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211
doc/guix.texi
View file

@ -147,6 +147,7 @@ Package Management
* Invoking guix gc:: Running the garbage collector.
* Invoking guix pull:: Fetching the latest Guix and distribution.
* Channels:: Customizing the package collection.
* Inferiors:: Interacting with another revision of Guix.
* Invoking guix describe:: Display information about your Guix revision.
* Invoking guix pack:: Creating software bundles.
* Invoking guix archive:: Exporting and importing store files.
@ -1699,6 +1700,7 @@ guix package -i emacs-guix
* Invoking guix gc:: Running the garbage collector.
* Invoking guix pull:: Fetching the latest Guix and distribution.
* Channels:: Customizing the package collection.
* Inferiors:: Interacting with another revision of Guix.
* Invoking guix describe:: Display information about your Guix revision.
* Invoking guix pack:: Creating software bundles.
* Invoking guix archive:: Exporting and importing store files.
@ -3053,6 +3055,135 @@ package it defines.
This gives you super powers, allowing you to track the provenance of binary
artifacts with very fine grain, and to reproduce software environments at
will---some sort of ``meta reproducibility'' capabilities, if you will.
@xref{Inferiors}, for another way to take advantage of these super powers.
@node Inferiors
@section Inferiors
@c TODO: Remove this once we're more confident about API stability.
@quotation Note
The functionality described here is a ``technology preview'' as of version
@value{VERSION}. As such, the interface is subject to change.
@end quotation
@cindex inferiors
@cindex composition of Guix revisions
Sometimes you might need to mix packages from the revision of Guix you're
currently running with packages available in a different revision of Guix.
Guix @dfn{inferiors} allow you to achieve that by composing different Guix
revisions in arbitrary ways.
@cindex inferior packages
Technically, an ``inferior'' is essentially a separate Guix process connected
to your main Guix process through a REPL (@pxref{Invoking guix repl}). The
@code{(guix inferior)} module allows you to create inferiors and to
communicate with them. It also provides a high-level interface to browse and
manipulate the packages that an inferior provides---@dfn{inferior packages}.
When combined with channels (@pxref{Channels}), inferiors provide a simple way
to interact with a separate revision of Guix. For example, let's assume you
want to install in your profile the current @code{guile} package, along with
the @code{guile-json} as it existed in an older revision of Guix---perhaps
because the newer @code{guile-json} has an incompatible API and you want to
run your code against the old API@. To do that, you could write a manifest for
use by @code{guix package --manifest} (@pxref{Invoking guix package}); in that
manifest, you would create an inferior for that old Guix revision you care
about, and you would look up the @code{guile-json} package in the inferior:
@lisp
(use-modules (guix inferior) (guix channels)
(srfi srfi-1)) ;for 'first'
(define channels
;; This is the old revision from which we want to
;; extract guile-json.
(list (channel
(name 'guix)
(url "https://git.savannah.gnu.org/git/guix.git")
(commit
"65956ad3526ba09e1f7a40722c96c6ef7c0936fe"))))
(define inferior
;; An inferior representing the above revision.
(inferior-for-channels channels))
;; Now create a manifest with the current "guile" package
;; and the old "guile-json" package.
(packages->manifest
(list (first (lookup-inferior-packages inferior "guile-json"))
(specification->package "guile")))
@end lisp
On its first run, @command{guix package --manifest} might have to build the
channel you specified before it can create the inferior; subsequent runs will
be much faster because the Guix revision will be cached.
The @code{(guix inferior)} module provides the following procedures to open an
inferior:
@deffn {Scheme Procedure} inferior-for-channels @var{channels} @
[#:cache-directory] [#:ttl]
Return an inferior for @var{channels}, a list of channels. Use the cache at
@var{cache-directory}, where entries can be reclaimed after @var{ttl} seconds.
This procedure opens a new connection to the build daemon.
As a side effect, this procedure may build or substitute binaries for
@var{channels}, which can take time.
@end deffn
@deffn {Scheme Procedure} open-inferior @var{directory} @
[#:command "bin/guix"]
Open the inferior Guix in @var{directory}, running
@code{@var{directory}/@var{command} repl} or equivalent. Return @code{#f} if
the inferior could not be launched.
@end deffn
@cindex inferior packages
The procedures listed below allow you to obtain and manipulate inferior
packages.
@deffn {Scheme Procedure} inferior-packages @var{inferior}
Return the list of packages known to @var{inferior}.
@end deffn
@deffn {Scheme Procedure} lookup-inferior-packages @var{inferior} @var{name} @
[@var{version}]
Return the sorted list of inferior packages matching @var{name} in
@var{inferior}, with highest version numbers first. If @var{version} is true,
return only packages with a version number prefixed by @var{version}.
@end deffn
@deffn {Scheme Procedure} inferior-package? @var{obj}
Return true if @var{obj} is an inferior package.
@end deffn
@deffn {Scheme Procedure} inferior-package-name @var{package}
@deffnx {Scheme Procedure} inferior-package-version @var{package}
@deffnx {Scheme Procedure} inferior-package-synopsis @var{package}
@deffnx {Scheme Procedure} inferior-package-description @var{package}
@deffnx {Scheme Procedure} inferior-package-home-page @var{package}
@deffnx {Scheme Procedure} inferior-package-location @var{package}
@deffnx {Scheme Procedure} inferior-package-inputs @var{package}
@deffnx {Scheme Procedure} inferior-package-native-inputs @var{package}
@deffnx {Scheme Procedure} inferior-package-propagated-inputs @var{package}
@deffnx {Scheme Procedure} inferior-package-transitive-propagated-inputs @var{package}
@deffnx {Scheme Procedure} inferior-package-native-search-paths @var{package}
@deffnx {Scheme Procedure} inferior-package-transitive-native-search-paths @var{package}
@deffnx {Scheme Procedure} inferior-package-search-paths @var{package}
These procedures are the counterpart of package record accessors
(@pxref{package Reference}). Most of them work by querying the inferior
@var{package} comes from, so the inferior must still be live when you call
these procedures.
@end deffn
Inferior packages can be used transparently like any other package or
file-like object in G-expressions (@pxref{G-Expressions}). They are also
transparently handled by the @code{packages->manifest} procedure, which is
commonly use in manifests (@pxref{Invoking guix package, the
@option{--manifest} option of @command{guix package}}). Thus you can insert
an inferior package pretty much anywhere you would insert a regular package:
in manifests, in the @code{packages} field of your @code{operating-system}
declaration, and so on.
@node Invoking guix describe
@section Invoking @command{guix describe}
@ -16757,6 +16888,86 @@ body of a named location block cannot contain location blocks.
@end table
@end deftp
@subsubheading Varnish Cache
@cindex Varnish
Varnish is a fast cache server that sits in between web applications
and end users. It proxies requests from clients and caches the
accessed URLs such that multiple requests for the same resource only
creates one request to the back-end.
@defvr {Scheme Variable} varnish-service-type
Service type for the Varnish daemon.
@end defvr
@deftp {Data Type} varnish-configuration
Data type representing the @code{varnish} service configuration.
This type has the following parameters:
@table @asis
@item @code{package} (default: @code{varnish})
The Varnish package to use.
@item @code{name} (default: @code{"default"})
A name for this Varnish instance. Varnish will create a directory in
@file{/var/varnish/} with this name and keep temporary files there. If
the name starts with a forward slash, it is interpreted as an absolute
directory name.
Pass the @code{-n} argument to other Varnish programs to connect to the
named instance, e.g. @command{varnishncsa -n default}.
@item @code{backend} (default: @code{"localhost:8080"})
The backend to use. This option has no effect if @code{vcl} is set.
@item @code{vcl} (default: #f)
The @dfn{VCL} (Varnish Configuration Language) program to run. If this
is @code{#f}, Varnish will proxy @code{backend} using the default
configuration. Otherwise this must be a file-like object with valid
VCL syntax.
@c Varnish does not support HTTPS, so keep this URL to avoid confusion.
For example, to mirror @url{http://www.gnu.org,www.gnu.org} with VCL you
can do something along these lines:
@example
(define %gnu-mirror
(plain-file
"gnu.vcl"
"vcl 4.1;
backend gnu @{ .host = "www.gnu.org"; @}"))
(operating-system
...
(services (cons (service varnish-service-type
(varnish-configuration
(listen '(":80"))
(vcl %gnu-mirror)))
%base-services)))
@end example
The configuration of an already running Varnish instance can be inspected
and changed using the @command{varnishadm} program.
Consult the @url{https://varnish-cache.org/docs/,Varnish User Guide} and
@url{https://book.varnish-software.com/4.0/,Varnish Book} for
comprehensive documentation on Varnish and its configuration language.
@item @code{listen} (default: @code{'("localhost:80")})
List of addresses Varnish will listen on.
@item @code{storage} (default: @code{'("malloc,128m")})
List of storage backends that will be available in VCL.
@item @code{parameters} (default: @code{'()})
List of run-time parameters in the form @code{'(("parameter" . "value"))}.
@item @code{extra-options} (default: @code{'()})
Additional arguments to pass to the @command{varnishd} process.
@end table
@end deftp
@subsubheading FastCGI
@cindex fastcgi
@cindex fcgiwrap
FastCGI is an interface between the front-end and the back-end of a web

6
gnu/local.mk
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@ -808,14 +808,12 @@ dist_patch_DATA = \
%D%/packages/patches/hdf-eos5-remove-gctp.patch \
%D%/packages/patches/hdf-eos5-fix-szip.patch \
%D%/packages/patches/hdf-eos5-fortrantests.patch \
%D%/packages/patches/hmmer-remove-cpu-specificity.patch \
%D%/packages/patches/higan-remove-march-native-flag.patch \
%D%/packages/patches/hubbub-sort-entities.patch \
%D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch \
%D%/packages/patches/hydra-disable-darcs-test.patch \
%D%/packages/patches/icecat-avoid-bundled-libraries.patch \
%D%/packages/patches/icecat-bug-1413868-pt1.patch \
%D%/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch \
%D%/packages/patches/icecat-CVE-2018-12383.patch \
%D%/packages/patches/icecat-use-system-graphite2.patch \
%D%/packages/patches/icecat-use-system-harfbuzz.patch \
%D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch \
@ -918,6 +916,7 @@ dist_patch_DATA = \
%D%/packages/patches/libutils-remove-damaging-includes.patch \
%D%/packages/patches/libvdpau-va-gl-unbundle.patch \
%D%/packages/patches/libvpx-CVE-2016-2818.patch \
%D%/packages/patches/libvpx-use-after-free-in-postproc.patch \
%D%/packages/patches/libxslt-generated-ids.patch \
%D%/packages/patches/libxt-guix-search-paths.patch \
%D%/packages/patches/lierolibre-check-unaligned-access.patch \
@ -1114,7 +1113,6 @@ dist_patch_DATA = \
%D%/packages/patches/reptyr-fix-gcc-7.patch \
%D%/packages/patches/ripperx-missing-file.patch \
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
%D%/packages/patches/rsem-makefile.patch \
%D%/packages/patches/rtags-separate-rct.patch \
%D%/packages/patches/racket-store-checksum-override.patch \
%D%/packages/patches/ruby-rubygems-276-for-ruby24.patch \

20
gnu/packages/admin.scm
View file

@ -869,7 +869,7 @@ (define-public clusterssh
(define-public rename
(package
(name "rename")
(version "0.35")
(version "1.00")
(source (origin
(method url-fetch)
(uri (string-append
@ -877,8 +877,24 @@ (define-public rename
version ".tar.gz"))
(sha256
(base32
"052iqmn7ya3w1nadpiyavmr3rx566r0lbflx94y8b5wx9q5c16rq"))))
"03yhf8nmqsb0zyliv501fdvwlp589jqfn44yqkrflmpzrbik3zxl"))))
(build-system perl-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'find-itself
;; Fix run-time 'Can't locate File/Rename.pm in @INC' failure.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(with-directory-excursion bin
(for-each
(lambda (program)
(wrap-program program
`("PERL5LIB" ":" prefix
(,(string-append out "/lib/perl5/site_perl")))))
(find-files "." ".*")))
#t))))))
(native-inputs
`(("perl-module-build" ,perl-module-build)
("perl-test-pod" ,perl-test-pod)

4
gnu/packages/audio.scm
View file

@ -2015,14 +2015,14 @@ (define-public patchage
(define-public qjackctl
(package
(name "qjackctl")
(version "0.5.3")
(version "0.5.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
version "/qjackctl-" version ".tar.gz"))
(sha256
(base32
"0x08af8m5l8qy9av3dlldsg58ny9nc69h1s4i6hqkvj24jwy6fw1"))))
"0qr71nb93gkz5q53nfcl5g168z173wc6s8w1yjs3rfn3m4hg0bcq"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f)) ; no check target

248
gnu/packages/bioinformatics.scm
View file

@ -2936,18 +2936,15 @@ (define-public hisat2
(define-public hmmer
(package
(name "hmmer")
(version "3.1b2")
(version "3.2.1")
(source
(origin
(method url-fetch)
(uri (string-append
"http://eddylab.org/software/hmmer"
(version-major version) "/"
version "/hmmer-" version ".tar.gz"))
"http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz"))
(sha256
(base32
"0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
(patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
"171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(home-page "http://hmmer.org/")
@ -2957,12 +2954,10 @@ (define-public hmmer
sequences, and for making protein sequence alignments. It implements methods
using probabilistic models called profile hidden Markov models (profile
HMMs).")
(license (list license:gpl3+
;; The bundled library 'easel' is distributed
;; under The Janelia Farm Software License.
(license:non-copyleft
"file://easel/LICENSE"
"See easel/LICENSE in the distribution.")))))
;; hmmer uses non-portable SSE intrinsics so building fails on other
;; platforms.
(supported-systems '("x86_64-linux" "i686-linux"))
(license license:bsd-3)))
(define-public htseq
(package
@ -4800,66 +4795,79 @@ (define-public raxml
(define-public rsem
(package
(name "rsem")
(version "1.2.20")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri
(string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/deweylab/RSEM.git")
(commit (string-append "v" version))))
(sha256
(base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
(patches (search-patches "rsem-makefile.patch"))
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
(file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
'(begin
;; remove bundled copy of boost
;; remove bundled copy of boost and samtools
(delete-file-recursively "boost")
(delete-file-recursively "samtools-1.3")
#t))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:make-flags
(list (string-append "BOOST="
(assoc-ref %build-inputs "boost")
"/include/")
(string-append "SAMHEADERS="
(assoc-ref %build-inputs "htslib")
"/include/htslib/sam.h")
(string-append "SAMLIBS="
(assoc-ref %build-inputs "htslib")
"/lib/libhts.a"))
#:phases
(modify-phases %standard-phases
;; No "configure" script.
;; Do not build bundled samtools library.
(replace 'configure
(lambda _
(substitute* "Makefile"
(("^all : sam/libbam.a") "all : "))
#t))
(lambda _
(substitute* "Makefile"
(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
(("^\\$\\(SAMLIBS\\).*") ""))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(perl (string-append out "/lib/perl5/site_perl")))
(mkdir-p bin)
(mkdir-p perl)
(for-each (lambda (file)
(install-file file bin))
(find-files "." "rsem-.*"))
(install-file "rsem_perl_utils.pm" perl))
#t))
(add-after
'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (prog)
(wrap-program (string-append out "/bin/" prog)
`("PERL5LIB" ":" prefix
(,(string-append out "/lib/perl5/site_perl")))))
'("rsem-plot-transcript-wiggles"
"rsem-calculate-expression"
"rsem-generate-ngvector"
"rsem-run-ebseq"
"rsem-prepare-reference")))
#t)))))
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(perl (string-append out "/lib/perl5/site_perl")))
(mkdir-p bin)
(mkdir-p perl)
(for-each (lambda (file)
(install-file file bin))
(find-files "." "rsem-.*"))
(install-file "rsem_perl_utils.pm" perl))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (prog)
(wrap-program (string-append out "/bin/" prog)
`("PERL5LIB" ":" prefix
(,(string-append out "/lib/perl5/site_perl")))))
'("rsem-calculate-expression"
"rsem-control-fdr"
"rsem-generate-data-matrix"
"rsem-generate-ngvector"
"rsem-plot-transcript-wiggles"
"rsem-prepare-reference"
"rsem-run-ebseq"
"rsem-run-prsem-testing-procedure")))
#t)))))
(inputs
`(("boost" ,boost)
("ncurses" ,ncurses)
("r-minimal" ,r-minimal)
("perl" ,perl)
("samtools" ,samtools-0.1)
("htslib" ,htslib-1.3)
("zlib" ,zlib)))
(home-page "http://deweylab.biostat.wisc.edu/rsem/")
(synopsis "Estimate gene expression levels from RNA-Seq data")
@ -13723,3 +13731,141 @@ (define-public python-hic2cool
cooler). Both @code{hic} and @code{cool} files describe Hi-C contact
matrices.")
(license license:expat)))
(define-public r-pore
(package
(name "r-pore")
(version "0.24")
(source
(origin
(method url-fetch)
(uri
(string-append "mirror://sourceforge/rpore/" version
"/poRe_" version ".tar.gz"))
(sha256
(base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
(properties `((upstream-name . "poRe")))
(build-system r-build-system)
(propagated-inputs
`(("r-bit64" ,r-bit64)
("r-data-table" ,r-data-table)
("r-rhdf5" ,r-rhdf5)
("r-shiny" ,r-shiny)
("r-svdialogs" ,r-svdialogs)))
(home-page "https://sourceforge.net/projects/rpore/")
(synopsis "Visualize Nanopore sequencing data")
(description
"This package provides graphical user interfaces to organize and visualize Nanopore
sequencing data.")
;; This is free software but the license variant is unclear:
;; <https://github.com/mw55309/poRe_docs/issues/10>.
(license license:bsd-3)))
(define-public r-xbioc
(let ((revision "1")
(commit "f798c187e376fd1ba27abd559f47bbae7e3e466b"))
(package
(name "r-xbioc")
(version (git-version "0.1.15" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/renozao/xbioc.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-assertthat" ,r-assertthat)
("r-biobase" ,r-biobase)
("r-biocinstaller" ,r-biocinstaller)
("r-digest" ,r-digest)
("r-pkgmaker" ,r-pkgmaker)
("r-plyr" ,r-plyr)
("r-reshape2" ,r-reshape2)
("r-stringr" ,r-stringr)))
(home-page "https://github.com/renozao/xbioc/")
(synopsis "Extra base functions for Bioconductor")
(description "This package provides extra utility functions to perform
common tasks in the analysis of omics data, leveraging and enhancing features
provided by Bioconductor packages.")
(license license:gpl3+))))
(define-public r-cssam
(let ((revision "1")
(commit "9ec58c982fa551af0d80b1a266890d92954833f2"))
(package
(name "r-cssam")
(version (git-version "1.4" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shenorrLab/csSAM.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-formula" ,r-formula)
("r-ggplot2" ,r-ggplot2)
("r-pkgmaker" ,r-pkgmaker)
("r-plyr" ,r-plyr)
("r-rngtools" ,r-rngtools)
("r-scales" ,r-scales)))
(home-page "https://github.com/shenorrLab/csSAM/")
(synopsis "Cell type-specific statistical analysis of microarray")
(description "This package implements the method csSAM that computes
cell-specific differential expression from measured cell proportions using
SAM.")
;; Any version
(license license:lgpl2.1+))))
(define-public r-bseqsc
(let ((revision "1")
(commit "fef3f3e38dcf3df37103348b5780937982b43b98"))
(package
(name "r-bseqsc")
(version (git-version "1.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shenorrLab/bseqsc.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-cssam" ,r-cssam)
("r-dplyr" ,r-dplyr)
("r-e1071" ,r-e1071)
("r-edger" ,r-edger)
("r-ggplot2" ,r-ggplot2)
("r-nmf" ,r-nmf)
("r-openxlsx" ,r-openxlsx)
("r-pkgmaker" ,r-pkgmaker)
("r-plyr" ,r-plyr)
("r-preprocesscore" ,r-preprocesscore)
("r-rngtools" ,r-rngtools)
("r-scales" ,r-scales)
("r-stringr" ,r-stringr)
("r-xbioc" ,r-xbioc)))
(home-page "https://github.com/shenorrLab/bseqsc")
(synopsis "Deconvolution of bulk sequencing experiments using single cell data")
(description "BSeq-sc is a bioinformatics analysis pipeline that
leverages single-cell sequencing data to estimate cell type proportion and
cell type-specific gene expression differences from RNA-seq data from bulk
tissue samples. This is a companion package to the publication \"A
single-cell transcriptomic map of the human and mouse pancreas reveals inter-
and intra-cell population structure.\" Baron et al. Cell Systems (2016)
@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
(license license:gpl2+))))

6
gnu/packages/bittorrent.scm
View file

@ -409,7 +409,7 @@ (define-public libtorrent-rasterbar
(define-public qbittorrent
(package
(name "qbittorrent")
(version "4.0.4")
(version "4.1.3")
(source (origin
(method url-fetch)
(uri (string-append
@ -418,7 +418,7 @@ (define-public qbittorrent
(file-name (string-append name "-release-" version ".tar.gz"))
(sha256
(base32
"145r4lv7rqdhrm5znn3ndxsfdf579n46zvj7c53c422am8ir5xhp"))))
"00zrpnwanq9f7maky2z4wnzw08xy902s77scm2gcvxxxankr4j92"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -434,7 +434,7 @@ (define-public qbittorrent
`(("boost" ,boost)
("libtorrent-rasterbar" ,libtorrent-rasterbar)
("openssl" ,openssl)
("python" ,python)
("python" ,python-wrapper)
("qtbase" ,qtbase)
("qtsvg" ,qtsvg)
("zlib" ,zlib)))

4
gnu/packages/check.scm
View file

@ -1920,14 +1920,14 @@ (define-public python2-nose-randomly
(define-public python-nose-timer
(package
(name "python-nose-timer")
(version "0.7.2")
(version "0.7.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "nose-timer" version))
(sha256
(base32
"0ywg223p528014z5s0vzck74r4xyw3kvcp2casfnc85dkvir1zj7"))))
"0hfz5aqnhf493i9kyb6prm4zm8vx7wmfsyg3nvsnh24lzh2kwx44"))))
(build-system python-build-system)
(propagated-inputs
`(("python-nose" ,python-nose)

20
gnu/packages/cran.scm
View file

@ -5875,3 +5875,23 @@ (define-public r-abps
calculate other scores used in anti-doping programs, such as the ratio of
hemoglobin to reticulocytes (OFF-score), as well as example data.")
(license license:gpl2+)))
(define-public r-parmigene
(package
(name "r-parmigene")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "parmigene" version))
(sha256
(base32
"1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/parmigene/")
(synopsis "Mutual information estimation for gene network reconstruction")
(description
"This package provides a parallel estimation of the mutual information
based on entropy estimates from k-nearest neighbors distances and algorithms
for the reconstruction of gene regulatory networks.")
(license license:agpl3+)))

6
gnu/packages/databases.scm
View file

@ -1457,15 +1457,15 @@ (define-public perl-dbd-pg
(define-public perl-dbd-mysql
(package
(name "perl-dbd-mysql")
(version "4.047")
(version "4.048")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/C/CA/CAPTTOFU/"
(uri (string-append "mirror://cpan/authors/id/M/MI/MICHIELB/"
"DBD-mysql-" version ".tar.gz"))
(sha256
(base32
"0idizgr0hr7sj92fbdlb3gv6cva15jkpaq28wrdw4j4p7awx2mls"))))
"1zqmch6c9gq06z90mkmk1skajk2kaggriw19ym5w04l7wv5gydqp"))))
(build-system perl-build-system)
(arguments
`(#:phases

7
gnu/packages/debian.scm
View file

@ -1,6 +1,9 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
@ -71,7 +74,7 @@ (define-public debian-archive-keyring
(define-public ubuntu-keyring
(package
(name "ubuntu-keyring")
(version "2018.02.28")
(version "2018.09.18.1")
(source
(origin
(method url-fetch)
@ -79,7 +82,7 @@ (define-public ubuntu-keyring
"+files/" name "_" version ".tar.gz"))
(sha256
(base32
"1zj3012cz7rlx9pm39wnwa0lmi1h38n6bkgbz81vnmcsvqsc9a3a"))))
"0csx2n62rj9rxjv4y8qhby7l9rbybfwrb0406pc2cjr7f2yk91af"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))

4
gnu/packages/education.scm
View file

@ -243,7 +243,7 @@ (define-public tipp10
(define-public snap
(package
(name "snap")
(version "4.2.1.3")
(version "4.2.1.4")
(source
(origin
(method git-fetch)
@ -253,7 +253,7 @@ (define-public snap
(file-name (git-file-name name version))
(sha256
(base32
"0n32hg8rx6alk5j58l76gzmicrg1bp7jagz5mh1zrg7591aicjal"))))
"0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))

184
gnu/packages/emacs.scm
View file

@ -118,6 +118,7 @@ (define-module (gnu packages emacs)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages video)
#:use-module (gnu packages haskell)
#:use-module (gnu packages wordnet)
#:use-module (guix utils)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
@ -334,9 +335,9 @@ (define-public guile-emacs
;;; Emacs hacking.
;;;
(define-public geiser
(define-public emacs-geiser
(package
(name "geiser")
(name "emacs-geiser")
(version "0.10")
(source (origin
(method url-fetch)
@ -369,7 +370,10 @@ (define-public geiser
metadata.")
(license license:bsd-3)))
(define-public paredit
(define-public geiser
(deprecated-package "geiser" emacs-geiser))
(define-public emacs-paredit
(package
(name "emacs-paredit")
(version "24")
@ -394,6 +398,9 @@ (define-public paredit
when typing parentheses directly or commenting out code line by line.")
(license license:gpl3+)))
(define-public paredit
(deprecated-package "paredit" emacs-paredit))
(define-public git-modes
(package
(name "emacs-git-modes")
@ -443,9 +450,9 @@ (define-public emacs-with-editor
on stdout instead of using a socket as the Emacsclient does.")
(license license:gpl3+)))
(define-public magit
(define-public emacs-magit
(package
(name "magit")
(name "emacs-magit")
(version "2.13.0")
(source (origin
(method url-fetch)
@ -511,9 +518,12 @@ (define-public magit
operations.")
(license license:gpl3+)))
(define-public magit-svn
(define-public magit
(deprecated-package "magit" emacs-magit))
(define-public emacs-magit-svn
(package
(name "magit-svn")
(name "emacs-magit-svn")
(version "2.2.0")
(source (origin
(method url-fetch)
@ -530,7 +540,7 @@ (define-public magit-svn
("gzip" ,gzip)))
(propagated-inputs `(("dash" ,emacs-dash)
("with-editor" ,emacs-with-editor)
("magit" ,magit)))
("magit" ,emacs-magit)))
(arguments
`(#:modules ((guix build utils)
(guix build emacs-utils))
@ -576,6 +586,9 @@ (define-public magit-svn
support for Git-SVN.")
(license license:gpl3+)))
(define-public magit-svn
(deprecated-package "magit-svn" emacs-magit-svn))
(define-public emacs-magit-popup
(package
(name "emacs-magit-popup")
@ -640,9 +653,9 @@ (define-public emacs-ghub
only a handful of functions that are not resource-specific.")
(license license:gpl3+)))
(define-public haskell-mode
(define-public emacs-haskell-mode
(package
(name "haskell-mode")
(name "emacs-haskell-mode")
(version "16.1")
(source (origin
(method url-fetch)
@ -730,7 +743,10 @@ (define (copy-to-dir dir files)
programs.")
(license license:gpl3+)))
(define-public flycheck
(define-public haskell-mode
(deprecated-package "haskell-mode" emacs-haskell-mode))
(define-public emacs-flycheck
(package
(name "emacs-flycheck")
(version "31")
@ -766,6 +782,9 @@ (define-public flycheck
provides an optional IDE-like error list.")
(license license:gpl3+))) ;+GFDLv1.3+ for the manual
(define-public flycheck
(deprecated-package "flycheck" emacs-flycheck))
;;;
;;; Web browsing.
@ -909,7 +928,7 @@ (define-public emacs-wget
;;; Multimedia.
;;;
(define-public emms
(define-public emacs-emms
(package
(name "emacs-emms")
(version "5.0")
@ -1047,9 +1066,12 @@ (define-public emms
(home-page "https://www.gnu.org/software/emms/")
(license license:gpl3+)))
(define-public emms
(deprecated-package "emacs-emms" emacs-emms))
(define-public emacs-emms-player-mpv
;; A new mpv backend is included in Emms from 5.0.
(deprecated-package "emacs-emms-player-mpv" emms))
(deprecated-package "emacs-emms-player-mpv" emacs-emms))
(define-public emacs-emms-mode-line-cycle
(package
@ -1079,9 +1101,9 @@ (define-public emacs-emms-mode-line-cycle
;;; Miscellaneous.
;;;
(define-public bbdb
(define-public emacs-bbdb
(package
(name "bbdb")
(name "emacs-bbdb")
(version "3.1.2")
(source (origin
(method url-fetch)
@ -1120,6 +1142,9 @@ (define-public bbdb
mode, Rmail, Gnus, MH-E, and VM). BBDB is fully customizable.")
(license license:gpl3+)))
(define-public bbdb
(deprecated-package "bbdb" emacs-bbdb))
(define-public emacs-aggressive-indent
(package
(name "emacs-aggressive-indent")
@ -1720,7 +1745,7 @@ (define-public emacs-guix
`(("guile" ,guile-2.2)
("guix" ,guix)))
(propagated-inputs
`(("geiser" ,geiser)
`(("geiser" ,emacs-geiser)
("guile-gcrypt" ,guile-gcrypt)
("dash" ,emacs-dash)
("bui" ,emacs-bui)
@ -2376,7 +2401,7 @@ (define-public emacs-string-inflection
"1k0sm552iawi49v4zis6dbb81d1rzgky9v0dpv7nj31gnb7bmy7k"))))
(build-system emacs-build-system)
(native-inputs
`(("ert-runner" ,ert-runner)))
`(("ert-runner" ,emacs-ert-runner)))
(arguments
`(#:tests? #t
#:test-command '("ert-runner")))
@ -2662,7 +2687,7 @@ (define-public emacs-deferred
(native-inputs
`(("emacs-ert-expectations" ,emacs-ert-expectations)
("emacs-undercover" ,emacs-undercover)
("ert-runner" ,ert-runner)))
("ert-runner" ,emacs-ert-runner)))
(synopsis "Simple asynchronous functions for Emacs Lisp")
(description
"The @code{deferred.el} library provides support for asynchronous tasks.
@ -2671,7 +2696,7 @@ (define-public emacs-deferred
for asynchronous tasks.")
(license license:gpl3+)))
(define-public butler
(define-public emacs-butler
(package
(name "emacs-butler")
(version "0.2.4")
@ -2697,6 +2722,9 @@ (define-public butler
build jobs.")
(license license:gpl3+)))
(define-public butler
(deprecated-package "emacs-butler" emacs-butler))
(define-public emacs-company
(package
(name "emacs-company")
@ -2822,7 +2850,7 @@ (define-public emacs-multiple-cursors
simultaneous cursors.")
(license license:gpl3+)))
(define-public typo
(define-public emacs-typo
(package
(name "emacs-typo")
(version "1.1")
@ -2846,6 +2874,9 @@ (define-public typo
on context.")
(license license:gpl3+)))
(define-public typo
(deprecated-package "emacs-typo" emacs-typo))
(define-public emacs-scheme-complete
(let ((commit "9b5cf224bf2a5994bc6d5b152ff487517f1a9bb5"))
(package
@ -3981,7 +4012,7 @@ (define-public emacs-clojure-mode
(native-inputs
`(("emacs-dash" ,emacs-dash)
("emacs-s" ,emacs-s)
("ert-runner" ,ert-runner)))
("ert-runner" ,emacs-ert-runner)))
(arguments
`(#:tests? #t
#:test-command '("ert-runner")))
@ -4353,7 +4384,7 @@ (define-public emacs-tide
(propagated-inputs
`(("emacs-dash" ,emacs-dash)
("emacs-s" ,emacs-s)
("emacs-flycheck" ,flycheck)
("emacs-flycheck" ,emacs-flycheck)
("emacs-typescript-mode" ,emacs-typescript-mode)))
(home-page "https://github.com/ananthakumaran/tide")
(synopsis "Typescript IDE for Emacs")
@ -4518,7 +4549,7 @@ (define-public emacs-mocker
`(#:tests? #t
#:test-command '("ert-runner")))
(native-inputs
`(("ert-runner" ,ert-runner)))
`(("ert-runner" ,emacs-ert-runner)))
(propagated-inputs
`(("emacs-el-x" ,emacs-el-x)))
(home-page "https://github.com/sigma/mocker.el")
@ -4584,7 +4615,7 @@ (define-public emacs-pyvenv
#:tests? #t
#:test-command '("ert-runner")))
(native-inputs
`(("ert-runner" ,ert-runner)
`(("ert-runner" ,emacs-ert-runner)
("emacs-mocker" ,emacs-mocker)))
(home-page "https://github.com/jorgenschaefer/pyvenv")
(synopsis "Virtualenv minor mode for Emacs")
@ -4669,7 +4700,7 @@ (define-public emacs-elpy
("pyvenv" ,emacs-pyvenv)
("s" ,emacs-s)))
(native-inputs
`(("ert-runner" ,ert-runner)
`(("ert-runner" ,emacs-ert-runner)
("emacs-f" ,emacs-f)
("python" ,python-wrapper)
("python-autopep8" ,python-autopep8)
@ -5252,7 +5283,7 @@ (define-public emacs-monroe
(define-public emacs-orgalist
(package
(name "emacs-orgalist")
(version "1.8")
(version "1.9")
(source
(origin
(method url-fetch)
@ -5260,7 +5291,7 @@ (define-public emacs-orgalist
"orgalist-" version ".el"))
(sha256
(base32
"1wqwnmn08i0qkxm8b2iclvf6cydcn68h1p3h7r1kig2bdn5b8948"))))
"1rmmcyiiqkq54hn74nhzxzl4nvd902hv6gq341jwhrm7yiagffi6"))))
(build-system emacs-build-system)
(home-page "http://elpa.gnu.org/packages/orgalist.html")
(synopsis "Manage Org-like lists in non-Org buffers")
@ -5318,14 +5349,14 @@ (define-public emacs-org
(name "emacs-org")
;; emacs-org-contrib inherits from this package. Please update its sha256
;; checksum as well.
(version "9.1.13")
(version "9.1.14")
(source (origin
(method url-fetch)
(uri (string-append "http://elpa.gnu.org/packages/org-"
version ".tar"))
(sha256
(base32
"1vx0n32gvrgy2bl2b4pvxf00cywxwm57gi46f2b2zlrnmd5n85pr"))))
"17vd9hig26rqv90l6y92hc2i0x29g44lsdsp0xd4m53s8r3zdikz"))))
(build-system emacs-build-system)
(home-page "https://orgmode.org/")
(synopsis "Outline-based notes management and organizer")
@ -5507,14 +5538,15 @@ (define-public emacs-auto-complete
(define-public m17n-db
(package
(name "m17n-db")
(version "1.7.0")
(version "1.8.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://savannah/m17n/m17n-db-"
version ".tar.gz"))
(sha256
(base32 "1w08hnsbknrcjlzp42c99bgwc9hzsnf5m4apdv0dacql2s09zfm2"))))
(base32
"0vfw7z9i2s9np6nmx1d4dlsywm044rkaqarn7akffmb6bf1j6zv5"))))
(build-system gnu-build-system)
(inputs
`(("gettext" ,gettext-minimal)))
@ -5541,14 +5573,15 @@ (define-public m17n-db
(define-public m17n-lib
(package
(name "m17n-lib")
(version "1.7.0")
(version "1.8.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://savannah/m17n/m17n-lib-"
version ".tar.gz"))
(sha256
(base32 "10yv730i25g1rpzv6q49m6xn4p8fjm7jdwvik2h70sn8w3hm7f4f"))))
(base32
"0jp61y09xqj10mclpip48qlfhniw8gwy8b28cbzxy8hq8pkwmfkq"))))
(build-system gnu-build-system)
(inputs
`(("fribidi" ,fribidi)
@ -6931,9 +6964,9 @@ (define-public emacs-commander
;; Tests for ert-runner have a circular dependency with ecukes, and therefore
;; cannot be run
(define-public ert-runner
(define-public emacs-ert-runner
(package
(name "ert-runner")
(name "emacs-ert-runner")
(version "0.7.0")
(source
(origin
@ -6976,6 +7009,9 @@ (define-public ert-runner
running tests easier.")
(license license:gpl3+)))
(define-public ert-runner
(deprecated-package "ert-runner" emacs-ert-runner))
(define-public emacs-disable-mouse
(package
(name "emacs-disable-mouse")
@ -7019,7 +7055,7 @@ (define-public emacs-json-reformat
(native-inputs
`(("emacs-dash" ,emacs-dash)
("emacs-shut-up" ,emacs-shut-up)
("ert-runner" ,ert-runner)))
("ert-runner" ,emacs-ert-runner)))
(arguments
`(#:tests? #t
#:test-command '("ert-runner")))
@ -7250,7 +7286,7 @@ (define-public emacs-ws-butler
"1a4b0lsmwq84qfx51c5xy4fryhb1ysld4fhgw2vr37izf53379sb"))))
(build-system emacs-build-system)
(native-inputs
`(("ert-runner" ,ert-runner)))
`(("ert-runner" ,emacs-ert-runner)))
(arguments
`(#:tests? #t
#:test-command '("ert-runner" "tests")))
@ -7506,7 +7542,7 @@ (define-public emacs-browse-at-remote
`(("emacs-f" ,emacs-f)
("emacs-s" ,emacs-s)))
(native-inputs
`(("ert-runner" ,ert-runner)))
`(("ert-runner" ,emacs-ert-runner)))
(arguments
`(#:tests? #t
#:test-command '("ert-runner")))
@ -7976,9 +8012,9 @@ (define-public emacs-bongo
@code{afplay}.")
(license license:gpl2+)))
(define-public groovy-emacs-modes
(define-public emacs-groovy-modes
(package
(name "groovy-emacs-modes")
(name "emacs-groovy-modes")
(version "2.0")
(source (origin
(method url-fetch)
@ -8000,7 +8036,10 @@ (define-public groovy-emacs-modes
navigation with the grails mode.")
(license license:gpl3+)))
(define-public org-tree-slide
(define-public groovy-emacs-modes
(deprecated-package "groovy-emacs-modes" emacs-groovy-modes))
(define-public emacs-org-tree-slide
(let ((commit "dff8f1a4a64c8dd0a1fde0b0131e2fe186747134")
(revision "0"))
(package
@ -8022,6 +8061,9 @@ (define-public org-tree-slide
@kbd{C-<} to jump to the next and previous slide.")
(license license:gpl3+))))
(define-public org-tree-slide
(deprecated-package "emacs-org-tree-slide" emacs-org-tree-slide))
(define-public emacs-scratch-el
(let ((commit "2cdf2b841ce7a0987093f65b0cc431947549f897")
(revision "1"))
@ -8394,7 +8436,7 @@ (define-public emacs-ergoemacs-mode
(define-public emacs-password-store
(package
(name "emacs-password-store")
(version "1.7.2")
(version "1.7.3")
(source (origin
(method url-fetch)
(uri
@ -8402,7 +8444,7 @@ (define-public emacs-password-store
"password-store-" version ".tar.xz"))
(sha256
(base32
"1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27"))))
"1x53k5dn3cdmvy8m4fqdld4hji5n676ksl0ql4armkmsds26av1b"))))
(build-system emacs-build-system)
(arguments
`(#:phases
@ -10094,7 +10136,7 @@ (define-public emacs-benchmark-init
(define-public emacs-emms-player-simple-mpv
;; A new mpv backend is included in Emms from 5.0.
(deprecated-package "emacs-emms-player-simple-mpv" emms))
(deprecated-package "emacs-emms-player-simple-mpv" emacs-emms))
(define-public emacs-magit-org-todos-el
(let ((commit "df206287737b9671f2e36ae7b1474ebbe9940d2a"))
@ -10112,7 +10154,7 @@ (define-public emacs-magit-org-todos-el
(base32
"0kdp7k7jnnrkhsg0xh1c3h7iz0vgi120gf5xwl1hxy61avivnxrn"))))
(propagated-inputs
`(("magit" ,magit)))
`(("magit" ,emacs-magit)))
(build-system emacs-build-system)
(home-page "https://github.com/danielma/magit-org-todos.el")
(synopsis "Get todo.org into Emacs Magit status")
@ -10951,7 +10993,7 @@ (define-public emacs-dumb-jump
`(("emacs-el-mock" ,emacs-el-mock)
("emacs-noflet" ,emacs-noflet)
("emacs-undercover" ,emacs-undercover)
("ert-runner" ,ert-runner)))
("ert-runner" ,emacs-ert-runner)))
(propagated-inputs
`(("emacs-f" ,emacs-f)
("emacs-popup" ,emacs-popup)))
@ -11138,7 +11180,7 @@ (define-public emacs-evil-magit
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-evil" ,emacs-evil)
("magit" ,magit)))
("magit" ,emacs-magit)))
(home-page
"https://github.com/emacs-evil/evil-magit")
(synopsis "Evil-based key bindings for Magit")
@ -11411,7 +11453,7 @@ (define-public emacs-helm-emms
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)
("emacs-emms" ,emms)))
("emacs-emms" ,emacs-emms)))
(home-page
"https://github.com/emacs-helm/helm-emms")
(synopsis "Emms for Helm")
@ -11466,7 +11508,7 @@ (define-public emacs-helm-flycheck
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-dash" ,emacs-dash)
("emacs-flycheck" ,flycheck)
("emacs-flycheck" ,emacs-flycheck)
("emacs-helm" ,emacs-helm)))
(home-page "https://github.com/yasuyk/helm-flycheck")
(synopsis "Show Flycheck errors with Helm")
@ -11705,8 +11747,8 @@ (define-public emacs-mu4e-conversation
(synopsis
"Show a complete thread in a single buffer")
(description
"This package offers an alternate view to mu4e e-mail display. It
shows all e-mails of a thread in a single view, where each correspondant has
"This package offers an alternate view to mu4e's e-mail display. It
shows all e-mails of a thread in a single view, where each correspondent has
their own face. Threads can be displayed linearly (in which case e-mails are
displayed in chronological order) or as an Org document where the node tree
maps the thread tree.")
@ -12028,7 +12070,7 @@ (define-public emacs-magit-todos
("emacs-dash" ,emacs-dash)
("emacs-f" ,emacs-f)
("emacs-hl-todo" ,emacs-hl-todo)
("magit" ,magit)
("magit" ,emacs-magit)
("emacs-pcre2el" ,emacs-pcre2el)
("emacs-s" ,emacs-s)))
(home-page "https://github.com/alphapapa/magit-todos")
@ -12197,3 +12239,41 @@ (define-public emacs-blimp
some commands) and hints displayed in prompt using @command{eimp.el} to
execute its commands and resize images.")
(license license:gpl3+))))
(define-public emacs-synosaurus
(let ((commit "8bf95b935976ec0a1964cf175ed57cc5f6f93bdb"))
(package
(name "emacs-synosaurus")
(version (git-version "0.1.0" "1" commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/hpdeifel/synosaurus")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"15by9jccab6kyplxa6k0glzaivxkqdigl33gl2qi2cvy6f2q7gva"))))
(build-system emacs-build-system)
(propagated-inputs
`(("wordnet" ,wordnet)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((wn (assoc-ref inputs "wordnet")))
;; .el is read-only in git.
(chmod "synosaurus-wordnet.el" #o644)
;; Specify the absolute file names of the various
;; programs so that everything works out-of-the-box.
(emacs-substitute-variables
"synosaurus-wordnet.el"
("wordnet-command"
(string-append wn "/bin/wn")))))))))
(home-page "https://github.com/hpdeifel/synosaurus")
(synopsis "Extensible thesaurus mode for Emacs")
(description "Synosaurus is a thesaurus fontend for Emacs with pluggable
backends, including the @command{wordnet} offline backend.")
(license license:gpl3+))))

58
gnu/packages/enchant.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -19,34 +20,41 @@
(define-module (gnu packages enchant)
#:use-module (gnu packages)
#:use-module (gnu packages aspell)
#:use-module (gnu packages check)
#:use-module (gnu packages glib)
#:use-module (gnu packages pkg-config)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (guix licenses))
#:use-module (guix licenses)
#:use-module (srfi srfi-1))
(define-public enchant
(package
(name "enchant")
(version "1.6.0")
(source
(origin
(method url-fetch)
(uri
(string-append "http://www.abisource.com/downloads/" name "/" version
"/" name "-" version ".tar.gz"))
(sha256
(base32 "0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g"))))
(version "2.2.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/AbiWord/enchant/releases"
"/download/v" version "/enchant-"
version ".tar.gz"))
(sha256
(base32
"0v87p1ls0gym95qirijpclk650sjbkcjjl6ssk059zswcwaykn5b"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--disable-static"
;; Tests require a relocatable build.
"--enable-relocatable")))
(inputs
`(("aspell" ,aspell) ;; Currently, the only supported backend in Guix
("glib" ,glib))) ;; is aspell. (This information might be old)
`(("aspell" ,aspell))) ;; Currently, the only supported backend in Guix
(propagated-inputs ;; is aspell. (This information might be old)
;; Required by enchant.pc.
`(("glib" ,glib)))
(native-inputs
`(("glib:bin" ,glib "bin")
("pkg-config" ,pkg-config)))
("pkg-config" ,pkg-config)
("unittest-cpp" ,unittest-cpp)))
(synopsis "Multi-backend spell-checking library wrapper")
(description
"On the surface, Enchant appears to be a generic spell checking library.
@ -57,5 +65,23 @@ (define-public enchant
and implement certain features that may be lacking in any individual provider
library. Everything should \"just work\" for any and every definition of \"just
working\".")
(home-page "http://www.abisource.com/projects/enchant")
(home-page "https://abiword.github.io/enchant/")
(license lgpl2.1+)))
;; Some packages are not ready for the 2.x API yet, so we keep this version
;; around. The library and executables of Enchant 2 have been designed not to
;; conflict with 1.x, so it's OK if both end up in the same profile.
(define-public enchant-1.6
(package
(inherit enchant)
(version "1.6.0")
(arguments '(#:configure-flags '("--disable-static")))
(native-inputs (alist-delete "unittest-cpp"
(package-native-inputs enchant)))
(source (origin
(method url-fetch)
(uri (string-append "http://www.abisource.com/downloads/enchant/"
version "/enchant-" version ".tar.gz"))
(sha256
(base32
"0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g"))))))

2
gnu/packages/fcitx.scm
View file

@ -75,7 +75,7 @@ (define-public fcitx
("pkg-config" ,pkg-config)))
(inputs
`(("dbus" ,dbus)
("enchant" ,enchant)
("enchant" ,enchant-1.6)
("gettext" ,gettext-minimal)
("gtk2" ,gtk+-2)
("gtk3" ,gtk+)

16
gnu/packages/ftp.scm
View file

@ -170,15 +170,15 @@ (define-public weex
(define-public libfilezilla
(package
(name "libfilezilla")
(version "0.13.1")
(version "0.13.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://download.filezilla-project.org/"
(uri (string-append "https://download.filezilla-project.org/"
name "/" name "-" version ".tar.bz2"))
(sha256
(base32
"0347zkapp0wrhfm1yzw7wa1v3lww65ch176scifxn8f9068f1ixb"))))
"0z9cqscca4w94j9npgcknrrw8gfwn5ids903042fczlr977j0i19"))))
(build-system gnu-build-system)
(native-inputs
`(("cppunit" ,cppunit)
@ -207,16 +207,14 @@ (define-public libfilezilla
(define-public filezilla
(package
(name "filezilla")
(version "3.31.0")
(version "3.37.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://sourceforge.net/projects/" name
"/files/FileZilla_Client/" version
"/FileZilla_" version "_src" ".tar.bz2"))
(uri (string-append "https://download.filezilla-project.org/client/"
"FileZilla_" version "_src.tar.bz2"))
(sha256
(base32
"1rfysb8dil35a7bzj2kw0mzzkys39d7yn6ipsbk8l6rkwfvnii8l"))))
(base32 "1bbxlm8gc0r5jing8xmkdbhj5a1qfbjn8varhny3mrk1am4m7s7l"))))
(build-system gnu-build-system)
(arguments
;; Don't let filezilla phone home to check for updates.

13
gnu/packages/gl.scm
View file

@ -725,7 +725,7 @@ (define-public gl2ps
(define-public virtualgl
(package
(name "virtualgl")
(version "2.5.2")
(version "2.6")
(source
(origin
(method url-fetch)
@ -734,16 +734,17 @@ (define-public virtualgl
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0rnid3hwrry9d5d4m7sygq00xxx976rgk00a3557m9r5kxbmy476"))))
"1ck1d0w19cgyqvrb9mdlj6l5db90xf18yln71kdninlqxvpgj6h7"))))
(arguments
`(#:tests? #f ;; no tests are available
`(#:tests? #f ; no tests are available
#:configure-flags (list
(string-append "-DCMAKE_INSTALL_LIBDIR="
(assoc-ref %outputs "out") "/lib")
"-DVGL_USESSL=1"))) ;; use OpenSSL
(string-append "-DCMAKE_INSTALL_LIBDIR="
(assoc-ref %outputs "out") "/lib")
"-DVGL_USESSL=1"))) ; use OpenSSL
(build-system cmake-build-system)
(inputs `(("glu" ,glu)
("libjpeg-turbo" ,libjpeg-turbo)
("libxtst" ,libxtst)
("mesa" ,mesa)
("openssl" ,openssl)))
(native-inputs `(("pkg-config" ,pkg-config)))

60
gnu/packages/gnome.scm
View file

@ -115,6 +115,8 @@ (define-module (gnu packages gnome)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages rdesktop)
#:use-module (gnu packages scanner)
#:use-module (gnu packages selinux)
@ -4094,35 +4096,27 @@ (define-public simple-scan
(define-public eolie
(package
(name "eolie")
(version "0.9.15")
(version "0.9.37")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/gnumdk/eolie/"
"releases/download/" version
"/eolie-" version ".tar.xz"))
(uri (string-append "https://gitlab.gnome.org/World/eolie/"
"uploads/4341cb428b7a45670308ee3fb3fa07dd/"
"eolie-" version ".tar.xz"))
(sha256
(base32
"0glydxp1xh85gfidk1l9miqn6qxdbvvk5s3iy0pjlv8nrs3263jd"))))
(build-system glib-or-gtk-build-system)
"126m0nwwy3lqv7z8aj9hiwangih03b1nlkg3xja9p7wbf7zcvp2n"))))
(build-system meson-build-system)
(arguments
`(#:phases
`(#:glib-or-gtk? #t
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda* (#:key outputs #:allow-other-keys)
(zero? (system* "meson" "build"
"--prefix" (assoc-ref outputs "out")))))
(replace 'check
(lambda _ (zero? (system* "ninja" "-C" "build" "test"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(zero? (system* "ninja" "-C" "build" "install"))))
(add-after 'wrap 'wrap-more
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
;; These libraries must be on LD_LIBRARY_PATH.
(libs '("gtkspell3" "webkitgtk" "libsoup" "libsecret"
"atk" "gtk+" "gsettings-desktop-schemas"
"gcc:lib" ; needed b/c webkitgtk is built with gcc-7
"gobject-introspection"))
(path (string-join
(map (lambda (lib)
@ -4135,12 +4129,12 @@ (define-public eolie
`("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))
#t)))))
(native-inputs
`(("intltool" ,intltool)
`(("gcc:lib" ,gcc-7 "lib") ; needed because webkitgtk is built with gcc-7
("intltool" ,intltool)
("itstool" ,itstool)
("pkg-config" ,pkg-config)
("meson" ,meson-for-build)
("ninja" ,ninja)
("python" ,python)
("glib:bin" ,glib "bin")
("gtk+" ,gtk+ "bin")))
(inputs
`(("gobject-introspection" ,gobject-introspection)
@ -4150,12 +4144,14 @@ (define-public eolie
("atk" ,atk) ; propagated by gtk+, but we need it in LD_LIBRARY_PATH
("python" ,python-wrapper)
("python-dateutil" ,python-dateutil)
("python-pyfxa" ,python-pyfxa)
("python-pygobject" ,python-pygobject)
("python-pycairo" ,python-pycairo)
("python-pycrypto" ,python-pycrypto)
("libsecret" ,libsecret)
("gtkspell3" ,gtkspell3)
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("webkitgtk" ,webkitgtk)))
("webkitgtk" ,webkitgtk-2.22)))
(home-page "https://wiki.gnome.org/Apps/Eolie")
(synopsis "Web browser for GNOME")
(description
@ -4193,6 +4189,7 @@ (define-public epiphany
`(("dconf" ,dconf)))
(native-inputs
`(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
("gcc" ,gcc-7) ; needed because webkitgtk-2.22 is compiled with gcc-7
("glib:bin" ,glib "bin") ; for glib-mkenums
("gtk+:bin" ,gtk+ "bin") ; for gtk-update-icon-cache
("intltool" ,intltool)
@ -4213,7 +4210,7 @@ (define-public epiphany
("libxslt" ,libxslt)
("nettle" ,nettle) ; for hogweed
("sqlite" ,sqlite)
("webkitgtk" ,webkitgtk)))
("webkitgtk" ,webkitgtk-2.22)))
(home-page "https://wiki.gnome.org/Apps/Web")
(synopsis "GNOME web browser")
(description
@ -6936,7 +6933,7 @@ (define-public orca
(define-public gspell
(package
(name "gspell")
(version "1.4.2")
(version "1.8.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -6944,7 +6941,7 @@ (define-public gspell
name "-" version ".tar.xz"))
(sha256
(base32
"1683vyyfq3q0ph665jj6id8hnlyid4qxzmqiwpv97gmz8zksg6x5"))
"1rdv873ixhwr15jwgc2z6k6y0hj353fqnwsy7zkh0c30qwiiv6l1"))
(patches (search-patches "gspell-dash-test.patch"))))
(build-system glib-or-gtk-build-system)
(arguments
@ -6978,7 +6975,7 @@ (define-public gspell
("aspell-dict-en" ,aspell-dict-en)
("xorg-server" ,xorg-server)))
(propagated-inputs
`(("enchant" ,enchant))) ; enchant.pc is required by gspell-1.pc
`(("enchant" ,enchant))) ;enchant.pc is required by gspell-1.pc
(home-page "https://wiki.gnome.org/Projects/gspell")
(synopsis "GNOME's alternative spell checker")
(description
@ -7230,7 +7227,7 @@ (define-public sound-juicer
(license license:gpl2+)))
(define-public workrave
(let ((commit "v1_10_20"))
(let ((commit "v1_10_21"))
(package
(name "workrave")
(version (string-map (match-lambda
@ -7242,18 +7239,11 @@ (define-public workrave
(uri (git-reference
(url "https://github.com/rcaelers/workrave.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(file-name (git-file-name name version))
(sha256
(base32
"099a87zkrkmsgfz9isrfm89dh545x52891jh6qxmn19h6wwsi941"))))
"150qca8c552fakjlzkgarsxgp87l1xcwn19svqsa9d0cygqxjgia"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autogen.sh")
#t)))))
(propagated-inputs `(("glib" ,glib)
("gtk+" ,gtk+)
("gdk-pixbuf" ,gdk-pixbuf)

166
gnu/packages/gnuzilla.scm
View file

@ -35,6 +35,7 @@ (define-module (gnu packages gnuzilla)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cargo)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages databases)
@ -58,6 +59,7 @@ (define-module (gnu packages gnuzilla)
#:use-module (gnu packages xorg)
#:use-module (gnu packages gl)
#:use-module (gnu packages assembly)
#:use-module (gnu packages rust)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages video)
#:use-module (gnu packages xdisorg)
@ -467,10 +469,10 @@ (define-public nss
(license license:mpl2.0)))
(define (mozilla-patch file-name changeset hash)
"Return an origin for CHANGESET from the mozilla-esr52 repository."
"Return an origin for CHANGESET from the mozilla-esr60 repository."
(origin
(method url-fetch)
(uri (string-append "https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/"
(uri (string-append "https://hg.mozilla.org/releases/mozilla-esr60/raw-rev/"
changeset))
(sha256 (base32 hash))
(file-name file-name)))
@ -478,112 +480,27 @@ (define (mozilla-patch file-name changeset hash)
(define-public icecat
(package
(name "icecat")
(version "52.6.0-gnu1")
(version "60.2.0-gnu1")
(source
(origin
(method url-fetch)
;; Temporary URL pending official release:
(uri "https://alpha.gnu.org/gnu/gnuzilla/60.2.0/icecat-60.2.0-gnu1.tar.bz2")
#;
(uri (string-append "mirror://gnu/gnuzilla/"
(first (string-split version #\-))
"/" name "-" version ".tar.bz2"))
(sha256
(base32
"09fn54glqg1aa93hnz5zdcy07cps09dbni2b4200azh6nang630a"))
"0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl"))
(patches
(list
(search-patch "icecat-avoid-bundled-libraries.patch")
(search-patch "icecat-use-system-harfbuzz.patch")
(search-patch "icecat-use-system-graphite2.patch")
(mozilla-patch "icecat-bug-546387.patch" "d13e3fefb76e" "1b760r0bg2ydbl585wlmajljh1nlisrwxvjws5b28a3sgjy01i6k")
(mozilla-patch "icecat-bug-1350152.patch" "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj")
(mozilla-patch "icecat-bug-1411708.patch" "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip")
(mozilla-patch "icecat-bug-1375217.patch" "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv")
(mozilla-patch "icecat-CVE-2018-5145.patch" "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
(mozilla-patch "icecat-CVE-2018-5130.patch" "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
(mozilla-patch "icecat-CVE-2018-5125-pt1.patch" "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
(mozilla-patch "icecat-bug-1426087.patch" "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n")
(mozilla-patch "icecat-bug-1416307.patch" "54f2f7f93b30" "1ncjir16mqya37wgf6fy2rqki3vl433c4grjr3fypmlig6xfgg1l")
(mozilla-patch "icecat-CVE-2018-5127.patch" "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
(mozilla-patch "icecat-CVE-2018-5125-pt2.patch" "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
(mozilla-patch "icecat-CVE-2018-5125-pt3.patch" "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
(mozilla-patch "icecat-CVE-2018-5129.patch" "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
(mozilla-patch "icecat-bug-1334465-pt1.patch" "f95c5b881442" "0iaddhf65jd9cycj4bw0b207n2jiqkr4q84jifzyqn4ygs75wdqd")
(mozilla-patch "icecat-bug-1334465-pt2.patch" "8a4265c8fb41" "1d9zfdbrlw9wzr84b7pj7lxgy487lsx0kfd89287hjk0al8m6vrw")
(mozilla-patch "icecat-bug-1398021.patch" "28855df568d8" "1kmq836gniplxpjnvq8lhbcc1aqi56al628r1mzdy94b5yb0lis3")
(mozilla-patch "icecat-bug-1388020.patch" "e8ab2736499b" "0n28vcd65rxsyq3z22rfcfksryfndhm1i3g6ah3akg11jnagqf5v")
(mozilla-patch "icecat-CVE-2018-5125-pt4.patch" "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
(mozilla-patch "icecat-CVE-2018-5125-pt5.patch" "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
(mozilla-patch "icecat-CVE-2018-5144.patch" "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
(mozilla-patch "icecat-bug-1430173-pt1.patch" "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i")
(mozilla-patch "icecat-bug-1430173-pt2.patch" "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl")
(mozilla-patch "icecat-CVE-2018-5131.patch" "3102fbb97b32" "0kg0183v92gxjb9255xjwhxyd6gl77l9c0civx3040k975fybwlp")
(mozilla-patch "icecat-CVE-2018-5125-pt6.patch" "4904c0f4a645" "0lsq62ynksy1fbw0m87f1d741fyvrrp1vrznx5hx0l2p4g4frhv3")
(mozilla-patch "icecat-CVE-2018-5125-pt7.patch" "16b8073d5c30" "1dv94qqah1wjd3bxjvrkmjbb2f95d3d11zpm8mggdk52il575bwl")
(mozilla-patch "icecat-bug-1442127-pt1.patch" "f931f85b09da" "02s380w8a73g4w2wm810lbigh4z4rrlfy10ywwhv4lpkbk8xg7pr")
(mozilla-patch "icecat-bug-1442127-pt2.patch" "da5792b70f30" "116k9qja5ir9b3laazasp43f5jx59qq72nknmq5bn5v1ixya9r4l")
(mozilla-patch "icecat-CVE-2018-5125-pt8.patch" "62b831df8269" "109pn0hqn7s27580glv4z7qv1pmjzii9szvf3wkn97k5wybrzgkx")
(mozilla-patch "icecat-bug-1442504.patch" "8954ce68a364" "0bl65zw82bwqg0mmcri94pxqq6ibff7y5rclkzapb081p6yvf73q")
(mozilla-patch "icecat-CVE-2018-5125-pt9.patch" "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb")
(mozilla-patch "icecat-bug-1426603.patch" "ca0b92ecedee" "0dc3mdl4a3hrq4j384zjavf3splj6blv4masign710hk7svlgbhq")
(mozilla-patch "icecat-CVE-2018-5146.patch" "494e5d5278ba" "1yb4lxjw499ppwhk31vz0vzl0cfqvj9d4jwqag7ayj53ybwsqgjr")
(mozilla-patch "icecat-CVE-2018-5147.patch" "5cd5586a2f48" "10s774pwvj6xfk3kk6ivnhp2acc8x9sqq6na8z47nkhgwl2712i5")
(mozilla-patch "icecat-CVE-2018-5148.patch" "c3e447e07077" "0gmwy631f8ip4gr1mpbjk8bx1n1748wdls5zq4y8hpmpnq5g1wyx")
(mozilla-patch "icecat-CVE-2018-5178.patch" "17201199b18d" "1d0hcim1fwh0bklwpmnal1mv9d9kmyif1m15aj1nqkf1n3x4xc37")
(mozilla-patch "icecat-bug-1361699.patch" "a07d6c3ff262" "1z8mjg2487r8pxi0x951v6fwwr696q84f6hlzimc3r7bn5ds9r83")
(mozilla-patch "icecat-CVE-2018-5150-pt01.patch" "7127ccf8f88c" "0m4my7aflpp0wlqilr2m4axd7k2fyrs7jqdcz2rrz5pwivz1anvd")
(mozilla-patch "icecat-bug-1444231.patch" "57bd35fa8618" "0pl6x5amc5x6nhwl7qnmnff3jjjxmbs8r365bfzj58g7q5ihqwvf")
(mozilla-patch "icecat-CVE-2018-5150-pt02.patch" "2f3e1ccf1661" "0azl8g81kpc0w2xpjpgm1154ll12g0a8n6i7bl3s9nnrk2i26n74")
(mozilla-patch "icecat-CVE-2018-5159.patch" "8ff2c4d68e36" "0kz1rqhnz8ca4z20hnpcafidhsrwhnm0h2gmlgchni33h8pisr1f")
(mozilla-patch "icecat-CVE-2018-5154.patch" "b8c430253efd" "1arjcaps9axhxh5ff84n9bydhhzrihn7hbq7v69nvqwqrjp3lgg9")
(mozilla-patch "icecat-CVE-2018-5155.patch" "05cadfa3ac39" "0q0vh7vy7x0l8jp6376fn10qljfp4mnp4m9zfn90j4m19pfl86a0")
(mozilla-patch "icecat-CVE-2018-5168.patch" "48a678d7cb81" "1yfh7kxxxvqck2hpn98pwag4splyc6c9brc5haq28fp8x9r9qvlk")
(mozilla-patch "icecat-CVE-2018-5150-pt03.patch" "112032576872" "1x1hxyggbxlnlj0n9cbp03hjnfvm6cq8nqj0jizrd8cfyd5aig8p")
(mozilla-patch "icecat-CVE-2018-5150-pt04.patch" "ad9a885b0df4" "1hrk1q9mk59jww55g4lqmaflznk87x3vvjn2mxfgfbbjs8l1cyz4")
(mozilla-patch "icecat-bug-1452416.patch" "f89ab96a2532" "1dqchxdyznhgyxhfq0hm0vg1p597hjqflfzigc7j3s5vxf9rg2nv")
(mozilla-patch "icecat-CVE-2018-5150-pt05.patch" "af885a1bd293" "1wfpqhm2dp4fsx6zbrncngsqz7g2x09b625zcighixrbpvybyww3")
(mozilla-patch "icecat-CVE-2018-5150-pt06.patch" "666fc84ec72d" "0lml2wqd4yqidhi364x8r90f78397k2y0kq5z5bv8l8j4bhcnb9v")
(search-patch "icecat-CVE-2018-5157-and-CVE-2018-5158.patch")
(mozilla-patch "icecat-CVE-2018-5150-pt07.patch" "1ab40761a856" "1kgwypy7k5b33jwkni4025za4kcnv5m6klsx4wsswlixmljmkbc7")
(mozilla-patch "icecat-bug-1453339.patch" "0edb8dca7087" "0b30pipqryh311sc97rcmwnx9n8qdlbbz90b2hkybjnprmbhfxrm")
(mozilla-patch "icecat-CVE-2018-5150-pt08.patch" "134c728799c1" "16hbwx6fx1hrddsyjjbd3z954ql3pg348xs13h9riyblq8crzmam")
(mozilla-patch "icecat-CVE-2018-5150-pt09.patch" "14eab155eaa8" "0wr4xgblxzk4c2gvlnpl7ic1196mrhry1hgwdl1jivq0ji5cbvbd")
(mozilla-patch "icecat-bug-1452619.patch" "2b75d55ccf0e" "1g87aybw6ggv6hyk385bplv0lx63n020gwyq0d6d4pqld48hsm1i")
(mozilla-patch "icecat-CVE-2018-5156-pt1.patch" "89857f35df29" "0gzi47svrw5ajdlm3i12193psm702zx70x5h1rwp4gb7gxh4m4d9")
(mozilla-patch "icecat-CVE-2018-5150-pt10.patch" "3f2ec03c0405" "0w02952dlxd2gmwghck2nm4rjjmc5ylg62bw6m1rvi35kcr134lr")
(mozilla-patch "icecat-CVE-2018-5183.patch" "f729bf78fb3a" "0xkj6jwxwdqkvb5c7wi16b8cm8qrnlrd3s9jnd46jg03iykrx56f")
(mozilla-patch "icecat-CVE-2018-5188-pt01.patch" "eb896089db47" "10lppk4x2d3pim71a36ky1dmg08rs5ckfiljwvfnr1cw6934qxl4")
(mozilla-patch "icecat-CVE-2018-5188-pt02.patch" "2374dca97bde" "0y1g55wvj44nzb1qfkl271jcf8s1ik8lcl1785z0zim4qzn7qkpa")
(mozilla-patch "icecat-CVE-2018-5188-pt03.patch" "70b6298e0c9e" "0n5jfy6c421dkybk8m18vd61y95zz0r64g1p1zlya3fps5knfaqi")
(mozilla-patch "icecat-CVE-2018-12365-pt1.patch" "4ef79fe9b3b7" "1c32z1ki1i6xj1nbb0xlxwqnmz48ikmy8dmp37rkjz8ssn04wgfg")
(mozilla-patch "icecat-CVE-2018-12365-pt2.patch" "9ad16112044a" "0ayya67sx7avcb8bplfdxb92l9g4mjrb1s3hby283llhqv0ikg9b")
(mozilla-patch "icecat-CVE-2018-12359.patch" "11d8a87fb6d6" "1rkmdk18llw0x1jakix75hlhy0hpsmlminnflagbzrzjli81gwm1")
(mozilla-patch "icecat-CVE-2018-5188-pt04.patch" "407b10ad1273" "16qzsfirw045xag96f1qvpdlibm8lwdj9l1mlli4n1vz0db91v9q")
(mozilla-patch "icecat-CVE-2018-6126.patch" "e76e2e481b17" "0hnx13msjy28n3bpa2c24kpzalam4bdk5gnp0f9k671l48rs9yb3")
(mozilla-patch "icecat-CVE-2018-5188-pt05.patch" "2c75bfcd465c" "1pjinj8qypafqm2fk68s3hzcbzcijn09qzrpcxvzq6bl1yfc1xfd")
(mozilla-patch "icecat-CVE-2018-5188-pt06.patch" "042f80f3befd" "0av918kin4bkrq7gnjz0h9w8kkq8rk9l93250lfl5kqrinza1gsk")
(mozilla-patch "icecat-CVE-2018-5188-pt07+bugs-1455071+1433642+1456604+1458320.patch"
"bb0451c9c4a0" "1lhm1b2a7c6jwhzsg3c830hfhp17p8j9zbcmgchpb8c5jkc3vw0x")
(mozilla-patch "icecat-CVE-2018-5188-pt08.patch" "8189b262e3b9" "13rh86ddwmj1bhv3ibbil3sv5xbqq1c9v1czgbsna5hxxkzc1y3b")
(mozilla-patch "icecat-CVE-2018-5188-pt09.patch" "9f81ae3f6e1d" "05vfg8a8jrzd93n1wvncmvdmqgf9cgsl8ryxgjs3032gbbjkga7q")
(mozilla-patch "icecat-CVE-2018-12360.patch" "face7a3dd5d7" "0jclw30mf693w8lrmvn0iankggj21nh4j3zh51q5363rj5xncdzx")
(mozilla-patch "icecat-CVE-2018-5188-pt10.patch" "7afb58c046c8" "1r0569r76712x7x1sw6xr0x06ilv6iw3fncb0f8r8b9mp6wrpx34")
(mozilla-patch "icecat-CVE-2018-12362-pt1.patch" "f1a745f8c42d" "11q73pb7a8f09xjzil4rhg5nr49zrnz1vb0prni0kqvrnppf5s40")
(mozilla-patch "icecat-CVE-2018-12362-pt2.patch" "1f9a430881cc" "0f79rv7njliqxx33z07n60b50jg0a596d1km7ayz2hivbl2d0168")
(mozilla-patch "icecat-CVE-2018-5188-pt11.patch" "28f4fc0a5141" "1a8f9z6c80in8ccj82ysdrcr2lqypp29l4acs50kwncm0c0b01zl")
(mozilla-patch "icecat-CVE-2018-12363.patch" "ad5a53a1d2b1" "0rhl4r39ydb3lkfp5pkwvhhzqgfh33s9r7b7jccgkrx6f13xyq78")
(mozilla-patch "icecat-CVE-2018-5188-pt12.patch" "0ddfc03c0454" "1b0xw2kj9765lvpl8iwr3wwcz40bdfp3dp4y9f546a61qsi9q9d6")
(mozilla-patch "icecat-CVE-2018-5156-pt2.patch" "dbf36189a364" "1awbyhy0r79i03sns2p0m78f9hb6c7kp4hwia2khx4qszlsr4j95")
(mozilla-patch "icecat-CVE-2018-5188-pt13.patch" "32509dfde003" "0cc3c92dgf5qynk093prq610c9x815l2fa24ddrw9czdzbwblsdq")
(mozilla-patch "icecat-bug-1462912.patch" "f18535a212da" "0zkqz9il89f1s1yrp5c6hj6kysy2x02iy50vgwdj30lr56gkpzmk")
(mozilla-patch "icecat-CVE-2018-5188-pt14.patch" "e8e9e1ef79f2" "0dc8p6fsppq3bhbpmp41f8mjxbr31pvgpga0a73dqdaicq5ydgj4")
(search-patch "icecat-bug-1413868-pt1.patch")
(mozilla-patch "icecat-CVE-2018-5188-pt15.patch" "9d4d31b2630d" "1lcbmsyi09kp80h1jgxj5l45zl24xn22h1lq7drbyjxsn1kggq4g")
(mozilla-patch "icecat-CVE-2018-12366-pt1.patch" "edf2c7dff493" "06xmyk7nm54cm9m6qc59wz8cxxfa5r25mf2xzdzy74iq5hwa1ac8")
(mozilla-patch "icecat-CVE-2018-5188-pt16.patch" "05549a4d1b80" "10q68cllshmmhlrbirm9h4gyc3ffrcpsxihfpcbxh90nv2h16jci")
(mozilla-patch "icecat-CVE-2018-12364.patch" "67b2d8924841" "197riigbb6l30959pygr0zlv7vaims78dg1mh0pg33pa7cbna0ds")
(mozilla-patch "icecat-CVE-2018-12366-pt2.patch" "528d4d997bb3" "0f375i96a404dkn0fanmd9pgfj3wyrhjfc5dwslw2s44gwfjhljb")
(mozilla-patch "icecat-bug-1369771.patch" "fab16ad7f256" "0kd8qm04sjgfgfg8yw3ivcxazb1d7v430g86chw4n64qybsh9ka3")
(mozilla-patch "icecat-CVE-2018-5188-pt17.patch" "068e249d02b4" "1iy9by1mg5qhp8502h31m8zm99aq2hx0c5n3hadd5pk11lfnq6ll")
(mozilla-patch "icecat-bug-1413868-pt2.patch" "755067c14b06" "089dwqwzcdg1l6aimi0i65q4dgb2iny5h8yjx63h9zgv77n0700a")))
;; FIXME (search-patch "icecat-use-system-harfbuzz.patch")
;; FIXME (search-patch "icecat-use-system-graphite2.patch")
(mozilla-patch "icecat-CVE-2018-12385.patch" "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
(search-patch "icecat-CVE-2018-12383.patch")
(mozilla-patch "icecat-bug-1489744.patch" "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")))
(modules '((guix build utils)))
(snippet
'(begin
@ -613,13 +530,13 @@ (define-public icecat
"modules/freetype2"
"modules/zlib"
"modules/libbz2"
"ipc/chromium/src/third_party/libevent"
;; UNBUNDLE-ME "ipc/chromium/src/third_party/libevent"
"media/libjpeg"
"media/libvpx"
"security/nss"
"gfx/cairo"
"gfx/harfbuzz"
"gfx/graphite2"
;; UNBUNDLE-ME "gfx/cairo"
;; UNBUNDLE-ME "gfx/harfbuzz"
;; UNBUNDLE-ME "gfx/graphite2"
"js/src/ctypes/libffi"
"db/sqlite3"))
;; Delete .pyc files, typically present in icecat source tarballs
@ -633,29 +550,29 @@ (define-public icecat
(inputs
`(("alsa-lib" ,alsa-lib)
("bzip2" ,bzip2)
("cairo" ,cairo)
;; UNBUNDLE-ME ("cairo" ,cairo)
("cups" ,cups)
("dbus-glib" ,dbus-glib)
("gdk-pixbuf" ,gdk-pixbuf)
("glib" ,glib)
("gtk+" ,gtk+)
("gtk+-2" ,gtk+-2)
("graphite2" ,graphite2)
;; UNBUNDLE-ME ("graphite2" ,graphite2)
("pango" ,pango)
("freetype" ,freetype)
("harfbuzz" ,harfbuzz)
;; UNBUNDLE-ME ("harfbuzz" ,harfbuzz)
("hunspell" ,hunspell)
("libcanberra" ,libcanberra)
("libgnome" ,libgnome)
("libjpeg-turbo" ,libjpeg-turbo)
("libxft" ,libxft)
("libevent" ,libevent-2.0)
;; UNBUNDLE-ME ("libevent" ,libevent-2.0)
("libxinerama" ,libxinerama)
("libxscrnsaver" ,libxscrnsaver)
("libxcomposite" ,libxcomposite)
("libxt" ,libxt)
("libffi" ,libffi)
("ffmpeg" ,ffmpeg-3.4)
("ffmpeg" ,ffmpeg)
("libvpx" ,libvpx)
("icu4c" ,icu4c)
("pixman" ,pixman)
@ -670,7 +587,9 @@ (define-public icecat
("zip" ,zip)
("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)
`(("rust" ,rust)
("cargo" ,rust "cargo")
("perl" ,perl)
("python" ,python-2) ; Python 3 not supported
("python2-pysqlite" ,python2-pysqlite)
("yasm" ,yasm)
@ -687,11 +606,12 @@ (define-public icecat
;; practice somehow. See <http://hydra.gnu.org/build/378133>.
#:validate-runpath? #f
#:imported-modules ,%cargo-build-system-modules ;for `generate-checksums'
#:configure-flags '("--enable-default-toolkit=cairo-gtk3"
"--with-distribution-id=org.gnu"
"--enable-gio"
"--enable-startup-notification"
"--enable-pulseaudio"
@ -701,7 +621,9 @@ (define-public icecat
"--disable-maintenance-service"
"--disable-eme"
"--disable-gconf"
"--disable-gnomeui"
;; Stylo requires LLVM/clang. For now, disable it.
"--disable-stylo"
;; Building with debugging symbols takes ~5GiB, so
;; disable it.
@ -716,15 +638,15 @@ (define-public icecat
"--with-system-zlib"
"--with-system-bz2"
"--with-system-jpeg" ; must be libjpeg-turbo
"--with-system-libevent"
;; UNBUNDLE-ME "--with-system-libevent"
"--with-system-libvpx"
"--with-system-icu"
"--with-system-nspr"
"--with-system-nss"
"--with-system-harfbuzz"
"--with-system-graphite2"
;; UNBUNDLE-ME "--with-system-harfbuzz"
;; UNBUNDLE-ME "--with-system-graphite2"
"--enable-system-pixman"
"--enable-system-cairo"
;; UNBUNDLE-ME "--enable-system-cairo"
"--enable-system-ffi"
"--enable-system-hunspell"
"--enable-system-sqlite"
@ -774,6 +696,24 @@ (define-public icecat
'avcodec', 'avutil', 'pulse' ]\n\n"
all)))
#t))
(add-after 'patch-source-shebangs 'patch-cargo-checksums
(lambda* _
(use-modules (guix build cargo-build-system))
(let ((null-file "/dev/null")
(null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
(substitute* '("Cargo.lock" "servo/Cargo.lock")
(("(\"checksum .* = )\".*\"" all name)
(string-append name "\"" null-hash "\"")))
(for-each
(lambda (filename)
(delete-file filename)
(let ((dir (dirname filename)))
(display (string-append
"patch-cargo-checksums: generate-checksums for "
dir "\n"))
(generate-checksums dir null-file)))
(find-files "third_party/rust" ".cargo-checksum.json")))
#t))
(replace
'configure
;; configure does not work followed by both "SHELL=..." and

119
gnu/packages/golang.scm
View file

@ -12,6 +12,7 @@
;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright @ 2018 Katherine Cox-Buday <cox.katherine.e@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -499,6 +500,124 @@ (define-public go-1.10
(setenv "HOME" "/tmp")
#t)))))))))
(define-public go-1.11
(package
(inherit go-1.10)
(name "go")
(version "1.11")
(source
(origin
(method url-fetch)
(uri (string-append "https://storage.googleapis.com/golang/"
name version ".src.tar.gz"))
(sha256
(base32
"1ysj04jzds6xa8kdflkdsgyv3mg9fdn90zdf78g4g6p4bwpy3hdg"))))
(arguments
(substitute-keyword-arguments (package-arguments go-1.10)
((#:phases phases)
`(modify-phases ,phases
(replace 'prebuild
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((gcclib (string-append (assoc-ref inputs "gcc:lib") "/lib"))
(ld (string-append (assoc-ref inputs "libc") "/lib"))
(loader (car (find-files ld "^ld-linux.+")))
(net-base (assoc-ref inputs "net-base"))
(tzdata-path
(string-append (assoc-ref inputs "tzdata") "/share/zoneinfo"))
(output (assoc-ref outputs "out")))
(for-each delete-file
;; Removing net/ tests, which fail when attempting to access
;; network resources not present in the build container.
'("net/listen_test.go"
"net/parse_test.go"
"net/cgo_unix_test.go"
;; A side affect of these test scripts is testing
;; cgo. Attempts at using cgo flags and
;; directives with these scripts as specified
;; here (https://golang.org/cmd/cgo/) have not
;; worked. The tests continue to state that they
;; can not find crt1.o despite being present.
"cmd/go/testdata/script/list_compiled_imports.txt"
"cmd/go/testdata/script/mod_case_cgo.txt"
;; https://github.com/golang/go/issues/24884
"os/user/user_test.go"))
(substitute* "os/os_test.go"
(("/usr/bin") (getcwd))
(("/bin/pwd") (which "pwd"))
(("/bin/sh") (which "sh")))
(substitute* "cmd/vendor/golang.org/x/sys/unix/syscall_unix_test.go"
(("/usr/bin") "/tmp"))
;; Add libgcc to runpath
(substitute* "cmd/link/internal/ld/lib.go"
(("!rpath.set") "true"))
(substitute* "cmd/go/internal/work/gccgo.go"
(("cgoldflags := \\[\\]string\\{\\}")
(string-append "cgoldflags := []string{"
"\"-rpath=" gcclib "\""
"}"))
(("\"-lgcc_s\", ")
(string-append
"\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", ")))
(substitute* "cmd/go/internal/work/gc.go"
(("ldflags = setextld\\(ldflags, compiler\\)")
(string-append
"ldflags = setextld(ldflags, compiler)\n"
"ldflags = append(ldflags, \"-r\")\n"
"ldflags = append(ldflags, \"" gcclib "\")\n")))
;; Disable failing tests: these tests attempt to access
;; commands or network resources which are neither available
;; nor necessary for the build to succeed.
(for-each
(match-lambda
((file regex)
(substitute* file
((regex all before test_name)
(string-append before "Disabled" test_name)))))
'(("net/net_test.go" "(.+)(TestShutdownUnix.+)")
("net/dial_test.go" "(.+)(TestDialTimeout.+)")
("os/os_test.go" "(.+)(TestHostname.+)")
("time/format_test.go" "(.+)(TestParseInSydney.+)")
("time/format_test.go" "(.+)(TestParseInLocation.+)")
("os/exec/exec_test.go" "(.+)(TestEcho.+)")
("os/exec/exec_test.go" "(.+)(TestCommandRelativeName.+)")
("os/exec/exec_test.go" "(.+)(TestCatStdin.+)")
("os/exec/exec_test.go" "(.+)(TestCatGoodAndBadFile.+)")
("os/exec/exec_test.go" "(.+)(TestExitStatus.+)")
("os/exec/exec_test.go" "(.+)(TestPipes.+)")
("os/exec/exec_test.go" "(.+)(TestStdinClose.+)")
("os/exec/exec_test.go" "(.+)(TestIgnorePipeErrorOnSuccess.+)")
("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)")
("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")
("net/lookup_test.go" "(.+)(TestLookupPort.+)")
("syscall/exec_linux_test.go"
"(.+)(TestCloneNEWUSERAndRemapNoRootDisableSetgroups.+)")))
;; fix shebang for testar script
;; note the target script is generated at build time.
(substitute* "../misc/cgo/testcarchive/carchive_test.go"
(("#!/usr/bin/env") (string-append "#!" (which "env"))))
(substitute* "net/lookup_unix.go"
(("/etc/protocols") (string-append net-base "/etc/protocols")))
(substitute* "net/port_unix.go"
(("/etc/services") (string-append net-base "/etc/services")))
(substitute* "time/zoneinfo_unix.go"
(("/usr/share/zoneinfo/") tzdata-path))
(substitute* (find-files "cmd" "\\.go")
(("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader))
#t)))))))))
(define-public go go-1.9)
(define-public go-github-com-alsm-ioprogress

19
gnu/packages/gprolog.scm
View file

@ -27,15 +27,18 @@ (define-module (gnu packages gprolog)
(define-public gprolog
(package
(name "gprolog")
(version "1.4.4")
(version "1.4.5")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/gprolog/gprolog-" version
".tar.gz"))
(sha256
(base32
"13miyas47bmijmadm68cbvb21n4s156gjafz7kfx9brk9djfkh0q"))))
(origin
(method url-fetch)
;; Recent versions are not hosted on the GNU mirrors.
(uri (list (string-append "http://gprolog.org/gprolog-" version
".tar.gz")
(string-append "mirror://gnu/gprolog/gprolog-" version
".tar.gz")))
(sha256
(base32
"0z4cc42n3k6i35b8mr816iwsvrpxshw6d7dgz6s2h1hy0l7g1p5z"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags

8
gnu/packages/graphics.scm
View file

@ -406,7 +406,7 @@ (define-public openimageio
(define-public openscenegraph
(package
(name "openscenegraph")
(version "3.6.2")
(version "3.6.3")
(source
(origin
(method git-fetch)
@ -415,8 +415,8 @@ (define-public openscenegraph
(commit (string-append "OpenSceneGraph-" version))))
(sha256
(base32
"03jk6lclyd4biniaw04w7j0z1spkm69f1c19i37b8v9x3zv1p1id"))
(file-name (string-append name "-" version "-checkout"))))
"0h32z15sa8sbq276j0iib0n707m8bs4p5ji9z2ah411446paad9q"))
(file-name (git-file-name name version))))
(properties
`((upstream-name . "OpenSceneGraph")))
(build-system cmake-build-system)
@ -437,8 +437,6 @@ (define-public openscenegraph
("jasper" ,jasper)
("librsvg" ,librsvg)
("libxrandr" ,libxrandr)
("pth" ,pth)
("qtbase" ,qtbase)
("ffmpeg" ,ffmpeg)
("mesa" ,mesa)))
(synopsis "High performance real-time graphics toolkit")

9
gnu/packages/graphviz.scm
View file

@ -220,17 +220,18 @@ (define-public xdot
(define-public python-pydot
(package
(name "python-pydot")
(version "1.2.3")
(version "1.2.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pydot" version))
(sha256
(base32
"00imlz0033dygb9gdag1xr0cybn33gk5jsdi9ffbszzr97rd7dgd"))))
"1dhy4jpp646jslh2yks6klwwbaxcs905byyny880gl1iap8y5llj"))))
(build-system python-build-system)
;; FIXME: No tests in PyPi release tarball.
(arguments '(#:tests? #f))
(native-inputs
;; For tests.
`(("python-chardet" ,python-chardet)))
(propagated-inputs
`(("python-pyparsing" ,python-pyparsing)))
(home-page "https://github.com/erocarrera/pydot")

5
gnu/packages/gtk.scm
View file

@ -1579,12 +1579,11 @@ (define-public gtkspell3
`(("intltool" ,intltool)
("pkg-config" ,pkg-config)))
(inputs
`(("enchant" ,enchant)
("gobject-introspection" ,gobject-introspection)
`(("gobject-introspection" ,gobject-introspection)
("gtk+" ,gtk+)
("pango" ,pango)))
(propagated-inputs
`(("enchant" ,enchant))) ; gtkspell3-3.0.pc refers to it.
`(("enchant" ,enchant-1.6))) ;gtkspell3-3.0.pc refers to it
(home-page "http://gtkspell.sourceforge.net")
(synopsis "Spell-checking addon for GTK's TextView widget")
(description

40
gnu/packages/guile.scm
View file

@ -286,7 +286,45 @@ (define-public guile-2.2/fixed
; when heavily loaded)
(define-public guile-next
(deprecated-package "guile-next" guile-2.2))
;; This is the upcoming Guile 3.0, with JIT support.
(let ((commit "a74b4a45fab1a78e34954bce5f031e8a9765f827")
(revision "0"))
(package
(inherit guile-2.2)
(name "guile-next")
(version (git-version "2.99" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://git.savannah.gnu.org/git/guile.git")
(commit commit)))
(sha256
(base32
"0kq6mabv7j4gdlwmpz3iaddv98sc7awkl2358sg8j50sg10yw8nx"))
(file-name (git-file-name name version))))
(native-inputs
`(("autoconf", autoconf)
("automake" ,automake)
("libtool" ,libtool)
("gettext" ,gnu-gettext)
("texinfo" ,texinfo)
("flex" ,flex)
,@(package-native-inputs guile-2.2)))
(arguments
(substitute-keyword-arguments (package-arguments guile-2.2)
((#:phases phases '%standard-phases)
;; XXX: The default 'bootstrap' phase tries to execute the
;; ./bootstrap directory.
`(modify-phases ,phases
(replace 'bootstrap
(lambda _
(patch-shebang "build-aux/git-version-gen")
(invoke "autoreconf" "-vfi")))
(add-before 'check 'skip-version-test
(lambda _
;; Remove this test that's bound to fail.
(delete-file "test-suite/tests/version.test")
#t)))))))))
(define (make-guile-readline guile)
(package

9
gnu/packages/haskell.scm
View file

@ -6729,7 +6729,7 @@ (define-public ghc-xml-types
(define-public ghc-xml-conduit
(package
(name "ghc-xml-conduit")
(version "1.7.1.2")
(version "1.8.0.1")
(source
(origin
(method url-fetch)
@ -6737,11 +6737,12 @@ (define-public ghc-xml-conduit
"xml-conduit-" version ".tar.gz"))
(sha256
(base32
"0n4k0rq9j5cc9kdvj9xbx8gmiqlyk5x6pw8yxzw5wfsw7qkych2s"))))
"177gmyigxql1pn3ncz0r8annwv5cbxnihbgrrg1dhm4gmc9jy2wq"))))
(build-system haskell-build-system)
(inputs
`(("ghc-conduit" ,ghc-conduit)
("ghc-conduit-extra" ,ghc-conduit-extra)
("ghc-doctest" ,ghc-doctest)
("ghc-resourcet" ,ghc-resourcet)
("ghc-text" ,ghc-text)
("ghc-xml-types" ,ghc-xml-types)
@ -6762,7 +6763,7 @@ (define-public ghc-xml-conduit
(define-public ghc-pandoc-citeproc
(package
(name "ghc-pandoc-citeproc")
(version "0.12.2.5")
(version "0.14.3.1")
(source
(origin
(method url-fetch)
@ -6771,7 +6772,7 @@ (define-public ghc-pandoc-citeproc
version ".tar.gz"))
(sha256
(base32
"1l58nbflcnlznc93qimkk7ghk2gv8kipf45zf88piqa2zys41yyx"))))
"0yj6rckwsc9vig40cm15ry0j3d01xpk04qma9n4byhal6v4b5h22"))))
(build-system haskell-build-system)
(arguments
`(#:phases

37
gnu/packages/ibus.scm
View file

@ -44,7 +44,7 @@ (define-module (gnu packages ibus)
(define-public ibus
(package
(name "ibus")
(version "1.5.17")
(version "1.5.19")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/ibus/ibus/"
@ -52,22 +52,29 @@ (define-public ibus
version "/ibus-" version ".tar.gz"))
(sha256
(base32
"06fj7lawww5d5w73pk249191lvmpz7shlxfxia74bjkpb42shiq3"))))
"0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:tests? #f ; tests fail because there's no connection to dbus
#:configure-flags '("--disable-emoji-dict" ; cannot find emoji.json path
#:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
"--disable-python2"
"--enable-python-library"
,(string-append "--with-ucd-dir="
(getcwd) "/ucd")
"--enable-wayland")
#:make-flags
(list "CC=gcc"
(string-append "pyoverridesdir="
(assoc-ref %outputs "out")
"/lib/python2.7/site-packages/gi/overrides/")
(string-append "py2overridesdir="
(assoc-ref %outputs "out")
"/lib/python2.7/site-packages/gi/overrides/"))
"/lib/python3.6/site-packages/gi/overrides/"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'prepare-ucd-dir
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "../ucd")
(symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
(symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
#t))
(add-before 'configure 'disable-dconf-update
(lambda _
(substitute* "data/dconf/Makefile.in"
@ -117,11 +124,23 @@ (define-public ibus
("wayland" ,wayland)
("xmodmap" ,xmodmap)
("iso-codes" ,iso-codes)
("pygobject2" ,python2-pygobject)
("python2" ,python-2)))
("pygobject2" ,python-pygobject)
("python" ,python)))
(native-inputs
`(("glib" ,glib "bin") ; for glib-genmarshal
("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
("unicode-nameslist"
,(origin
(method url-fetch)
(uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
(sha256
(base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
("unicode-blocks"
,(origin
(method url-fetch)
(uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
(sha256
(base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
("vala" ,vala)
("pkg-config" ,pkg-config)))
(native-search-paths

12
gnu/packages/image.scm
View file

@ -1347,16 +1347,18 @@ (define-public gpick
(define-public libiptcdata
(package
(name "libiptcdata")
(version "1.0.4")
(version "1.0.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/" name "/" name "/"
version "/" name "-" version ".tar.gz"))
(uri (string-append "https://github.com/ianw/libiptcdata"
"/releases/download/release_"
(string-join (string-split version #\.) "_")
"/" name "-" version ".tar.gz"))
(sha256
(base32
"03pfvkmmx762iydq0q207x2028d275pbdysfsgpmrr0ywy63pxkr"))))
"17m2bscc76r1bymjgb44fbbfrdsjfqyb2ivg9wchyllm8pgx1560"))))
(build-system gnu-build-system)
(home-page "http://libiptcdata.sourceforge.net/")
(home-page "https://github.com/ianw/libiptcdata")
(synopsis "IPTC metadata manipulation library")
(description
"Libiptcdata is a C library for manipulating the International Press

27
gnu/packages/kodi.scm
View file

@ -2,6 +2,7 @@
;;; Copyright © 2015 David Thompson <davet@gnu.org>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -92,22 +93,22 @@ (define-public crossguid
(arguments
'(#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(delete 'configure) ; no configure script
;; There's no build system here, so we have to do it ourselves.
(replace 'build
(lambda _
(and (zero? (system* "g++" "-c" "guid.cpp" "-o" "guid.o"
"-std=c++11" "-DGUID_LIBUUID"))
(zero? (system* "ar" "rvs" "libcrossguid.a" "guid.o")))))
(invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
"-std=c++11" "-DGUID_LIBUUID")
(invoke "ar" "rvs" "libcrossguid.a" "guid.o")))
(replace 'check
(lambda _
(and (zero? (system* "g++" "-c" "test.cpp" "-o" "test.o"
"-std=c++11"))
(zero? (system* "g++" "-c" "testmain.cpp" "-o" "testmain.o"
"-std=c++11"))
(zero? (system* "g++" "test.o" "guid.o" "testmain.o"
"-o" "test" "-luuid"))
(zero? (system* (string-append (getcwd) "/test"))))))
(invoke "g++" "-c" "test.cpp" "-o" "test.o"
"-std=c++11")
(invoke "g++" "-c" "testmain.cpp" "-o" "testmain.o"
"-std=c++11")
(invoke "g++" "test.o" "guid.o" "testmain.o"
"-o" "test" "-luuid")
(invoke (string-append (getcwd) "/test"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@ -294,7 +295,7 @@ (define-public kodi
"lib/cpluff")))
(every (lambda (third-party)
(with-directory-excursion third-party
(zero? (system* "autoreconf" "-vif"))))
(invoke "autoreconf" "-vif")))
dirs))))
(add-after 'bootstrap-bundled-software 'patch-stuff
(lambda* (#:key inputs #:allow-other-keys)
@ -335,7 +336,7 @@ (define-public kodi
#t))
(add-before 'check 'build-kodi-test
(lambda _
(zero? (system* "make" "kodi-test")))))))
(invoke "make" "kodi-test"))))))
;; TODO: Add dependencies for:
;; - nfs
;; - cec

16
gnu/packages/linux.scm
View file

@ -399,8 +399,8 @@ (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux" "a
;; supports qemu "virt" machine and possibly a large number of ARM boards.
;; See : https://wiki.debian.org/DebianKernel/ARMMP.
(define %linux-libre-version "4.18.8")
(define %linux-libre-hash "163awpba1yd0x33xzj5dczimk4y96xc28syc4w2ad0qafgapng8l")
(define %linux-libre-version "4.18.9")
(define %linux-libre-hash "0wwmhnfvcsdlqhzwwwyz1x5a3ldjky6l0xir1pi6pysr0lak402x")
(define %linux-libre-4.18-patches
(list %boot-logo-patch
@ -430,8 +430,8 @@ (define-public linux-libre
#:patches %linux-libre-4.18-patches
#:configuration-file kernel-config))
(define %linux-libre-4.14-version "4.14.70")
(define %linux-libre-4.14-hash "138v51m6k57wnvlf9c22dad0w819mfb8f95i6w99mlg69qpwdvag")
(define %linux-libre-4.14-version "4.14.71")
(define %linux-libre-4.14-hash "1akvykaccy7ikl8v04grwxvgs4z2rrs7drf2s85ysqwq79mdh3gq")
(define-public linux-libre-4.14
(make-linux-libre %linux-libre-4.14-version
@ -440,14 +440,14 @@ (define-public linux-libre-4.14
#:configuration-file kernel-config))
(define-public linux-libre-4.9
(make-linux-libre "4.9.127"
"0q7h5gnl3ikic0pvwrxp78pz56yvijhz6s84gb92xywi1v3dd8mh"
(make-linux-libre "4.9.128"
"0lww23xcyyg0dwzrap5x9d700gy3lbxln55n6sqqkm7m89dkqwha"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
(make-linux-libre "4.4.156"
"13j4jb4hifh3fah2ysy2425fakwqqdh2z23lf4i0frxa1xl974h2"
(make-linux-libre "4.4.157"
"00bnfqwkr0jfdabmwx5qk5bqxn5vwnnzwqbm5rfg7lggii74kk54"
%intel-compatible-systems
#:configuration-file kernel-config))

4
gnu/packages/lxde.scm
View file

@ -164,7 +164,7 @@ (define-public lxtask
(define-public lxterminal
(package
(name "lxterminal")
(version "0.3.1")
(version "0.3.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/lxde/LXTerminal"
@ -172,7 +172,7 @@ (define-public lxterminal
version "/" name "-" version ".tar.xz"))
(sha256
(base32
"0jrc3m0hbxcmcgahwjlm46s2350gh80ggb6a90xy0h6xqa3z73fd"))))
"1124pghrhnx6q4391ri8nvi6bsmvbj1dx81an08mird8jf2b2rii"))))
(build-system gnu-build-system)
(inputs `(("gtk+" ,gtk+-2)
("vte" ,vte/gtk+-2)))

19
gnu/packages/machine-learning.scm
View file

@ -750,7 +750,24 @@ (define-public python-scikit-learn
(license license:bsd-3)))
(define-public python2-scikit-learn
(package-with-python2 python-scikit-learn))
(let ((parent (package-with-python2 python-scikit-learn)))
(package (inherit parent)
(arguments
(substitute-keyword-arguments (package-arguments parent)
((#:phases phases)
`(modify-phases ,phases
(replace 'check
(lambda _
;; Restrict OpenBLAS threads to prevent segfaults while testing!
(setenv "OPENBLAS_NUM_THREADS" "1")
;; Some tests expect to be able to write to HOME.
(setenv "HOME" "/tmp")
;; Disable tests that require network access
(delete-file "sklearn/datasets/tests/test_kddcup99.py")
(delete-file "sklearn/datasets/tests/test_mldata.py")
(delete-file "sklearn/datasets/tests/test_rcv1.py")
(invoke "pytest" "sklearn")
#t)))))))))
(define-public python-autograd
(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")

2
gnu/packages/mate.scm
View file

@ -1411,7 +1411,7 @@ (define-public pluma
(inputs
`(("atk" ,atk)
("cairo" ,cairo)
("enchant" ,enchant)
("enchant" ,enchant-1.6)
("glib" ,glib)
("gtk+" ,gtk+)
("gtksourceview" ,gtksourceview)

21
gnu/packages/maths.scm
View file

@ -814,8 +814,11 @@ (define-public hdf5
(mkdir-p flib)
(mkdir-p finc)
(mkdir-p fex)
(rename-file (string-append bin "/h5fc")
(string-append fbin "/h5fc"))
;; Note: When built with --enable-parallel, the 'h5fc' file
;; doesn't exist, hence this condition.
(when (file-exists? (string-append bin "/h5fc"))
(rename-file (string-append bin "/h5fc")
(string-append fbin "/h5fc")))
(for-each (lambda (file)
(rename-file file
(string-append flib "/" (basename file))))
@ -1034,10 +1037,13 @@ (define-public hdf5-parallel-openmpi
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
(substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
,@(package-arguments hdf5))
(substitute-keyword-arguments (package-arguments hdf5)
((#:configure-flags flags)
``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
((#:phases phases)
`(modify-phases ,phases
(add-after 'build 'mpi-setup
,%openmpi-setup)
(add-before 'check 'patch-tests
(lambda _
;; OpenMPI's mpirun will exit with non-zero status if it
@ -1396,6 +1402,13 @@ (define-public octave
("less" ,less)
("ghostscript" ,ghostscript)
("gnuplot" ,gnuplot)))
;; Octave code uses this variable to detect directories holding multiple CA
;; certificates to verify peers with. This is required for the networking
;; functions that require encryption to work properly.
(native-search-paths
(list (search-path-specification
(variable "CURLOPT_CAPATH")
(files '("etc/ssl/certs")))))
(arguments
`(#:configure-flags
(list (string-append "--with-shell="

17
gnu/packages/messaging.scm
View file

@ -1135,7 +1135,7 @@ (define-public ytalk
(define-public gloox
(package
(name "gloox")
(version "1.0.17")
(version "1.0.21")
(source
(origin
(method url-fetch)
@ -1143,7 +1143,7 @@ (define-public gloox
version ".tar.bz2"))
(sha256
(base32
"09c01jr5nrm7f1ly42wg0pqqscmp48pv8y2fjx1vwbavjxdq59ri"))))
"1k57qgif1yii515m6jaqaibkdysfab6394bpawd2l67321f1a4rw"))))
(build-system gnu-build-system)
(inputs
`(("libidn" ,libidn)
@ -1472,15 +1472,16 @@ (define-public freetalk
(define-public libmesode
(package
(name "libmesode")
(version "0.9.1")
(version "0.9.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/boothj5/libmesode/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/boothj5/libmesode.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0iaj56fkd5bjvqpvq3324ni895rmbj1akbfqipjydnghfwaym4z6"))))
"06f5nfaypvxrbsinxa1k2vrxrs7kqmg38g4wwwk5d63hpn1pj8ak"))))
(build-system gnu-build-system)
(inputs
`(("expat" ,expat)

4
gnu/packages/nano.scm
View file

@ -30,7 +30,7 @@ (define-module (gnu packages nano)
(define-public nano
(package
(name "nano")
(version "3.0")
(version "3.1")
(source
(origin
(method url-fetch)
@ -38,7 +38,7 @@ (define-public nano
version ".tar.xz"))
(sha256
(base32
"1868hg9s584fwjrh0fzdrixmxc2qhw520z4q5iv68kjiajivr9g0"))))
"17kinzyv6vwgyx2d0ym1kp65qbf7kxzwpyg21ic1rijv1aj2rh0l"))))
(build-system gnu-build-system)
(inputs
`(("gettext" ,gettext-minimal)

56
gnu/packages/networking.scm
View file

@ -87,6 +87,7 @@ (define-module (gnu packages networking)
#:use-module (gnu packages perl-check)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages ssh)
@ -651,7 +652,7 @@ (define-public wireshark
(define-public fping
(package
(name "fping")
(version "4.0")
(version "4.1")
(source
(origin
(method url-fetch)
@ -659,9 +660,9 @@ (define-public fping
version ".tar.gz"))
(sha256
(base32
"1kp81wchi79l8z8rrj602fpjrd8bi84y3i7fsaclzlwap5943sv7"))))
"0wxbvm480vij8dy4v1pi8f0c7010rx6bidg3qhsvkdf2ijhy4cr7"))))
(build-system gnu-build-system)
(home-page "http://fping.org/")
(home-page "https://fping.org/")
(synopsis "Send ICMP ECHO_REQUEST packets to network hosts")
(description
"fping is a ping like program which uses the Internet Control Message
@ -673,6 +674,55 @@ (define-public fping
fashion.")
(license license:expat)))
(define-public gandi.cli
(package
(name "gandi.cli")
(version "1.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
(base32 "0vfzkw1avybjkf6fwqpf5m4kjz4c0qkkmj62f3jd0zx00vh5ly1d"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'embed-store-file-names
(lambda _
(substitute* (list "gandi/cli/modules/cert.py"
"gandi/cli/tests/commands/test_certificate.py")
(("openssl") (which "openssl")))
#t))
(add-after 'install 'install-documentation
;; The included man page may be outdated but we install it anyway,
;; since it's mentioned in 'gandi --help' and better than nothing.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man1 (string-append out "/share/man/man1")))
(mkdir-p man1)
(with-output-to-file (string-append man1 "/gandi.1")
(lambda _
(invoke "rst2man.py" "gandicli.man.rst")))
#t))))))
(native-inputs
`(("python-docutils" ,python-docutils) ; for rst2man.py
("python-pytest-cov" ,python-pytest-cov)
("python-tox" ,python-tox)))
(inputs
`(("openssl" ,openssl)
("python-click" ,python-click)
("python-ipy" ,python-ipy)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)))
(home-page "https://cli.gandi.net")
(synopsis "Command-line interface to the Gandi.net Web API")
(description
"This package provides a command-line client (@command{gandi}) to buy,
manage, and delete Internet resources from Gandi.net such as domain names,
virtual machines, and certificates.")
(license license:gpl3+)))
(define-public httping
(package
(name "httping")

34
gnu/packages/node.scm
View file

@ -5,6 +5,7 @@
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -86,6 +87,14 @@ (define-public node
(modify-phases %standard-phases
(add-before 'configure 'patch-files
(lambda* (#:key inputs #:allow-other-keys)
;; This phase is inherited by Node LTS, which does not have all
;; the files listed here. Use this helper for convenience.
(define (delete-if-exists file)
(if (file-exists? file)
(delete-file file)
'()))
;; Fix hardcoded /bin/sh references.
(substitute* '("lib/child_process.js"
"lib/internal/v8_prof_polyfill.js"
@ -103,7 +112,7 @@ (define-public node
;; FIXME: These tests depend on being able to install eslint.
;; See https://github.com/nodejs/node/issues/17098.
(for-each delete-file
(for-each delete-if-exists
'("test/parallel/test-eslint-alphabetize-errors.js"
"test/parallel/test-eslint-buffer-constructor.js"
"test/parallel/test-eslint-documented-errors.js"
@ -111,7 +120,7 @@ (define-public node
;; FIXME: These tests fail in the build container, but they don't
;; seem to be indicative of real problems in practice.
(for-each delete-file
(for-each delete-if-exists
'("test/async-hooks/test-ttywrap.readstream.js"
"test/parallel/test-util-inspect.js"
"test/parallel/test-v8-serdes.js"
@ -125,6 +134,14 @@ (define-public node
"test/sequential/test-child-process-emfile.js"
"test/sequential/test-benchmark-child-process.js"
"test/sequential/test-http-regr-gh-2928.js"))
;; These tests have an expiry date: they depend on the validity of
;; TLS certificates that are bundled with the source. We want this
;; package to be reproducible forever, so remove those.
;; TODO: Regenerate certs instead.
(for-each delete-if-exists
'("test/parallel/test-tls-passphrase.js"
"test/parallel/test-tls-server-verify.js"))
#t))
(replace 'configure
;; Node's configure script is actually a python script, so we can't
@ -180,3 +197,16 @@ (define-public node
(home-page "https://nodejs.org/")
(license expat)
(properties '((timeout . 3600))))) ; 1 h
(define-public node-lts
(package
(inherit node)
(name "node-lts")
(version "8.12.0")
(source (origin
(inherit (package-source node))
(uri (string-append "https://nodejs.org/dist/v" version
"/node-v" version ".tar.xz"))
(sha256
(base32
"16j1rrxkhmvpcw689ndw1raql1gz4jqn7n82z55zn63c05cgz7as"))))))

12
gnu/packages/ocaml.scm
View file

@ -65,6 +65,7 @@ (define-module (gnu packages ocaml)
#:use-module (guix build-system gnu)
#:use-module (guix build-system ocaml)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix svn-download)
@ -1650,12 +1651,13 @@ (define-public ocaml-ssl
(version "0.5.5")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/savonet/ocaml-ssl/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/savonet/ocaml-ssl.git")
(commit version)))
(file-name (git-file-name name version))
(sha256 (base32
"15p7652cvzdrlqxc1af11mg07wasxr1fsaj44gcmmh6bmav7wfzq"))))
"0fviq8xhp3qk7pmkl7knchywsipxgb7p0z489hj8qnf2sx8xzdmy"))))
(build-system ocaml-build-system)
(arguments `(#:tests? #f
#:make-flags (list "OCAMLFIND_LDCONF=ignore")

1
gnu/packages/openldap.scm
View file

@ -293,6 +293,7 @@ (define-public 389-ds-base
("nspr" ,nspr)
("nss" ,nss)
("openldap" ,openldap)
("openssl" ,openssl) ; #included by net-snmp
("pcre" ,pcre)
("perl" ,perl)
("python" ,python)

4
gnu/packages/package-management.scm
View file

@ -566,13 +566,13 @@ (define-public rpm
(define-public diffoscope
(package
(name "diffoscope")
(version "100")
(version "102")
(source (origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
(base32
"0sh7g26i5ndpa8l7xq6rnijbi3jz5izjn0b98zcnm6wpgghszw48"))))
"0v2z98xx7n4viw12yq83flpb9ir5ahy1gn44pic0i3dam18xhcm6"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases

6
gnu/packages/parallel.scm
View file

@ -48,7 +48,7 @@ (define-module (gnu packages parallel)
(define-public parallel
(package
(name "parallel")
(version "20180822")
(version "20180922")
(source
(origin
(method url-fetch)
@ -56,7 +56,7 @@ (define-public parallel
version ".tar.bz2"))
(sha256
(base32
"0jjs7fpvdjjb5v0j39a6k7hq9h5ap3db1j7vg1r2dq4swk23h9bm"))))
"07q7lzway2qf8mx6fb4q45jmirsc8pw6rgv03ifrp32jw3q8w1za"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -66,7 +66,7 @@ (define-public parallel
(for-each
(lambda (file)
(substitute* file
;; Patch hard coded '/bin/sh' in the lin ending in:
;; Patch hard coded '/bin/sh' in the line ending in:
;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
;; parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
(("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))

22
gnu/packages/patches/hmmer-remove-cpu-specificity.patch
View file

@ -1,22 +0,0 @@
This patch removes compilation flags which make the build for the machine
where compilation takes place, rendering the build not reproducible.
diff --git a/configure b/configure
index 8b6aaef..49a6afc 100755
--- a/configure
+++ b/configure
@@ -6125,14 +6125,6 @@ fi # guess arch
if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then
for arch in $ax_gcc_arch; do
- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code
- flags="-mtune=$arch"
- # -mcpu=$arch and m$arch generate nonportable code on every arch except
- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr.
- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac
- else
- flags="-march=$arch -mcpu=$arch -m$arch"
- fi
for flag in $flags; do
as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh`
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5

103
gnu/packages/patches/icecat-CVE-2018-12383.patch Normal file
View file

@ -0,0 +1,103 @@
Based on upstream changeset:
https://hg.mozilla.org/releases/mozilla-esr60/rev/300efdbc9fe1
but with the git binary patch and related test changes omitted,
and adapted to apply cleanly to GNU IceCat.
# HG changeset patch
# User David Keeler <dkeeler@mozilla.com>
# Date 1531860660 25200
# Node ID 300efdbc9fe1f9165428c7934861033935b5abfa
# Parent 80a4a7ef281374dbb2afda8edac54665b14b9ef8
Bug 1475775 - Clean up old NSS DB file after upgrade if necessary. r=franziskus, r=mattn, a=RyanVM
Reviewers: franziskus, mattn
Bug #: 1475775
Differential Revision: https://phabricator.services.mozilla.com/D2202
diff --git a/security/manager/ssl/nsNSSComponent.cpp b/security/manager/ssl/nsNSSComponent.cpp
--- a/security/manager/ssl/nsNSSComponent.cpp
+++ b/security/manager/ssl/nsNSSComponent.cpp
@@ -1935,16 +1935,61 @@ AttemptToRenameBothPKCS11ModuleDBVersion
NS_NAMED_LITERAL_CSTRING(sqlModuleDBFilename, "pkcs11.txt");
nsresult rv = AttemptToRenamePKCS11ModuleDB(profilePath,
legacyModuleDBFilename);
if (NS_FAILED(rv)) {
return rv;
}
return AttemptToRenamePKCS11ModuleDB(profilePath, sqlModuleDBFilename);
}
+
+// When we changed from the old dbm database format to the newer sqlite
+// implementation, the upgrade process left behind the existing files. Suppose a
+// user had not set a password for the old key3.db (which is about 99% of
+// users). After upgrading, both the old database and the new database are
+// unprotected. If the user then sets a password for the new database, the old
+// one will not be protected. In this scenario, we should probably just remove
+// the old database (it would only be relevant if the user downgraded to a
+// version of IceCat before 58, but we have to trade this off against the
+// user's old private keys being unexpectedly unprotected after setting a
+// password).
+// This was never an issue on Android because we always used the new
+// implementation.
+static void
+MaybeCleanUpOldNSSFiles(const nsACString& profilePath)
+{
+ UniquePK11SlotInfo slot(PK11_GetInternalKeySlot());
+ if (!slot) {
+ return;
+ }
+ // Unfortunately we can't now tell the difference between "there already was a
+ // password when the upgrade happened" and "there was not a password but then
+ // the user added one after upgrading".
+ bool hasPassword = PK11_NeedLogin(slot.get()) &&
+ !PK11_NeedUserInit(slot.get());
+ if (!hasPassword) {
+ return;
+ }
+ nsCOMPtr<nsIFile> dbFile = do_CreateInstance("@mozilla.org/file/local;1");
+ if (!dbFile) {
+ return;
+ }
+ nsresult rv = dbFile->InitWithNativePath(profilePath);
+ if (NS_FAILED(rv)) {
+ return;
+ }
+ NS_NAMED_LITERAL_CSTRING(keyDBFilename, "key3.db");
+ rv = dbFile->AppendNative(keyDBFilename);
+ if (NS_FAILED(rv)) {
+ return;
+ }
+ // Since this isn't a directory, the `recursive` argument to `Remove` is
+ // irrelevant.
+ Unused << dbFile->Remove(false);
+}
#endif // ifndef ANDROID
// Given a profile directory, attempt to initialize NSS. If nocertdb is true,
// (or if we don't have a profile directory) simply initialize NSS in no DB mode
// and return. Otherwise, first attempt to initialize in read/write mode, and
// then read-only mode if that fails. If both attempts fail, we may be failing
// to initialize an NSS DB collection that has FIPS mode enabled. Attempt to
// ascertain if this is the case, and if so, rename the offending PKCS#11 module
@@ -1966,16 +2011,19 @@ InitializeNSSWithFallbacks(const nsACStr
// Try read/write mode. If we're in safeMode, we won't load PKCS#11 modules.
#ifndef ANDROID
PRErrorCode savedPRErrorCode1;
#endif // ifndef ANDROID
SECStatus srv = ::mozilla::psm::InitializeNSS(profilePath, false, !safeMode);
if (srv == SECSuccess) {
MOZ_LOG(gPIPNSSLog, LogLevel::Debug, ("initialized NSS in r/w mode"));
+#ifndef ANDROID
+ MaybeCleanUpOldNSSFiles(profilePath);
+#endif // ifndef ANDROID
return NS_OK;
}
#ifndef ANDROID
savedPRErrorCode1 = PR_GetError();
PRErrorCode savedPRErrorCode2;
#endif // ifndef ANDROID
// That failed. Try read-only mode.
srv = ::mozilla::psm::InitializeNSS(profilePath, true, !safeMode);

441
gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch
View file

@ -1,441 +0,0 @@
Based on <https://hg.mozilla.org/releases/mozilla-esr52/rev/608e76ec5ba2>
Adapted to apply cleanly to GNU IceCat.
# HG changeset patch
# User Ryan VanderMeulen <ryanvm@gmail.com>
# Date 1523630807 14400
# Node ID 608e76ec5ba25cec2271d2b400c7bce2d4c5ef79
# Parent 10b7f43b536f93151201d44d304c991aa9af5d0c
Bug 1452075 - Backport some upstream pdf.js fixes to ESR52. r=bdahl, r=yury, a=RyanVM
diff --git a/browser/extensions/pdfjs/content/PdfStreamConverter.jsm b/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
--- a/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
+++ b/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
@@ -24,17 +24,18 @@ const Cc = Components.classes;
const Ci = Components.interfaces;
const Cr = Components.results;
const Cu = Components.utils;
// True only if this is the version of pdf.js that is included with icecat.
const MOZ_CENTRAL = JSON.parse('true');
const PDFJS_EVENT_ID = 'pdf.js.message';
const PDF_CONTENT_TYPE = 'application/pdf';
const PREF_PREFIX = 'pdfjs';
-const PDF_VIEWER_WEB_PAGE = 'resource://pdf.js/web/viewer.html';
+const PDF_VIEWER_ORIGIN = "resource://pdf.js";
+const PDF_VIEWER_WEB_PAGE = "resource://pdf.js/web/viewer.html";
const MAX_NUMBER_OF_PREFS = 50;
const MAX_STRING_PREF_LENGTH = 128;
Cu.import('resource://gre/modules/XPCOMUtils.jsm');
Cu.import('resource://gre/modules/Services.jsm');
Cu.import('resource://gre/modules/NetUtil.jsm');
XPCOMUtils.defineLazyModuleGetter(this, 'NetworkManager',
@@ -105,21 +106,25 @@ function log(aMsg) {
if (!getBoolPref(PREF_PREFIX + '.pdfBugEnabled', false)) {
return;
}
var msg = 'PdfStreamConverter.js: ' + (aMsg.join ? aMsg.join('') : aMsg);
Services.console.logStringMessage(msg);
dump(msg + '\n');
}
-function getDOMWindow(aChannel) {
+function getDOMWindow(aChannel, aPrincipal) {
var requestor = aChannel.notificationCallbacks ?
aChannel.notificationCallbacks :
aChannel.loadGroup.notificationCallbacks;
var win = requestor.getInterface(Components.interfaces.nsIDOMWindow);
+ // Ensure the window wasn't navigated to something that is not PDF.js.
+ if (!win.document.nodePrincipal.equals(aPrincipal)) {
+ return null;
+ }
return win;
}
function getLocalizedStrings(path) {
var stringBundle = Cc['@mozilla.org/intl/stringbundle;1'].
getService(Ci.nsIStringBundleService).
createBundle('chrome://pdf.js/locale/' + path);
@@ -627,31 +632,31 @@ var RangedChromeActions = (function Rang
data = this.dataListener.readData();
this.dataListener.onprogress = function (loaded, total) {
self.domWindow.postMessage({
pdfjsLoadAction: 'progressiveRead',
loaded: loaded,
total: total,
chunk: self.dataListener.readData()
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
};
this.dataListener.oncomplete = function () {
self.dataListener = null;
};
}
this.domWindow.postMessage({
pdfjsLoadAction: 'supportsRangedLoading',
rangeEnabled: this.rangeEnabled,
streamingEnabled: this.streamingEnabled,
pdfUrl: this.pdfUrl,
length: this.contentLength,
data: data
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
return true;
};
proto.requestDataRange = function RangedChromeActions_requestDataRange(args) {
if (!this.rangeEnabled) {
return;
}
@@ -663,23 +668,23 @@ var RangedChromeActions = (function Rang
// errors from chrome code for non-range requests, so this doesn't
// seem high-pri
this.networkManager.requestRange(begin, end, {
onDone: function RangedChromeActions_onDone(args) {
domWindow.postMessage({
pdfjsLoadAction: 'range',
begin: args.begin,
chunk: args.chunk
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
},
onProgress: function RangedChromeActions_onProgress(evt) {
domWindow.postMessage({
pdfjsLoadAction: 'rangeProgress',
loaded: evt.loaded,
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
}
});
};
proto.abortLoading = function RangedChromeActions_abortLoading() {
this.networkManager.abortAllRequests();
if (this.originalRequest) {
this.originalRequest.cancel(Cr.NS_BINDING_ABORTED);
@@ -718,26 +723,26 @@ var StandardChromeActions = (function St
var self = this;
this.dataListener.onprogress = function ChromeActions_dataListenerProgress(
loaded, total) {
self.domWindow.postMessage({
pdfjsLoadAction: 'progress',
loaded: loaded,
total: total
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
};
this.dataListener.oncomplete =
function StandardChromeActions_dataListenerComplete(data, errorCode) {
self.domWindow.postMessage({
pdfjsLoadAction: 'complete',
data: data,
errorCode: errorCode
- }, '*');
+ }, PDF_VIEWER_ORIGIN);
self.dataListener = null;
self.originalRequest = null;
};
return true;
};
@@ -972,31 +977,35 @@ PdfStreamConverter.prototype = {
var proxy = {
onStartRequest: function(request, context) {
listener.onStartRequest(aRequest, aContext);
},
onDataAvailable: function(request, context, inputStream, offset, count) {
listener.onDataAvailable(aRequest, aContext, inputStream,
offset, count);
},
- onStopRequest: function(request, context, statusCode) {
- // We get the DOM window here instead of before the request since it
- // may have changed during a redirect.
- var domWindow = getDOMWindow(channel);
+ onStopRequest(request, context, statusCode) {
+ var domWindow = getDOMWindow(channel, resourcePrincipal);
+ if (!Components.isSuccessCode(statusCode) || !domWindow) {
+ // The request may have been aborted and the document may have been
+ // replaced with something that is not PDF.js, abort attaching.
+ listener.onStopRequest(aRequest, context, statusCode);
+ return;
+ }
var actions;
if (rangeRequest || streamRequest) {
actions = new RangedChromeActions(
domWindow, contentDispositionFilename, aRequest,
rangeRequest, streamRequest, dataListener);
} else {
actions = new StandardChromeActions(
domWindow, contentDispositionFilename, aRequest, dataListener);
}
var requestListener = new RequestListener(actions);
- domWindow.addEventListener(PDFJS_EVENT_ID, function(event) {
+ domWindow.document.addEventListener(PDFJS_EVENT_ID, function(event) {
requestListener.receive(event);
}, false, true);
if (actions.supportsIntegratedFind()) {
var findEventManager = new FindEventManager(domWindow);
findEventManager.bind();
}
listener.onStopRequest(aRequest, aContext, statusCode);
diff --git a/browser/extensions/pdfjs/content/build/pdf.worker.js b/browser/extensions/pdfjs/content/build/pdf.worker.js
--- a/browser/extensions/pdfjs/content/build/pdf.worker.js
+++ b/browser/extensions/pdfjs/content/build/pdf.worker.js
@@ -41648,16 +41648,32 @@
var error = sharedUtil.error;
var info = sharedUtil.info;
var isArray = sharedUtil.isArray;
var isBool = sharedUtil.isBool;
var isDict = corePrimitives.isDict;
var isStream = corePrimitives.isStream;
var PostScriptLexer = corePsParser.PostScriptLexer;
var PostScriptParser = corePsParser.PostScriptParser;
+ function toNumberArray(arr) {
+ if (!Array.isArray(arr)) {
+ return null;
+ }
+ var length = arr.length;
+ for (var i = 0; i < length; i++) {
+ if (typeof arr[i] !== 'number') {
+ var result = new Array(length);
+ for (var j = 0; j < length; j++) {
+ result[j] = +arr[j];
+ }
+ return result;
+ }
+ }
+ return arr;
+ }
var PDFFunction = function PDFFunctionClosure() {
var CONSTRUCT_SAMPLED = 0;
var CONSTRUCT_INTERPOLATED = 2;
var CONSTRUCT_STICHED = 3;
var CONSTRUCT_POSTSCRIPT = 4;
return {
getSampleArray: function PDFFunction_getSampleArray(size, outputSize, bps, str) {
var i, ii;
@@ -41747,43 +41763,43 @@
out[index] = [
arr[i],
arr[i + 1]
];
++index;
}
return out;
}
- var domain = dict.getArray('Domain');
- var range = dict.getArray('Range');
+ var domain = toNumberArray(dict.getArray('Domain'));
+ var range = toNumberArray(dict.getArray('Range'));
if (!domain || !range) {
error('No domain or range');
}
var inputSize = domain.length / 2;
var outputSize = range.length / 2;
domain = toMultiArray(domain);
range = toMultiArray(range);
- var size = dict.get('Size');
+ var size = toNumberArray(dict.get('Size'));
var bps = dict.get('BitsPerSample');
var order = dict.get('Order') || 1;
if (order !== 1) {
// No description how cubic spline interpolation works in PDF32000:2008
// As in poppler, ignoring order, linear interpolation may work as good
info('No support for cubic spline interpolation: ' + order);
}
- var encode = dict.getArray('Encode');
+ var encode = toNumberArray(dict.getArray('Encode'));
if (!encode) {
encode = [];
for (var i = 0; i < inputSize; ++i) {
- encode.push(0);
- encode.push(size[i] - 1);
- }
- }
- encode = toMultiArray(encode);
- var decode = dict.getArray('Decode');
+ encode.push([0, size[i] - 1]);
+ }
+ } else {
+ encode = toMultiArray(encode);
+ }
+ var decode = toNumberArray(dict.getArray('Decode'));
if (!decode) {
decode = range;
} else {
decode = toMultiArray(decode);
}
var samples = this.getSampleArray(size, outputSize, bps, str);
return [
CONSTRUCT_SAMPLED,
@@ -41868,22 +41884,19 @@
// Decode_2j, Decode_2j+1)
rj = interpolate(rj, 0, 1, decode[j][0], decode[j][1]);
// y_j = min(max(r_j, range_2j), range_2j+1)
dest[destOffset + j] = Math.min(Math.max(rj, range[j][0]), range[j][1]);
}
};
},
constructInterpolated: function PDFFunction_constructInterpolated(str, dict) {
- var c0 = dict.getArray('C0') || [0];
- var c1 = dict.getArray('C1') || [1];
+ var c0 = toNumberArray(dict.getArray('C0')) || [0];
+ var c1 = toNumberArray(dict.getArray('C1')) || [1];
var n = dict.get('N');
- if (!isArray(c0) || !isArray(c1)) {
- error('Illegal dictionary for interpolated function');
- }
var length = c0.length;
var diff = [];
for (var i = 0; i < length; ++i) {
diff.push(c1[i] - c0[i]);
}
return [
CONSTRUCT_INTERPOLATED,
c0,
@@ -41899,49 +41912,45 @@
return function constructInterpolatedFromIRResult(src, srcOffset, dest, destOffset) {
var x = n === 1 ? src[srcOffset] : Math.pow(src[srcOffset], n);
for (var j = 0; j < length; ++j) {
dest[destOffset + j] = c0[j] + x * diff[j];
}
};
},
constructStiched: function PDFFunction_constructStiched(fn, dict, xref) {
- var domain = dict.getArray('Domain');
+ var domain = toNumberArray(dict.getArray('Domain'));
if (!domain) {
error('No domain');
}
var inputSize = domain.length / 2;
if (inputSize !== 1) {
error('Bad domain for stiched function');
}
var fnRefs = dict.get('Functions');
var fns = [];
for (var i = 0, ii = fnRefs.length; i < ii; ++i) {
- fns.push(PDFFunction.getIR(xref, xref.fetchIfRef(fnRefs[i])));
- }
- var bounds = dict.getArray('Bounds');
- var encode = dict.getArray('Encode');
+ fns.push(PDFFunction.parse(xref, xref.fetchIfRef(fnRefs[i])));
+ }
+ var bounds = toNumberArray(dict.getArray('Bounds'));
+ var encode = toNumberArray(dict.getArray('Encode'));
return [
CONSTRUCT_STICHED,
domain,
bounds,
encode,
fns
];
},
constructStichedFromIR: function PDFFunction_constructStichedFromIR(IR) {
var domain = IR[1];
var bounds = IR[2];
var encode = IR[3];
- var fnsIR = IR[4];
- var fns = [];
+ var fns = IR[4];
var tmpBuf = new Float32Array(1);
- for (var i = 0, ii = fnsIR.length; i < ii; i++) {
- fns.push(PDFFunction.fromIR(fnsIR[i]));
- }
return function constructStichedFromIRResult(src, srcOffset, dest, destOffset) {
var clip = function constructStichedFromIRClip(v, min, max) {
if (v > max) {
v = max;
} else if (v < min) {
v = min;
}
return v;
@@ -41968,18 +41977,18 @@
// Prevent the value from becoming NaN as a result
// of division by zero (fixes issue6113.pdf).
tmpBuf[0] = dmin === dmax ? rmin : rmin + (v - dmin) * (rmax - rmin) / (dmax - dmin);
// call the appropriate function
fns[i](tmpBuf, 0, dest, destOffset);
};
},
constructPostScript: function PDFFunction_constructPostScript(fn, dict, xref) {
- var domain = dict.getArray('Domain');
- var range = dict.getArray('Range');
+ var domain = toNumberArray(dict.getArray('Domain'));
+ var range = toNumberArray(dict.getArray('Range'));
if (!domain) {
error('No domain.');
}
if (!range) {
error('No range.');
}
var lexer = new PostScriptLexer(fn);
var parser = new PostScriptParser(lexer);
@@ -42928,18 +42937,18 @@
case 'IndexedCS':
var baseIndexedCS = IR[1];
var hiVal = IR[2];
var lookup = IR[3];
return new IndexedCS(ColorSpace.fromIR(baseIndexedCS), hiVal, lookup);
case 'AlternateCS':
var numComps = IR[1];
var alt = IR[2];
- var tintFnIR = IR[3];
- return new AlternateCS(numComps, ColorSpace.fromIR(alt), PDFFunction.fromIR(tintFnIR));
+ var tintFn = IR[3];
+ return new AlternateCS(numComps, ColorSpace.fromIR(alt), tintFn);
case 'LabCS':
whitePoint = IR[1];
blackPoint = IR[2];
var range = IR[3];
return new LabCS(whitePoint, blackPoint, range);
default:
error('Unknown name ' + name);
}
@@ -43067,22 +43076,22 @@
var name = xref.fetchIfRef(cs[1]);
numComps = 1;
if (isName(name)) {
numComps = 1;
} else if (isArray(name)) {
numComps = name.length;
}
alt = ColorSpace.parseToIR(cs[2], xref, res);
- var tintFnIR = PDFFunction.getIR(xref, xref.fetchIfRef(cs[3]));
+ var tintFn = PDFFunction.parse(xref, xref.fetchIfRef(cs[3]));
return [
'AlternateCS',
numComps,
alt,
- tintFnIR
+ tintFn
];
case 'Lab':
params = xref.fetchIfRef(cs[1]);
whitePoint = params.getArray('WhitePoint');
blackPoint = params.getArray('BlackPoint');
var range = params.getArray('Range');
return [
'LabCS',
@@ -52483,9 +52492,9 @@
initializeWorker();
}
exports.setPDFNetworkStreamClass = setPDFNetworkStreamClass;
exports.WorkerTask = WorkerTask;
exports.WorkerMessageHandler = WorkerMessageHandler;
}));
}.call(pdfjsLibs));
exports.WorkerMessageHandler = pdfjsLibs.pdfjsCoreWorker.WorkerMessageHandler;
-}));
\ No newline at end of file
+}));

20
gnu/packages/patches/icecat-avoid-bundled-libraries.patch
View file

@ -1,8 +1,8 @@
Fixes needed when avoiding bundled libraries.
--- icecat-52.0.2/xpcom/build/moz.build.orig
+++ icecat-52.0.2/xpcom/build/moz.build
@@ -93,10 +93,5 @@
--- icecat-60.2.0/xpcom/build/moz.build.orig 2018-09-13 17:46:49.000000000 -0400
+++ icecat-60.2.0/xpcom/build/moz.build 2018-09-22 04:26:50.659564554 -0400
@@ -99,10 +99,5 @@
'/docshell/base',
]
@ -13,9 +13,9 @@ Fixes needed when avoiding bundled libraries.
-
if CONFIG['MOZ_WIDGET_TOOLKIT'] == 'cocoa':
CXXFLAGS += CONFIG['TK_CFLAGS']
--- icecat-52.0.2/storage/moz.build.orig
+++ icecat-52.0.2/storage/moz.build
@@ -114,7 +114,6 @@
--- icecat-60.2.0/storage/moz.build.orig 2018-09-13 17:51:11.000000000 -0400
+++ icecat-60.2.0/storage/moz.build 2018-09-22 04:26:50.659564554 -0400
@@ -117,7 +117,6 @@
DEFINES['MOZ_MEMORY_TEMP_STORE_PRAGMA'] = True
LOCAL_INCLUDES += [
@ -23,13 +23,13 @@ Fixes needed when avoiding bundled libraries.
'/dom/base',
]
--- icecat-52.0.2/dom/indexedDB/moz.build.orig
+++ icecat-52.0.2/dom/indexedDB/moz.build
@@ -101,7 +101,6 @@
--- icecat-60.2.0/dom/indexedDB/moz.build.orig 2018-09-13 17:49:42.000000000 -0400
+++ icecat-60.2.0/dom/indexedDB/moz.build 2018-09-22 04:26:50.663564574 -0400
@@ -102,7 +102,6 @@
CXXFLAGS += ['-Wno-error=shadow']
LOCAL_INCLUDES += [
- '/db/sqlite3/src',
'/dom/base',
'/dom/storage',
'/dom/workers',
'/ipc/glue',

663
gnu/packages/patches/icecat-bug-1413868-pt1.patch
View file

@ -1,663 +0,0 @@
Based on <https://hg.mozilla.org/releases/mozilla-esr52/rev/431fa5dd4016>
Adapted to apply cleanly to GNU IceCat.
# HG changeset patch
# User Honza Bambas <honzab.moz@firemni.cz>
# Date 1528830658 14400
# Node ID 431fa5dd4016bdab7e4bb0d3c4df85468fe337b0
# Parent e8e9e1ef79f2a18c61ec1b87cfb214c8d4960f8e
Bug 1413868. r=valentin, a=RyanVM
diff --git a/toolkit/xre/nsAppRunner.cpp b/toolkit/xre/nsAppRunner.cpp
--- a/toolkit/xre/nsAppRunner.cpp
+++ b/toolkit/xre/nsAppRunner.cpp
@@ -4,16 +4,17 @@
* file, You can obtain one at http://mozilla.org/MPL/2.0/. */
#include "mozilla/dom/ContentParent.h"
#include "mozilla/dom/ContentChild.h"
#include "mozilla/ipc/GeckoChildProcessHost.h"
#include "mozilla/ArrayUtils.h"
#include "mozilla/Attributes.h"
+#include "mozilla/FilePreferences.h"
#include "mozilla/ChaosMode.h"
#include "mozilla/IOInterposer.h"
#include "mozilla/Likely.h"
#include "mozilla/MemoryChecking.h"
#include "mozilla/Poison.h"
#include "mozilla/Preferences.h"
#include "mozilla/ScopeExit.h"
#include "mozilla/Services.h"
@@ -4304,16 +4305,20 @@ XREMain::XRE_mainRun()
// Need to write out the fact that the profile has been removed and potentially
// that the selected/default profile changed.
mProfileSvc->Flush();
}
}
mDirProvider.DoStartup();
+ // As FilePreferences need the profile directory, we must initialize right here.
+ mozilla::FilePreferences::InitDirectoriesWhitelist();
+ mozilla::FilePreferences::InitPrefs();
+
OverrideDefaultLocaleIfNeeded();
#ifdef MOZ_CRASHREPORTER
nsCString userAgentLocale;
// Try a localized string first. This pref is always a localized string in
// IceCatMobile, and might be elsewhere, too.
if (NS_SUCCEEDED(Preferences::GetLocalizedCString("general.useragent.locale", &userAgentLocale))) {
CrashReporter::AnnotateCrashReport(NS_LITERAL_CSTRING("useragent_locale"), userAgentLocale);
diff --git a/toolkit/xre/nsEmbedFunctions.cpp b/toolkit/xre/nsEmbedFunctions.cpp
--- a/toolkit/xre/nsEmbedFunctions.cpp
+++ b/toolkit/xre/nsEmbedFunctions.cpp
@@ -46,16 +46,17 @@
#include "nsX11ErrorHandler.h"
#include "nsGDKErrorHandler.h"
#include "base/at_exit.h"
#include "base/command_line.h"
#include "base/message_loop.h"
#include "base/process_util.h"
#include "chrome/common/child_process.h"
+#include "mozilla/FilePreferences.h"
#include "mozilla/ipc/BrowserProcessSubThread.h"
#include "mozilla/ipc/GeckoChildProcessHost.h"
#include "mozilla/ipc/IOThreadChild.h"
#include "mozilla/ipc/ProcessChild.h"
#include "ScopedXREEmbed.h"
#include "mozilla/plugins/PluginProcessChild.h"
#include "mozilla/dom/ContentProcess.h"
@@ -680,16 +681,18 @@ XRE_InitChildProcess(int aArgc,
::SetProcessShutdownParameters(0x280 - 1, SHUTDOWN_NORETRY);
#endif
#if defined(MOZ_SANDBOX) && defined(XP_WIN)
// We need to do this after the process has been initialised, as
// InitLoggingIfRequired may need access to prefs.
mozilla::sandboxing::InitLoggingIfRequired(aChildData->ProvideLogFunction);
#endif
+ mozilla::FilePreferences::InitDirectoriesWhitelist();
+ mozilla::FilePreferences::InitPrefs();
OverrideDefaultLocaleIfNeeded();
#if defined(MOZ_CRASHREPORTER)
#if defined(MOZ_CONTENT_SANDBOX) && !defined(MOZ_WIDGET_GONK)
AddContentSandboxLevelAnnotation();
#endif
#endif
diff --git a/xpcom/io/FilePreferences.cpp b/xpcom/io/FilePreferences.cpp
new file mode 100644
--- /dev/null
+++ b/xpcom/io/FilePreferences.cpp
@@ -0,0 +1,271 @@
+/* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */
+/* vim: set ts=8 sts=2 et sw=2 tw=80: */
+/* This Source Code Form is subject to the terms of the Mozilla Public
+* License, v. 2.0. If a copy of the MPL was not distributed with this
+* file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+#include "FilePreferences.h"
+
+#include "mozilla/Preferences.h"
+#include "nsAppDirectoryServiceDefs.h"
+#include "nsDirectoryServiceDefs.h"
+#include "nsDirectoryServiceUtils.h"
+
+namespace mozilla {
+namespace FilePreferences {
+
+static bool sBlockUNCPaths = false;
+typedef nsTArray<nsString> Paths;
+
+static Paths& PathArray()
+{
+ static Paths sPaths;
+ return sPaths;
+}
+
+static void AllowDirectory(char const* directory)
+{
+ nsCOMPtr<nsIFile> file;
+ NS_GetSpecialDirectory(directory, getter_AddRefs(file));
+ if (!file) {
+ return;
+ }
+
+ nsString path;
+ if (NS_FAILED(file->GetTarget(path))) {
+ return;
+ }
+
+ // The whitelist makes sense only for UNC paths, because this code is used
+ // to block only UNC paths, hence, no need to add non-UNC directories here
+ // as those would never pass the check.
+ if (!StringBeginsWith(path, NS_LITERAL_STRING("\\\\"))) {
+ return;
+ }
+
+ if (!PathArray().Contains(path)) {
+ PathArray().AppendElement(path);
+ }
+}
+
+void InitPrefs()
+{
+ sBlockUNCPaths = Preferences::GetBool("network.file.disable_unc_paths", false);
+}
+
+void InitDirectoriesWhitelist()
+{
+ // NS_GRE_DIR is the installation path where the binary resides.
+ AllowDirectory(NS_GRE_DIR);
+ // NS_APP_USER_PROFILE_50_DIR and NS_APP_USER_PROFILE_LOCAL_50_DIR are the two
+ // parts of the profile we store permanent and local-specific data.
+ AllowDirectory(NS_APP_USER_PROFILE_50_DIR);
+ AllowDirectory(NS_APP_USER_PROFILE_LOCAL_50_DIR);
+}
+
+namespace { // anon
+
+class Normalizer
+{
+public:
+ Normalizer(const nsAString& aFilePath, const char16_t aSeparator);
+ bool Get(nsAString& aNormalizedFilePath);
+
+private:
+ bool ConsumeItem();
+ bool ConsumeSeparator();
+ bool IsEOF() { return mFilePathCursor == mFilePathEnd; }
+
+ bool ConsumeName();
+ bool CheckParentDir();
+ bool CheckCurrentDir();
+
+ nsString::const_char_iterator mFilePathCursor;
+ nsString::const_char_iterator mFilePathEnd;
+
+ nsDependentSubstring mItem;
+ char16_t const mSeparator;
+ nsTArray<nsDependentSubstring> mStack;
+};
+
+Normalizer::Normalizer(const nsAString& aFilePath, const char16_t aSeparator)
+ : mFilePathCursor(aFilePath.BeginReading())
+ , mFilePathEnd(aFilePath.EndReading())
+ , mSeparator(aSeparator)
+{
+}
+
+bool Normalizer::ConsumeItem()
+{
+ if (IsEOF()) {
+ return false;
+ }
+
+ nsString::const_char_iterator nameBegin = mFilePathCursor;
+ while (mFilePathCursor != mFilePathEnd) {
+ if (*mFilePathCursor == mSeparator) {
+ break; // don't include the separator
+ }
+ ++mFilePathCursor;
+ }
+
+ mItem.Rebind(nameBegin, mFilePathCursor);
+ return true;
+}
+
+bool Normalizer::ConsumeSeparator()
+{
+ if (IsEOF()) {
+ return false;
+ }
+
+ if (*mFilePathCursor != mSeparator) {
+ return false;
+ }
+
+ ++mFilePathCursor;
+ return true;
+}
+
+bool Normalizer::Get(nsAString& aNormalizedFilePath)
+{
+ aNormalizedFilePath.Truncate();
+
+ if (IsEOF()) {
+ return true;
+ }
+ if (ConsumeSeparator()) {
+ aNormalizedFilePath.Append(mSeparator);
+ }
+
+ if (IsEOF()) {
+ return true;
+ }
+ if (ConsumeSeparator()) {
+ aNormalizedFilePath.Append(mSeparator);
+ }
+
+ while (!IsEOF()) {
+ if (!ConsumeName()) {
+ return false;
+ }
+ }
+
+ for (auto const& name : mStack) {
+ aNormalizedFilePath.Append(name);
+ }
+
+ return true;
+}
+
+bool Normalizer::ConsumeName()
+{
+ if (!ConsumeItem()) {
+ return true;
+ }
+
+ if (CheckCurrentDir()) {
+ return true;
+ }
+
+ if (CheckParentDir()) {
+ if (!mStack.Length()) {
+ // This means there are more \.. than valid names
+ return false;
+ }
+
+ mStack.RemoveElementAt(mStack.Length() - 1);
+ return true;
+ }
+
+ if (mItem.IsEmpty()) {
+ // this means an empty name (a lone slash), which is illegal
+ return false;
+ }
+
+ if (ConsumeSeparator()) {
+ mItem.Rebind(mItem.BeginReading(), mFilePathCursor);
+ }
+ mStack.AppendElement(mItem);
+
+ return true;
+}
+
+bool Normalizer::CheckCurrentDir()
+{
+ if (mItem == NS_LITERAL_STRING(".")) {
+ ConsumeSeparator();
+ // EOF is acceptable
+ return true;
+ }
+
+ return false;
+}
+
+bool Normalizer::CheckParentDir()
+{
+ if (mItem == NS_LITERAL_STRING("..")) {
+ ConsumeSeparator();
+ // EOF is acceptable
+ return true;
+ }
+
+ return false;
+}
+
+} // anon
+
+bool IsBlockedUNCPath(const nsAString& aFilePath)
+{
+ if (!sBlockUNCPaths) {
+ return false;
+ }
+
+ if (!StringBeginsWith(aFilePath, NS_LITERAL_STRING("\\\\"))) {
+ return false;
+ }
+
+ nsAutoString normalized;
+ if (!Normalizer(aFilePath, L'\\').Get(normalized)) {
+ // Broken paths are considered invalid and thus inaccessible
+ return true;
+ }
+
+ for (const auto& allowedPrefix : PathArray()) {
+ if (StringBeginsWith(normalized, allowedPrefix)) {
+ if (normalized.Length() == allowedPrefix.Length()) {
+ return false;
+ }
+ if (normalized[allowedPrefix.Length()] == L'\\') {
+ return false;
+ }
+
+ // When we are here, the path has a form "\\path\prefixevil"
+ // while we have an allowed prefix of "\\path\prefix".
+ // Note that we don't want to add a slash to the end of a prefix
+ // so that opening the directory (no slash at the end) still works.
+ break;
+ }
+ }
+
+ return true;
+}
+
+void testing::SetBlockUNCPaths(bool aBlock)
+{
+ sBlockUNCPaths = aBlock;
+}
+
+void testing::AddDirectoryToWhitelist(nsAString const & aPath)
+{
+ PathArray().AppendElement(aPath);
+}
+
+bool testing::NormalizePath(nsAString const & aPath, nsAString & aNormalized)
+{
+ Normalizer normalizer(aPath, L'\\');
+ return normalizer.Get(aNormalized);
+}
+
+} // ::FilePreferences
+} // ::mozilla
diff --git a/xpcom/io/FilePreferences.h b/xpcom/io/FilePreferences.h
new file mode 100644
--- /dev/null
+++ b/xpcom/io/FilePreferences.h
@@ -0,0 +1,25 @@
+/* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */
+/* vim: set ts=8 sts=2 et sw=2 tw=80: */
+/* This Source Code Form is subject to the terms of the Mozilla Public
+* License, v. 2.0. If a copy of the MPL was not distributed with this
+* file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+#include "nsIObserver.h"
+
+namespace mozilla {
+namespace FilePreferences {
+
+void InitPrefs();
+void InitDirectoriesWhitelist();
+bool IsBlockedUNCPath(const nsAString& aFilePath);
+
+namespace testing {
+
+void SetBlockUNCPaths(bool aBlock);
+void AddDirectoryToWhitelist(nsAString const& aPath);
+bool NormalizePath(nsAString const & aPath, nsAString & aNormalized);
+
+}
+
+} // FilePreferences
+} // mozilla
diff --git a/xpcom/io/moz.build b/xpcom/io/moz.build
--- a/xpcom/io/moz.build
+++ b/xpcom/io/moz.build
@@ -79,24 +79,26 @@ EXPORTS += [
'nsUnicharInputStream.h',
'nsWildCard.h',
'SlicedInputStream.h',
'SpecialSystemDirectory.h',
]
EXPORTS.mozilla += [
'Base64.h',
+ 'FilePreferences.h',
'SnappyCompressOutputStream.h',
'SnappyFrameUtils.h',
'SnappyUncompressInputStream.h',
]
UNIFIED_SOURCES += [
'Base64.cpp',
'crc32c.c',
+ 'FilePreferences.cpp',
'nsAnonymousTemporaryFile.cpp',
'nsAppFileLocationProvider.cpp',
'nsBinaryStream.cpp',
'nsDirectoryService.cpp',
'nsEscape.cpp',
'nsInputStreamTee.cpp',
'nsIOUtil.cpp',
'nsLinebreakConverter.cpp',
diff --git a/xpcom/io/nsLocalFileWin.cpp b/xpcom/io/nsLocalFileWin.cpp
--- a/xpcom/io/nsLocalFileWin.cpp
+++ b/xpcom/io/nsLocalFileWin.cpp
@@ -41,16 +41,17 @@
#include <stdio.h>
#include <stdlib.h>
#include <mbstring.h>
#include "nsXPIDLString.h"
#include "prproces.h"
#include "prlink.h"
+#include "mozilla/FilePreferences.h"
#include "mozilla/Mutex.h"
#include "SpecialSystemDirectory.h"
#include "nsTraceRefcnt.h"
#include "nsXPCOMCIDInternal.h"
#include "nsThreadUtils.h"
#include "nsXULAppAPI.h"
@@ -1162,16 +1163,20 @@ nsLocalFile::InitWithPath(const nsAStrin
char16_t secondChar = *(++begin);
// just do a sanity check. if it has any forward slashes, it is not a Native path
// on windows. Also, it must have a colon at after the first char.
if (FindCharInReadable(L'/', begin, end)) {
return NS_ERROR_FILE_UNRECOGNIZED_PATH;
}
+ if (FilePreferences::IsBlockedUNCPath(aFilePath)) {
+ return NS_ERROR_FILE_ACCESS_DENIED;
+ }
+
if (secondChar != L':' && (secondChar != L'\\' || firstChar != L'\\')) {
return NS_ERROR_FILE_UNRECOGNIZED_PATH;
}
if (secondChar == L':') {
// Make sure we have a valid drive, later code assumes the drive letter
// is a single char a-z or A-Z.
if (PathGetDriveNumberW(aFilePath.Data()) == -1) {
@@ -1974,16 +1979,20 @@ nsLocalFile::CopySingleFile(nsIFile* aSo
bool path1Remote, path2Remote;
if (!IsRemoteFilePath(filePath.get(), path1Remote) ||
!IsRemoteFilePath(destPath.get(), path2Remote) ||
path1Remote || path2Remote) {
dwCopyFlags |= COPY_FILE_NO_BUFFERING;
}
}
+ if (FilePreferences::IsBlockedUNCPath(destPath)) {
+ return NS_ERROR_FILE_ACCESS_DENIED;
+ }
+
if (!move) {
copyOK = ::CopyFileExW(filePath.get(), destPath.get(), nullptr,
nullptr, nullptr, dwCopyFlags);
} else {
copyOK = ::MoveFileExW(filePath.get(), destPath.get(),
MOVEFILE_REPLACE_EXISTING);
// Check if copying the source file to a different volume,
diff --git a/xpcom/tests/gtest/TestFilePreferencesWin.cpp b/xpcom/tests/gtest/TestFilePreferencesWin.cpp
new file mode 100644
--- /dev/null
+++ b/xpcom/tests/gtest/TestFilePreferencesWin.cpp
@@ -0,0 +1,141 @@
+#include "gtest/gtest.h"
+
+#include "mozilla/FilePreferences.h"
+#include "nsIFile.h"
+#include "nsXPCOMCID.h"
+
+TEST(FilePreferencesWin, Normalization)
+{
+ nsAutoString normalized;
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("foo"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("foo"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\foo"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\foo"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("foo\\some"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("foo\\some"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.\\foo"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\."), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.\\."), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\."), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\.\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\..\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\.."), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\..\\bar\\..\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\..\\bar"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\bar"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\..\\..\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\.\\..\\.\\..\\"), normalized);
+ ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
+
+ bool result;
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.."), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\..\\"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.\\..\\"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\\\bar"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\foo\\bar\\..\\..\\..\\..\\"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\\\"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\.\\\\"), normalized);
+ ASSERT_FALSE(result);
+
+ result = mozilla::FilePreferences::testing::NormalizePath(
+ NS_LITERAL_STRING("\\\\..\\\\"), normalized);
+ ASSERT_FALSE(result);
+}
+
+TEST(FilePreferencesWin, AccessUNC)
+{
+ nsCOMPtr<nsIFile> lf = do_CreateInstance(NS_LOCAL_FILE_CONTRACTID);
+
+ nsresult rv;
+
+ mozilla::FilePreferences::testing::SetBlockUNCPaths(false);
+
+ rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
+ ASSERT_EQ(rv, NS_OK);
+
+ mozilla::FilePreferences::testing::SetBlockUNCPaths(true);
+
+ rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
+ ASSERT_EQ(rv, NS_ERROR_FILE_ACCESS_DENIED);
+
+ mozilla::FilePreferences::testing::AddDirectoryToWhitelist(NS_LITERAL_STRING("\\\\nice"));
+
+ rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\share"));
+ ASSERT_EQ(rv, NS_OK);
+
+ rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
+ ASSERT_EQ(rv, NS_ERROR_FILE_ACCESS_DENIED);
+}
diff --git a/xpcom/tests/gtest/moz.build b/xpcom/tests/gtest/moz.build
--- a/xpcom/tests/gtest/moz.build
+++ b/xpcom/tests/gtest/moz.build
@@ -51,16 +51,21 @@ UNIFIED_SOURCES += [
if CONFIG['MOZ_DEBUG'] and CONFIG['OS_ARCH'] not in ('WINNT') and CONFIG['OS_TARGET'] != 'Android':
# FIXME bug 523392: TestDeadlockDetector doesn't like Windows
# Bug 1054249: Doesn't work on Android
UNIFIED_SOURCES += [
'TestDeadlockDetector.cpp',
'TestDeadlockDetectorScalability.cpp',
]
+if CONFIG['OS_TARGET'] == 'WINNT':
+ UNIFIED_SOURCES += [
+ 'TestFilePreferencesWin.cpp',
+ ]
+
if CONFIG['WRAP_STL_INCLUDES'] and not CONFIG['CLANG_CL']:
UNIFIED_SOURCES += [
'TestSTLWrappers.cpp',
]
# Compile TestAllocReplacement separately so Windows headers don't pollute
# the global namespace for other files.
SOURCES += [

34
gnu/packages/patches/libvpx-use-after-free-in-postproc.patch Normal file
View file

@ -0,0 +1,34 @@
From 52add5896661d186dec284ed646a4b33b607d2c7 Mon Sep 17 00:00:00 2001
From: Jerome Jiang <jianj@google.com>
Date: Wed, 23 May 2018 15:43:00 -0700
Subject: [PATCH] VP8: Fix use-after-free in postproc.
The pointer in vp8 postproc refers to show_frame_mi which is only
updated on show frame. However, when there is a no-show frame which also
changes the size (thus new frame buffers allocated), show_frame_mi is
not updated with new frame buffer memory.
Change the pointer in postproc to mi which is always updated.
Bug: 842265
Change-Id: I33874f2112b39f74562cba528432b5f239e6a7bd
---
vp8/common/postproc.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/vp8/common/postproc.c b/vp8/common/postproc.c
index d67ee8a57..8c292d616 100644
--- a/vp8/common/postproc.c
+++ b/vp8/common/postproc.c
@@ -65,7 +65,7 @@ void vp8_deblock(VP8_COMMON *cm, YV12_BUFFER_CONFIG *source,
double level = 6.0e-05 * q * q * q - .0067 * q * q + .306 * q + .0065;
int ppl = (int)(level + .5);
- const MODE_INFO *mode_info_context = cm->show_frame_mi;
+ const MODE_INFO *mode_info_context = cm->mi;
int mbr, mbc;
/* The pixel thresholds are adjusted according to if or not the macroblock
--
2.19.0

682
gnu/packages/patches/rsem-makefile.patch
View file

@ -1,682 +0,0 @@
This patch simplifies the Makefile, making it much easier to build rsem
without the bundled version of samtools. It has already been submitted
upstream: https://github.com/bli25wisc/RSEM/pull/11
From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 14:51:07 +0200
Subject: [PATCH 1/7] remove all headers from Makefile
---
Makefile | 95 +++++++++++-----------------------------------------------------
1 file changed, 16 insertions(+), 79 deletions(-)
diff --git a/Makefile b/Makefile
index 54e2603..3a55ed8 100644
--- a/Makefile
+++ b/Makefile
@@ -10,133 +10,70 @@ all : $(PROGRAMS)
sam/libbam.a :
cd sam ; ${MAKE} all
-Transcript.h : utils.h
-
-Transcripts.h : utils.h my_assert.h Transcript.h
-
-rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
+rsem-extract-reference-transcripts : extractRef.cpp
$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
+rsem-synthesis-reference-transcripts : synthesisRef.cpp
$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-BowtieRefSeqPolicy.h : RefSeqPolicy.h
-
-RefSeq.h : utils.h
-
-Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
-
-
rsem-preref : preRef.o
$(CC) preRef.o -o rsem-preref
-preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
+preRef.o : preRef.cpp
$(CC) $(COFLAGS) preRef.cpp
-
-SingleRead.h : Read.h
-
-SingleReadQ.h : Read.h
-
-PairedEndRead.h : Read.h SingleRead.h
-
-PairedEndReadQ.h : Read.h SingleReadQ.h
-
-
-PairedEndHit.h : SingleHit.h
-
-HitContainer.h : GroupInfo.h
-
-
-SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
-
-
rsem-parse-alignments : parseIt.o sam/libbam.a
$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
-parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
+parseIt.o : parseIt.cpp
$(CC) -Wall -O2 -c -I. parseIt.cpp
-
-rsem-build-read-index : utils.h buildReadIndex.cpp
+rsem-build-read-index : buildReadIndex.cpp
$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
-
-simul.h : boost/random.hpp
-
-ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
-
-SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
-
-SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
-
-PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h
-
-PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
-
-HitWrapper.h : HitContainer.h
-
-sam_rsem_aux.h : sam/bam.h
-
-sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
-
-BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
-
-sampling.h : boost/random.hpp
-
-WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
-
rsem-run-em : EM.o sam/libbam.a
$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
+EM.o : EM.cpp
$(CC) $(COFLAGS) EM.cpp
-bc_aux.h : sam/bam.h
-
-BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
-
-rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
+rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
+wiggle.o: wiggle.cpp
$(CC) $(COFLAGS) wiggle.cpp
rsem-simulate-reads : simulation.o
$(CC) -o rsem-simulate-reads simulation.o
-simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
+simulation.o : simulation.cpp
$(CC) $(COFLAGS) simulation.cpp
rsem-run-gibbs : Gibbs.o
$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
-#some header files are omitted
-Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp
+Gibbs.o : Gibbs.cpp
$(CC) $(COFLAGS) Gibbs.cpp
-Buffer.h : my_assert.h
-
rsem-calculate-credibility-intervals : calcCI.o
$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-#some header files are omitted
-calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
+calcCI.o : calcCI.cpp
$(CC) $(COFLAGS) calcCI.cpp
-rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
+rsem-get-unique : getUnique.cpp sam/libbam.a
$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
+rsem-sam-validator : samValidator.cpp sam/libbam.a
$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
ebseq :
From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:06:41 +0200
Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
---
Makefile | 48 ++++++++++++++++++++++++------------------------
1 file changed, 24 insertions(+), 24 deletions(-)
diff --git a/Makefile b/Makefile
index 3a55ed8..1dd97ca 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
CC = g++
-CFLAGS = -Wall -c -I.
-COFLAGS = -Wall -O3 -ffast-math -c -I.
+CFLAGS = -Wall -I. -I./sam -I./boost
+COFLAGS = -O3 -ffast-math -c
PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
.PHONY : all ebseq clean
@@ -11,70 +11,70 @@ sam/libbam.a :
cd sam ; ${MAKE} all
rsem-extract-reference-transcripts : extractRef.cpp
- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
+ $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
rsem-synthesis-reference-transcripts : synthesisRef.cpp
- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
rsem-preref : preRef.o
- $(CC) preRef.o -o rsem-preref
+ $(CC) $(CFLAGS) preRef.o -o rsem-preref
preRef.o : preRef.cpp
- $(CC) $(COFLAGS) preRef.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
rsem-parse-alignments : parseIt.o sam/libbam.a
- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
+ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
parseIt.o : parseIt.cpp
- $(CC) -Wall -O2 -c -I. parseIt.cpp
+ $(CC) $(CFLAGS) -O2 -c parseIt.cpp
rsem-build-read-index : buildReadIndex.cpp
- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
+ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
rsem-run-em : EM.o sam/libbam.a
- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
+ $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
EM.o : EM.cpp
- $(CC) $(COFLAGS) EM.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
wiggle.o: wiggle.cpp
- $(CC) $(COFLAGS) wiggle.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
rsem-simulate-reads : simulation.o
- $(CC) -o rsem-simulate-reads simulation.o
+ $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
simulation.o : simulation.cpp
- $(CC) $(COFLAGS) simulation.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
rsem-run-gibbs : Gibbs.o
- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
+ $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
Gibbs.o : Gibbs.cpp
- $(CC) $(COFLAGS) Gibbs.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
rsem-calculate-credibility-intervals : calcCI.o
- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
+ $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
calcCI.o : calcCI.cpp
- $(CC) $(COFLAGS) calcCI.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
rsem-get-unique : getUnique.cpp sam/libbam.a
- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
rsem-sam-validator : samValidator.cpp sam/libbam.a
- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
ebseq :
cd EBSeq ; ${MAKE} all
From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:10:49 +0200
Subject: [PATCH 3/7] separate object rules from rules for executables
---
Makefile | 50 ++++++++++++++++++++++++++------------------------
1 file changed, 26 insertions(+), 24 deletions(-)
diff --git a/Makefile b/Makefile
index 1dd97ca..ae4de3b 100644
--- a/Makefile
+++ b/Makefile
@@ -10,6 +10,32 @@ all : $(PROGRAMS)
sam/libbam.a :
cd sam ; ${MAKE} all
+ebseq :
+ cd EBSeq ; ${MAKE} all
+
+
+calcCI.o : calcCI.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
+
+EM.o : EM.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
+
+Gibbs.o : Gibbs.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
+
+preRef.o : preRef.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
+
+parseIt.o : parseIt.cpp
+ $(CC) $(CFLAGS) -O2 -c parseIt.cpp
+
+simulation.o : simulation.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
+
+wiggle.o: wiggle.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
+
+
rsem-extract-reference-transcripts : extractRef.cpp
$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
@@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
rsem-preref : preRef.o
$(CC) $(CFLAGS) preRef.o -o rsem-preref
-preRef.o : preRef.cpp
- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
-
rsem-parse-alignments : parseIt.o sam/libbam.a
$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
-parseIt.o : parseIt.cpp
- $(CC) $(CFLAGS) -O2 -c parseIt.cpp
-
rsem-build-read-index : buildReadIndex.cpp
$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
rsem-run-em : EM.o sam/libbam.a
$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-EM.o : EM.cpp
- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
-
rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
@@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-wiggle.o: wiggle.cpp
- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
-
rsem-simulate-reads : simulation.o
$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
-simulation.o : simulation.cpp
- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
-
rsem-run-gibbs : Gibbs.o
$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
-Gibbs.o : Gibbs.cpp
- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
-
rsem-calculate-credibility-intervals : calcCI.o
$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-calcCI.o : calcCI.cpp
- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
-
rsem-get-unique : getUnique.cpp sam/libbam.a
$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
@@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-ebseq :
- cd EBSeq ; ${MAKE} all
-
clean :
rm -f *.o *~ $(PROGRAMS)
cd sam ; ${MAKE} clean
From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:28:30 +0200
Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam
---
Makefile | 36 ++++++++++++++++++------------------
1 file changed, 18 insertions(+), 18 deletions(-)
diff --git a/Makefile b/Makefile
index ae4de3b..a87cc4d 100644
--- a/Makefile
+++ b/Makefile
@@ -1,11 +1,11 @@
CC = g++
-CFLAGS = -Wall -I. -I./sam -I./boost
+CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
COFLAGS = -O3 -ffast-math -c
PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
.PHONY : all ebseq clean
-all : $(PROGRAMS)
+all : sam/libbam.a $(PROGRAMS)
sam/libbam.a :
cd sam ; ${MAKE} all
@@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
rsem-preref : preRef.o
$(CC) $(CFLAGS) preRef.o -o rsem-preref
-rsem-parse-alignments : parseIt.o sam/libbam.a
- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
+rsem-parse-alignments : parseIt.o
+ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
rsem-build-read-index : buildReadIndex.cpp
$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
-rsem-run-em : EM.o sam/libbam.a
- $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
+rsem-run-em : EM.o
+ $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
-rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
+rsem-tbam2gbam : tbam2gbam.cpp
+ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
-rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
+rsem-bam2wig : wiggle.o bam2wig.cpp
+ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
-rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
+rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
+ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
rsem-simulate-reads : simulation.o
$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
@@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o
rsem-calculate-credibility-intervals : calcCI.o
$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-rsem-get-unique : getUnique.cpp sam/libbam.a
- $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
+rsem-get-unique : getUnique.cpp
+ $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
-rsem-sam-validator : samValidator.cpp sam/libbam.a
- $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
+rsem-sam-validator : samValidator.cpp
+ $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
-rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
+ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
clean :
rm -f *.o *~ $(PROGRAMS)
From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:33:02 +0200
Subject: [PATCH 5/7] do not repeat target name, use $@ instead
---
Makefile | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/Makefile b/Makefile
index a87cc4d..7ec90a3 100644
--- a/Makefile
+++ b/Makefile
@@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp
rsem-extract-reference-transcripts : extractRef.cpp
- $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
+ $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
rsem-synthesis-reference-transcripts : synthesisRef.cpp
- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
rsem-preref : preRef.o
- $(CC) $(CFLAGS) preRef.o -o rsem-preref
+ $(CC) $(CFLAGS) preRef.o -o $@
rsem-parse-alignments : parseIt.o
- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
rsem-build-read-index : buildReadIndex.cpp
- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
+ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
rsem-run-em : EM.o
- $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
rsem-tbam2gbam : tbam2gbam.cpp
$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
@@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
rsem-simulate-reads : simulation.o
- $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
+ $(CC) $(CFLAGS) -o $@ simulation.o
rsem-run-gibbs : Gibbs.o
- $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
+ $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
rsem-calculate-credibility-intervals : calcCI.o
- $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
+ $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
rsem-get-unique : getUnique.cpp
$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:44:53 +0200
Subject: [PATCH 6/7] use automatic variables to refer to prerequisites
---
Makefile | 44 ++++++++++++++++++++++----------------------
1 file changed, 22 insertions(+), 22 deletions(-)
diff --git a/Makefile b/Makefile
index 7ec90a3..6540d81 100644
--- a/Makefile
+++ b/Makefile
@@ -15,71 +15,71 @@ ebseq :
calcCI.o : calcCI.cpp
- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
EM.o : EM.cpp
- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
Gibbs.o : Gibbs.cpp
- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
preRef.o : preRef.cpp
- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
parseIt.o : parseIt.cpp
- $(CC) $(CFLAGS) -O2 -c parseIt.cpp
+ $(CC) $(CFLAGS) -O2 -c $<
simulation.o : simulation.cpp
- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
wiggle.o: wiggle.cpp
- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
+ $(CC) $(CFLAGS) $(COFLAGS) $<
rsem-extract-reference-transcripts : extractRef.cpp
- $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
+ $(CC) $(CFLAGS) -O3 $< -o $@
rsem-synthesis-reference-transcripts : synthesisRef.cpp
- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
+ $(CC) $(CFLAGS) -O3 $< -o $@
rsem-preref : preRef.o
- $(CC) $(CFLAGS) preRef.o -o $@
+ $(CC) $(CFLAGS) $< -o $@
rsem-parse-alignments : parseIt.o
- $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
rsem-build-read-index : buildReadIndex.cpp
- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
+ $(CC) $(CFLAGS) -O3 $< -o $@
rsem-run-em : EM.o
- $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
rsem-tbam2gbam : tbam2gbam.cpp
- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
rsem-bam2wig : wiggle.o bam2wig.cpp
- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
rsem-simulate-reads : simulation.o
- $(CC) $(CFLAGS) -o $@ simulation.o
+ $(CC) $(CFLAGS) -o $@ $<
rsem-run-gibbs : Gibbs.o
- $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
+ $(CC) $(CFLAGS) -o $@ $< -lpthread
rsem-calculate-credibility-intervals : calcCI.o
- $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
+ $(CC) $(CFLAGS) -o $@ $< -lpthread
rsem-get-unique : getUnique.cpp
- $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
rsem-sam-validator : samValidator.cpp
- $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
clean :
rm -f *.o *~ $(PROGRAMS)
From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 15:49:19 +0200
Subject: [PATCH 7/7] split long line
---
Makefile | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/Makefile b/Makefile
index 6540d81..0ab04a5 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,22 @@
CC = g++
CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
COFLAGS = -O3 -ffast-math -c
-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
+PROGRAMS = \
+ rsem-extract-reference-transcripts \
+ rsem-synthesis-reference-transcripts \
+ rsem-preref \
+ rsem-parse-alignments \
+ rsem-build-read-index \
+ rsem-run-em \
+ rsem-tbam2gbam \
+ rsem-run-gibbs \
+ rsem-calculate-credibility-intervals \
+ rsem-simulate-reads \
+ rsem-bam2wig \
+ rsem-get-unique \
+ rsem-bam2readdepth \
+ rsem-sam-validator \
+ rsem-scan-for-paired-end-reads
.PHONY : all ebseq clean

6
gnu/packages/python-crypto.scm
View file

@ -203,14 +203,14 @@ (define-public python-pyblake2
(define-public python-paramiko
(package
(name "python-paramiko")
(version "2.4.1")
(version "2.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "paramiko" version))
(sha256
(base32
"1wx4s95i2cdh8hhi1c3jb8lzk71jifa3z9wjfsx905y7lrsngqrk"))))
"1jqgj2gl1pz7bi2aab1r2xq0ml0gskmm9p235cg9y32nydymm5x8"))))
(build-system python-build-system)
(arguments
`(;; FIXME: Tests require many unpackaged libraries, see dev-requirements.txt.
@ -220,7 +220,7 @@ (define-public python-paramiko
("python-pyasn1" ,python-pyasn1)
("python-pynacl" ,python-pynacl)
("python-cryptography" ,python-cryptography)))
(home-page "http://www.paramiko.org/")
(home-page "https://www.paramiko.org/")
(synopsis "SSHv2 protocol library")
(description "Paramiko is a python implementation of the SSHv2 protocol,
providing both client and server functionality. While it leverages a Python C

140
gnu/packages/python-web.scm
View file

@ -5,7 +5,7 @@
;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym+a@scratchpost.org>
;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
@ -1351,14 +1351,14 @@ (define-public awscli
(define-public python-wsgiproxy2
(package
(name "python-wsgiproxy2")
(version "0.4.4")
(version "0.4.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "WSGIProxy2" version ".tar.gz"))
(sha256
(base32
"16532rjc94h3w74x52jfckf3yzsp8h6z34522jk4xgjy82hpnd7r"))))
"19d9dva282vfjs784i0zkxp078lxfz4h3f621z30ij9wbf5rba6a"))))
(build-system python-build-system)
(native-inputs
`(("python-webtest" ,python-webtest)))
@ -1592,6 +1592,29 @@ (define-public python-responses
(define-public python2-responses
(package-with-python2 python-responses))
(define-public python-grequests
(package
(name "python-grequests")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "grequests" version))
(sha256
(base32
"1j9icncllbkv7x5719b20mx670c6q1jrdx1sakskkarvx3pc8h8g"))))
(build-system python-build-system)
(propagated-inputs
`(("python-gevent" ,python-gevent)
("python-requests" ,python-requests)))
(native-inputs
`(("python-nose" ,python-nose)))
(home-page "https://github.com/kennethreitz/grequests")
(synopsis "Python library for asynchronous HTTP requests")
(description "GRequests is a Python library that allows you to use
@code{Requests} with @code{Gevent} to make asynchronous HTTP Requests easily")
(license license:bsd-2)))
(define-public python-geventhttpclient
(package
(name "python-geventhttpclient")
@ -2030,21 +2053,36 @@ (define-public python2-flask-htmlmin
(define-public python-flask-login
(package
(name "python-flask-login")
(version "0.4.0")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/maxcountryman/flask-login/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/maxcountryman/flask-login.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1pdqp7a2gyb7k06xda004x0fi2w66s6kn2i0ndkqndmg12d83f9w"))))
(base32 "1rj0qwyxapxnp84fi4lhmvh3d91fdiwz7hibw77x3d5i72knqaa9"))))
(arguments
;; Tests fail PEP8 compliance. See:
;; https://github.com/maxcountryman/flask-login/issues/340
`(#:tests? #f))
`(#:phases
(modify-phases %standard-phases
(add-before 'check 'avoid-yanc
;; Work around '.nosetests-real: error: no such option: --with-yanc'.
(lambda _
(setenv "NOCOLOR" "set")
#t)))))
(build-system python-build-system)
(propagated-inputs
`(("python-flask" ,python-flask)))
(native-inputs
;; For tests.
`(("python-blinker" ,python-blinker)
("python-mock" ,python-mock)
("python-nose" ,python-nose)
("python-pep8" ,python-pep8)
("python-pyflakes" ,python-pyflakes)
("python-semantic-version" ,python-semantic-version)
("python-werkzeug" ,python-werkzeug)))
(home-page "https://github.com/maxcountryman/flask-login")
(synopsis "User session management for Flask")
(description
@ -2626,3 +2664,79 @@ (define-public python-google-api-client
(define-public python2-google-api-client
(package-with-python2 python-google-api-client))
(define-public python-hawkauthlib
(package
(name "python-hawkauthlib")
(version "2.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "hawkauthlib" version))
(sha256
(base32
"03ai47s4h8nfnrf25shbfvkm1b9n1ccd4nmmj280sg1fayi69zgg"))))
(build-system python-build-system)
(propagated-inputs
`(("python-requests" ,python-requests)
("python-webob" ,python-webob)))
(home-page "https://github.com/mozilla-services/hawkauthlib")
(synopsis "Hawk Access Authentication protocol")
(description
"This is a low-level Python library for implementing Hawk Access Authentication,
a simple HTTP request-signing scheme.")
(license license:mpl2.0)))
(define-public python-pybrowserid
(package
(name "python-pybrowserid")
(version "0.14.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyBrowserID" version))
(sha256
(base32
"1qvi79kfb8x9kxkm5lw2mp42hm82cpps1xknmsb5ghkwx1lpc8kc"))))
(build-system python-build-system)
(propagated-inputs
`(("python-requests" ,python-requests)))
(native-inputs
`(("python-mock" ,python-mock)))
(home-page "https://github.com/mozilla/PyBrowserID")
(synopsis "Python library for the BrowserID protocol")
(description
"This is a Python client library for the BrowserID protocol that
underlies Mozilla Persona.")
(license license:mpl2.0)))
(define-public python-pyfxa
(package
(name "python-pyfxa")
(version "0.6.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyFxA" version))
(sha256
(base32
"0axl16fyrz2r88gnw4b12mk7dpkqscv8c4wsc1y5hicl7bsbc4fm"))))
(build-system python-build-system)
(arguments '(#:tests? #f)) ; 17 tests require network access
(propagated-inputs
`(("python-cryptography" ,python-cryptography)
("python-hawkauthlib" ,python-hawkauthlib)
("python-pybrowserid" ,python-pybrowserid)
("python-requests" ,python-requests)
("python-six" ,python-six)))
(native-inputs
`(("python-grequests" ,python-grequests)
("python-mock" ,python-mock)
("python-responses" ,python-responses)
("python-unittest2" ,python-unittest2)))
(home-page "https://github.com/mozilla/PyFxA")
(synopsis "Firefox Accounts client library for Python")
(description
"This is a Python library for interacting with the Firefox Accounts
ecosystem.")
(license license:mpl2.0)))

75
gnu/packages/python.scm
View file

@ -715,8 +715,8 @@ (define-public python-hdf4
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(getenv "PYTHONPATH")))
(and (zero? (system* "./runexamples.sh"))
(zero? (system* "nosetests" "-v"))))))))
(invoke "./runexamples.sh")
(invoke "nosetests" "-v"))))))
(home-page "https://github.com/fhs/python-hdf4")
(synopsis "Python interface to the NCSA HDF4 library")
(description
@ -855,6 +855,34 @@ (define-public python-lockfile
(define-public python2-lockfile
(package-with-python2 python-lockfile))
(define-public python-semantic-version
(package
(name "python-semantic-version")
(version "2.6.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "semantic_version" version))
(sha256
(base32
"1h2l9xyg1zzsda6kjcmfcgycbvrafwci283vcr1v5sbk01l2hhra"))))
(build-system python-build-system)
(arguments
`(#:tests? #f)) ; PyPI tarball lacks tests
(home-page "https://github.com/rbarrois/python-semanticversion")
(synopsis "Semantic versioning module for Python")
(description
"The @code{semantic_version} class is a small library for handling
@uref{https://semver.org/, semantic versioning} (@dfn{SemVer}) in Python.
It can compare versions, generate a new version that represents a bump in one of
the version levels, and check whether any given string is a proper semantic
version identifier.")
(license license:bsd-3)))
(define-public python2-semantic-version
(package-with-python2 python-semantic-version))
(define-public python-setuptools
(package
(name "python-setuptools")
@ -3263,16 +3291,13 @@ (define-public python2-pygit2
(define-public python-pyparsing
(package
(name "python-pyparsing")
(version "2.2.0")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pyparsing/pyparsing"
"/pyparsing-" version
"/pyparsing-" version ".tar.gz"))
(uri (pypi-uri "pyparsing" version))
(sha256
(base32
"016b9gh606aa44sq92jslm89bg874ia0yyiyb643fa6dgbsbqch8"))))
(base32 "06dgd0iilvf8m0ssmfpcbh8l6jf0zkp8adbb84llksg17crfx4zl"))))
(build-system python-build-system)
(outputs '("out" "doc"))
(arguments
@ -3295,7 +3320,7 @@ (define-public python-pyparsing
(list "docs" "htmldoc" "examples")
(list doc html-doc examples))
#t))))))
(home-page "http://pyparsing.wikispaces.com")
(home-page "https://github.com/pyparsing/pyparsing")
(synopsis "Python parsing class library")
(description
"The pyparsing module is an alternative approach to creating and
@ -4239,15 +4264,14 @@ (define-public python2-cairocffi
(define-public python-decorator
(package
(name "python-decorator")
(version "4.2.1")
(version "4.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "decorator" version))
(sha256
(base32 "03iaf116rm3w8b4agb8hzf6z9331mrvi4khfxq35zkx17sgxsikx"))))
(base32 "0308djallnh00v112y5b7nadl657ysmkp6vc8xn51d6yzc9zm7n3"))))
(build-system python-build-system)
(arguments '(#:tests? #f)) ; no test target
(home-page "https://pypi.python.org/pypi/decorator/")
(synopsis "Python module to simplify usage of decorators")
(description
@ -4422,7 +4446,7 @@ (define-public python-pexpect
;; Why does it not work? Delete for now.
(delete-file "tests/test_socket.py")
#t))
(replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
(replace 'check (lambda _ (invoke "nosetests" "-v"))))))
(native-inputs
`(("python-nose" ,python-nose)
("python-pytest" ,python-pytest)
@ -5099,21 +5123,21 @@ (define-public python2-netifaces
(define-public python-networkx
(package
(name "python-networkx")
(version "2.1")
(version "2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "networkx" version ".zip"))
(sha256
(base32 "1ccb8mfz4m821k9y0cigkbq42q2sbb4dj5fbjshp0awp32j2q9v4"))))
(base32 "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5"))))
(build-system python-build-system)
;; python-decorator is needed at runtime
;; python-decorator is needed at runtime.
(propagated-inputs
`(("python-decorator" ,python-decorator)))
(native-inputs
`(("python-nose" ,python-nose)
("unzip" ,unzip)))
(home-page "http://networkx.github.io/")
(home-page "https://networkx.github.io/")
(synopsis "Python module for creating and manipulating graphs and networks")
(description
"NetworkX is a Python package for the creation, manipulation, and study
@ -12117,14 +12141,14 @@ (define-public python2-flex
(define-public python-marshmallow
(package
(name "python-marshmallow")
(version "3.0.0b3")
(version "3.0.0b14")
(source
(origin
(method url-fetch)
(uri (pypi-uri "marshmallow" version))
(sha256
(base32
"07mcrij1yvk85lvgx44wwr9pc80xryghvlgayb057g1cazcypysd"))))
"1digk3f5cfk7wmlka65mc7bzsd96pbsgcsvp6pimd5b4ff9zb5p3"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
@ -12391,15 +12415,24 @@ (define-public python2-pyopengl-accelerate
(define-public python-rencode
(package
(name "python-rencode")
(version "1.0.3")
(version "1.0.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "rencode" version))
(sha256
(base32
"08if5yax1xn5yfp8p3765ccjmfcv9di7i4m5jckgnwvdsgznwkbj"))))
"0mzwdq1is7kyyr32i5k4iz6g5xxdvmiyc132jnc60p9m6lnwjrpv"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'check 'delete-bogus-test
;; This test requires /home/aresch/Downloads, which is not provided by
;; the build environment.
(lambda _
(delete-file "rencode/t.py")
#t)))))
(native-inputs `(("pkg-config" ,pkg-config)
("python-cython" ,python-cython)))
(home-page "https://github.com/aresch/rencode")

57
gnu/packages/rust.scm
View file

@ -514,6 +514,26 @@ (define-public rust-1.20
(substitute-keyword-arguments (package-arguments rust-1.19)
((#:phases phases)
`(modify-phases ,phases
(add-after 'patch-tests 'patch-cargo-tests
(lambda _
(substitute* "src/tools/cargo/tests/build.rs"
(("/usr/bin/env") (which "env"))
;; Guix llvm is compiled without asmjs-unknown-emscripten.
(("fn wasm32_final_outputs") "#[ignore]\nfn wasm32_final_outputs"))
(substitute* "src/tools/cargo/tests/death.rs"
;; This is stuck when built in container.
(("fn ctrl_c_kills_everyone") "#[ignore]\nfn ctrl_c_kills_everyone"))
;; Prints test output in the wrong order when built on
;; i686-linux.
(substitute* "src/tools/cargo/tests/test.rs"
(("fn cargo_test_env") "#[ignore]\nfn cargo_test_env"))
#t))
(add-after 'patch-cargo-tests 'ignore-glibc-2.27-incompatible-test
;; https://github.com/rust-lang/rust/issues/47863
(lambda _
(substitute* "src/test/run-pass/out-of-stack.rs"
(("// ignore-android") "// ignore-test\n// ignore-android"))
#t))
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -542,7 +562,6 @@ (define-public rust-1.20
prefix = \"" out "\"
docdir = \"" doc "/share/doc/rust" "\"
sysconfdir = \"etc\"
localstatedir = \"var/lib\"
[rust]
default-linker = \"" gcc "/bin/gcc" "\"
channel = \"stable\"
@ -579,10 +598,11 @@ (define-public rust-1.20
(delete 'patch-cargo-tomls)
(add-before 'build 'reset-timestamps-after-changes
(lambda* _
(define ref (stat "README.md"))
(for-each
(lambda (filename)
(set-file-time filename ref))
;; Rust 1.20.0 treats timestamp 0 as "file doesn't exist".
;; Therefore, use timestamp 1.
(utime filename 1 1 1 1))
(find-files "." #:directories? #t))
#t))
(replace 'build
@ -651,34 +671,6 @@ (define-public rust-1.23
;; XXX: Revisit this when we use gcc 6.
(substitute* "src/binaryen/CMakeLists.txt"
(("ADD_COMPILE_FLAG\\(\\\"-march=native\\\"\\)") ""))
#t))
(add-after 'patch-tests 'patch-cargo-tests
(lambda _
(substitute* "src/tools/cargo/tests/build.rs"
(("/usr/bin/env") (which "env"))
;; Guix llvm is compiled without asmjs-unknown-emscripten.
(("fn wasm32_final_outputs") "#[ignore]\nfn wasm32_final_outputs"))
(substitute* "src/tools/cargo/tests/death.rs"
;; This is stuck when built in container.
(("fn ctrl_c_kills_everyone") "#[ignore]\nfn ctrl_c_kills_everyone"))
;; Prints test output in the wrong order when built on
;; i686-linux.
(substitute* "src/tools/cargo/tests/test.rs"
(("fn cargo_test_env") "#[ignore]\nfn cargo_test_env"))
#t))
(add-after 'patch-cargo-tests 'ignore-glibc-2.27-incompatible-test
;; https://github.com/rust-lang/rust/issues/47863
(lambda _
(substitute* "src/test/run-pass/out-of-stack.rs"
(("// ignore-android") "// ignore-test\n// ignore-android"))))
(add-after 'ignore-glibc-2.27-incompatible-test 'fix-mtime-bug
(lambda* _
(substitute* "src/build_helper/lib.rs"
;; Bug in Rust code.
;; Current implementation assume that if dst not exist then it's mtime
;; is 0, but in same time "src" have 0 mtime in guix build!
(("let threshold = mtime\\(dst\\);")
"if !dst.exists() {\nreturn false\n}\n let threshold = mtime(dst);"))
#t))))))))
(define-public rust-1.24
@ -698,8 +690,7 @@ (define-public rust-1.24
;; This test is known to fail on aarch64 and powerpc64le:
;; https://github.com/rust-lang/rust/issues/45410
(("fn test_loading_cosine") "#[ignore]\nfn test_loading_cosine"))
#t))
(delete 'fix-mtime-bug))))))))
#t)))))))))
(define-public rust-1.25
(let ((base-rust

4
gnu/packages/skarnet.scm
View file

@ -105,7 +105,7 @@ (define-public execline
(define-public s6
(package
(name "s6")
(version "2.7.2.0")
(version "2.7.2.1")
(source
(origin
(method url-fetch)
@ -113,7 +113,7 @@ (define-public s6
version ".tar.gz"))
(sha256
(base32
"02canrzmhr66gi16ldyylk378jlmyfl73vn72ayr12h2wyxgqm5g"))))
"0vyl4wr2l4mp9ams0dyg224qxhl8ksxsv2shs6606lhhp9g1rb6b"))))
(build-system gnu-build-system)
(inputs `(("skalibs" ,skalibs)
("execline" ,execline)))

3
gnu/packages/syndication.scm
View file

@ -1,6 +1,9 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at

6
gnu/packages/version-control.scm
View file

@ -712,13 +712,13 @@ (define-public python2-ghp-import
(define-public python-gitdb
(package
(name "python-gitdb")
(version "2.0.3")
(version "2.0.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "gitdb2" version))
(sha256
(base32
"02azg62mr99b7cllyjrly77np3vw32y8nrxpa2xjapiyaga2j3mn"))))
"0i608q9c47rdsmyac1cn6s0hzwwj7cb957y8fc9wacc5lnw8ak5v"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@ -733,7 +733,7 @@ (define-public python-gitdb
"file" (number->string filecount))
(lambda (port)
(format port "~a" filecount))))
(and
(begin
(invoke "git" "init")
(invoke "git" "config" "user.name" "Total Git")
(invoke "git" "config" "user.email" "git@localhost")

3
gnu/packages/video.scm
View file

@ -1242,7 +1242,8 @@ (define-public libvpx
(sha256
(base32
"0vvh89hvp8qg9an9vcmwb7d9k3nixhxaz6zi65qdjnd0i56kkcz6"))
(patches (search-patches "libvpx-CVE-2016-2818.patch"))))
(patches (search-patches "libvpx-use-after-free-in-postproc.patch"
"libvpx-CVE-2016-2818.patch"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list "--enable-shared"

4
gnu/packages/web.scm
View file

@ -5019,12 +5019,14 @@ (define-public varnish
"--localstatedir=/var")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-/bin/sh
(add-after 'unpack 'use-absolute-file-names
(lambda _
(substitute* '("bin/varnishtest/vtc_varnish.c"
"bin/varnishtest/vtc_process.c"
"bin/varnishd/mgt/mgt_vcc.c")
(("/bin/sh") (which "sh")))
(substitute* "bin/varnishd/mgt/mgt_shmem.c"
(("rm -rf") (string-append (which "rm") " -rf")))
#t))
(add-before 'install 'patch-Makefile
(lambda _

49
gnu/packages/webkit.scm
View file

@ -24,6 +24,7 @@ (define-module (gnu packages webkit)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
@ -32,6 +33,7 @@ (define-module (gnu packages webkit)
#:use-module (gnu packages databases)
#:use-module (gnu packages enchant)
#:use-module (gnu packages flex)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
@ -85,23 +87,7 @@ (define-public webkitgtk
;; XXX Disable WOFF2 ‘web fonts’. These were never
;; supported in our previous builds. Enabling them
;; requires building libwoff2 and possibly woff2dec.
"-DUSE_WOFF2=OFF")
#:phases
(modify-phases %standard-phases
(add-after
'set-paths 'add-gst-plugins-base-include-path
(lambda* (#:key inputs #:allow-other-keys)
;; XXX Work around a problem in the build system, which neglects
;; to add -I for gst-plugins-base when compiling
;; Source/WebKit2/UIProcess/WebPageProxy.cpp, apparently assuming
;; that it will be in the same directory as gstreamer's header
;; files.
(setenv "CPATH"
(string-append (getenv "C_INCLUDE_PATH")
":"
(assoc-ref inputs "gst-plugins-base")
"/include/gstreamer-1.0"))
#t)))))
"-DUSE_WOFF2=OFF")))
(native-inputs
`(("bison" ,bison)
("gettext" ,gettext-minimal)
@ -149,3 +135,32 @@ (define-public webkitgtk
license:lgpl2.1+
license:bsd-2
license:bsd-3))))
;; This version of webkitgtk needs to be kept separate, because it requires a
;; newer version of GCC than our default compiler, and this causes problems
;; when linked with C++ libraries built using our default compiler. For now,
;; we use this newer webkitgtk only for selected packages, e.g. epiphany.
(define-public webkitgtk-2.22
(package/inherit webkitgtk
(name "webkitgtk")
(version "2.22.2")
(source (origin
(method url-fetch)
(uri (string-append "https://www.webkitgtk.org/releases/"
name "-" version ".tar.xz"))
(sha256
(base32
"1flrbr8pzbrlwv09b4pmgh6vklw7jghd2lgrhcb72vl9s7a8fm1l"))))
(native-inputs
`(("gcc" ,gcc-7) ; webkitgtk-2.22 requires gcc-6 or newer
,@(package-native-inputs webkitgtk)))
(arguments
`(#:phases (modify-phases %standard-phases
(add-before 'configure 'work-around-gcc-7-include-path-issue
;; FIXME: Work around a problem with gcc-7 includes (see
;; <https://bugs.gnu.org/30756>).
(lambda _
(unsetenv "C_INCLUDE_PATH")
(unsetenv "CPLUS_INCLUDE_PATH")
#t)))
,@(package-arguments webkitgtk)))))

4
gnu/packages/wxwidgets.scm
View file

@ -49,7 +49,7 @@ (define-module (gnu packages wxwidgets)
(define-public wxwidgets
(package
(name "wxwidgets")
(version "3.0.3")
(version "3.0.4")
(source
(origin
(method url-fetch)
@ -57,7 +57,7 @@ (define-public wxwidgets
"releases/download/v" version
"/wxWidgets-" version ".tar.bz2"))
(sha256
(base32 "0yrhp5cs2g33cpbdwdzicmm5m4mfnlvxwv031x9266zc90zh7j08"))))
(base32 "1w7pgfqjab7n84lc4aarydl3g55d1hdgl2ilwml766r6inc7y5cn"))))
(build-system glib-or-gtk-build-system)
(inputs
`(("glu" ,glu)

11
gnu/packages/xml.scm
View file

@ -681,20 +681,23 @@ (define-public perl-xml-compile-tester
(define-public perl-xml-compile
(package
(name "perl-xml-compile")
(version "1.54")
(version "1.60")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/"
"XML-Compile-" version ".tar.gz"))
(sha256
(base32
"1hp41960bpqxvv1samv9hc0ghhmvs3i16r4rfl9yp54lp6jhsr2c"))))
"04vv7wy5v1l38xsfdbacvyd90qircvnrs2f3ysljm1nhq8mycmwm"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-log-report" ,perl-log-report)
`(("perl-carp" ,perl-carp)
("perl-log-report" ,perl-log-report)
("perl-xml-compile-tester" ,perl-xml-compile-tester)
("perl-xml-libxml" ,perl-xml-libxml)
("perl-test-deep" ,perl-test-deep)))
("perl-scalar-list-utils" ,perl-scalar-list-utils)
("perl-test-deep" ,perl-test-deep)
("perl-types-serialiser" ,perl-types-serialiser)))
(home-page "https://metacpan.org/release/XML-Compile")
(synopsis "Compilation-based XML processing")
(description

4
gnu/packages/xorg.scm
View file

@ -5910,7 +5910,7 @@ (define-public xcompmgr
(define-public xpra
(package
(name "xpra")
(version "2.3.3")
(version "2.3.4")
(source
(origin
(method url-fetch)
@ -5918,7 +5918,7 @@ (define-public xpra
version ".tar.xz"))
(sha256
(base32
"1azvvddjfq7lb5kmbn0ilgq2nf7pmymsc3b9lhbjld6w156qdv01"))))
"0wa3kx54himy3i1b2801hlzfilh3cf4kjk40k1cjl0ds28m5hija"))))
(build-system python-build-system)
(inputs `(("ffmpeg" ,ffmpeg)
("flac" ,flac)

96
gnu/services/web.scm
View file

@ -8,6 +8,7 @@
;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -190,7 +191,21 @@ (define-module (gnu services web)
tailon-configuration-config-file
tailon-configuration-package
tailon-service-type))
tailon-service-type
<varnish-configuration>
varnish-configuration
varnish-configuration?
varnish-configuration-package
varnish-configuration-name
varnish-configuration-backend
varnish-configuration-vcl
varnish-configuration-listen
varnish-configuration-storage
varnish-configuration-parameters
varnish-configuration-extra-options
varnish-service-type))
;;; Commentary:
;;;
@ -1162,3 +1177,82 @@ (define tailon-service-type
(files (append (tailon-configuration-file-files old-config-file)
files))))))))
(default-value (tailon-configuration))))
;;;
;;; Varnish
;;;
(define-record-type* <varnish-configuration>
varnish-configuration make-varnish-configuration
varnish-configuration?
(package varnish-configuration-package ;<package>
(default varnish))
(name varnish-configuration-name ;string
(default "default"))
(backend varnish-configuration-backend ;string
(default "localhost:8080"))
(vcl varnish-configuration-vcl ;#f | <file-like>
(default #f))
(listen varnish-configuration-listen ;list of strings
(default '("localhost:80")))
(storage varnish-configuration-storage ;list of strings
(default '("malloc,128m")))
(parameters varnish-configuration-parameters ;list of string pairs
(default '()))
(extra-options varnish-configuration-extra-options ;list of strings
(default '())))
(define %varnish-accounts
(list (user-group
(name "varnish")
(system? #t))
(user-account
(name "varnish")
(group "varnish")
(system? #t)
(comment "Varnish Cache User")
(home-directory "/var/varnish")
(shell (file-append shadow "/sbin/nologin")))))
(define varnish-shepherd-service
(match-lambda
(($ <varnish-configuration> package name backend vcl listen storage
parameters extra-options)
(list (shepherd-service
(provision (list (symbol-append 'varnish- (string->symbol name))))
(documentation (string-append "The Varnish Web Accelerator"
" (" name ")"))
(requirement '(networking))
(start #~(make-forkexec-constructor
(list #$(file-append package "/sbin/varnishd")
"-n" #$name
#$@(if vcl
#~("-f" #$vcl)
#~("-b" #$backend))
#$@(append-map (lambda (a) (list "-a" a)) listen)
#$@(append-map (lambda (s) (list "-s" s)) storage)
#$@(append-map (lambda (p)
(list "-p" (format #f "~a=~a"
(car p) (cdr p))))
parameters)
#$@extra-options)
;; Varnish will drop privileges to the "varnish" user when
;; it exists. Not passing #:user here allows the service
;; to bind to ports < 1024.
#:pid-file (if (string-prefix? "/" #$name)
(string-append #$name "/_.pid")
(string-append "/var/varnish/" #$name "/_.pid"))))
(stop #~(make-kill-destructor)))))))
(define varnish-service-type
(service-type
(name 'varnish)
(description "Run the Varnish cache server.")
(extensions
(list (service-extension account-service-type
(const %varnish-accounts))
(service-extension shepherd-root-service-type
varnish-shepherd-service)))
(default-value
(varnish-configuration))))

5
gnu/system/mapped-devices.scm
View file

@ -157,7 +157,10 @@ (define aliases
;; @dots{}
(initrd-modules (append (list~{ ~s~})
%base-initrd-modules)))
@end example\n")
@end example
If you think this diagnostic is inaccurate, use the @option{--skip-checks}
option of @command{guix system}.\n")
missing)))
(&error-location
(location (source-properties->location location)))))))))

20
gnu/system/vm.scm
View file

@ -99,21 +99,28 @@ (define %linux-vm-file-systems
(device "store")
(type "9p")
(needed-for-boot? #t)
(options "trans=virtio")
(flags '(read-only))
(options "trans=virtio,cache=loose")
(check? #f))
;; The 9p documentation says that cache=loose is "intended for
;; exclusive, read-only mounts", without additional details. In
;; practice it seems to work well for these, and it's much faster than
;; the default cache=none, especially when copying and registering
;; store items.
(file-system
(mount-point "/xchg")
(device "xchg")
(type "9p")
(needed-for-boot? #t)
(options "trans=virtio")
(options "trans=virtio,cache=loose")
(check? #f))
(file-system
(mount-point "/tmp")
(device "tmp")
(type "9p")
(needed-for-boot? #t)
(options "trans=virtio")
(options "trans=virtio,cache=loose")
(check? #f))))
(define not-config?
@ -390,7 +397,12 @@ (define schema
#:closures graphs
#:copy-closures? #$copy-inputs?
#:register-closures? #$register-closures?
#:system-directory #$os-drv))
#:system-directory #$os-drv
;; Disable deduplication to speed things up,
;; and because it doesn't help much for a
;; single system generation.
#:deduplicate? #f))
(root-size #$(if (eq? 'guess disk-image-size)
#~(max
;; Minimum 20 MiB root size

41
gnu/tests/web.scm
View file

@ -32,6 +32,7 @@ (define-module (gnu tests web)
#:use-module (guix store)
#:export (%test-httpd
%test-nginx
%test-varnish
%test-php-fpm
%test-hpcguix-web
%test-tailon))
@ -167,6 +168,46 @@ (define %test-nginx
(value (run-webserver-test name %nginx-os
#:log-file "/var/log/nginx/access.log"))))
;;;
;;; Varnish
;;;
(define %varnish-vcl
(mixed-text-file
"varnish-test.vcl"
"vcl 4.0;
backend dummy { .host = \"127.1.1.1\"; }
sub vcl_recv { return(synth(200, \"OK\")); }
sub vcl_synth {
synthetic(\"" %index.html-contents "\");
set resp.http.Content-Type = \"text/plain\";
return(deliver);
}"))
(define %varnish-os
(simple-operating-system
(dhcp-client-service)
;; Pretend to be a web server that serves %index.html-contents.
(service varnish-service-type
(varnish-configuration
(name "/tmp/server")
;; Use a small VSL buffer to fit in the test VM.
(parameters '(("vsl_space" . "4M")))
(vcl %varnish-vcl)))
;; Proxy the "server" using the builtin configuration.
(service varnish-service-type
(varnish-configuration
(parameters '(("vsl_space" . "4M")))
(backend "localhost:80")
(listen '(":8080"))))))
(define %test-varnish
(system-test
(name "varnish")
(description "Test the Varnish Cache server.")
(value (run-webserver-test "varnish-default" %varnish-os))))
;;;
;;; PHP-FPM

23
guix/build/store-copy.scm
View file

@ -19,6 +19,7 @@
(define-module (guix build store-copy)
#:use-module (guix build utils)
#:use-module (guix sets)
#:use-module (guix progress)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-9)
#:use-module (srfi srfi-26)
@ -167,7 +168,8 @@ (define items
(reduce + 0 (map file-size items)))
(define* (populate-store reference-graphs target)
(define* (populate-store reference-graphs target
#:key (log-port (current-error-port)))
"Populate the store under directory TARGET with the items specified in
REFERENCE-GRAPHS, a list of reference-graph files."
(define store
@ -183,9 +185,20 @@ (define (graph-from-file file)
(mkdir-p store)
(chmod store #o1775)
(for-each (lambda (thing)
(copy-recursively thing
(string-append target thing)))
(things-to-copy)))
(let* ((things (things-to-copy))
(len (length things))
(progress (progress-reporter/bar len
(format #f "copying ~a store items"
len)
log-port)))
(call-with-progress-reporter progress
(lambda (report)
(for-each (lambda (thing)
(copy-recursively thing
(string-append target thing)
#:log (%make-void-port "w"))
(report))
things)))))
;;; store-copy.scm ends here

16
guix/channels.scm
View file

@ -47,9 +47,9 @@ (define-module (guix channels)
channel-instance-checkout
latest-channel-instances
channel-instance-derivations
latest-channel-derivation
channel-instances->manifest))
channel-instances->manifest
channel-instances->derivation))
;;; Commentary:
;;;
@ -294,13 +294,17 @@ (define instance->entry
(zip instances derivations))))
(return (manifest entries))))
(define (channel-instances->derivation instances)
"Return the derivation of the profile containing INSTANCES, a list of
channel instances."
(mlet %store-monad ((manifest (channel-instances->manifest instances)))
(profile-derivation manifest)))
(define latest-channel-instances*
(store-lift latest-channel-instances))
(define* (latest-channel-derivation #:optional (channels %default-channels))
"Return as a monadic value the derivation that builds the profile for the
latest instances of CHANNELS."
(mlet* %store-monad ((instances ((store-lift latest-channel-instances)
channels))
(manifest (channel-instances->manifest instances)))
(profile-derivation manifest)))
(mlet %store-monad ((instances (latest-channel-instances* channels)))
(channel-instances->derivation instances)))

15
guix/git-download.scm
View file

@ -156,22 +156,23 @@ (define (git-file-list directory)
The result is similar to that of the 'git ls-files' command, except that it
also includes directories, not just regular files. The returned file names
are relative to DIRECTORY, which is not necessarily the root of the checkout."
(let* ((directory (canonicalize-path directory))
(let* (;; 'repository-working-directory' always returns a trailing "/",
;; so add one here to ease the comparisons below.
(directory (string-append (canonicalize-path directory) "/"))
(dot-git (repository-discover directory))
(top (dirname dot-git))
(repository (repository-open dot-git))
;; XXX: This procedure is mistakenly private in Guile-Git 0.1.0.
(workdir ((@@ (git repository) repository-working-directory)
repository))
(head (repository-head repository))
(oid (reference-target head))
(commit (commit-lookup repository oid))
(tree (commit-tree commit))
(files (tree-list tree)))
(repository-close! repository)
(if (string=? top directory)
(if (string=? workdir directory)
files
(let ((relative (string-append
(string-drop directory
(+ 1 (string-length top)))
"/")))
(let ((relative (string-drop directory (string-length workdir))))
(filter-map (lambda (file)
(and (string-prefix? relative file)
(string-drop file (string-length relative))))

2
guix/gnupg.scm
View file

@ -57,7 +57,7 @@ (define current-keyring
(define %openpgp-key-server
;; The default key server. Note that keys.gnupg.net appears to be
;; unreliable.
(make-parameter "pgp.mit.edu"))
(make-parameter "pool.sks-keyservers.net"))
(define* (gnupg-verify sig file
#:optional (keyring (current-keyring)))

366
guix/inferior.scm
View file

@ -19,24 +19,68 @@
(define-module (guix inferior)
#:use-module (srfi srfi-9)
#:use-module (srfi srfi-9 gnu)
#:use-module ((guix utils) #:select (source-properties->location))
#:use-module ((guix utils)
#:select (%current-system
source-properties->location
call-with-temporary-directory
version>? version-prefix?
cache-directory))
#:use-module ((guix store)
#:select (nix-server-socket
nix-server-major-version
nix-server-minor-version
store-lift))
#:use-module ((guix derivations)
#:select (read-derivation-from-file))
#:use-module (guix gexp)
#:use-module (guix search-paths)
#:use-module (guix profiles)
#:use-module (guix channels)
#:use-module (guix monads)
#:use-module (guix store)
#:use-module (guix derivations)
#:use-module (guix base32)
#:use-module (gcrypt hash)
#:autoload (guix cache) (maybe-remove-expired-cache-entries)
#:autoload (guix ui) (show-what-to-build*)
#:autoload (guix build utils) (mkdir-p)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:autoload (ice-9 ftw) (scandir)
#:use-module (ice-9 match)
#:use-module (ice-9 popen)
#:use-module (ice-9 vlist)
#:use-module (ice-9 binary-ports)
#:use-module ((rnrs bytevectors) #:select (string->utf8))
#:export (inferior?
open-inferior
close-inferior
inferior-eval
inferior-object?
inferior-packages
lookup-inferior-packages
inferior-package?
inferior-package-name
inferior-package-version
inferior-packages
inferior-package-synopsis
inferior-package-description
inferior-package-home-page
inferior-package-location))
inferior-package-location
inferior-package-inputs
inferior-package-native-inputs
inferior-package-propagated-inputs
inferior-package-transitive-propagated-inputs
inferior-package-native-search-paths
inferior-package-transitive-native-search-paths
inferior-package-search-paths
inferior-package-derivation
inferior-package->manifest-entry
%inferior-cache-directory
inferior-for-channels))
;;; Commentary:
;;;
@ -48,11 +92,13 @@ (define-module (guix inferior)
;; Inferior Guix process.
(define-record-type <inferior>
(inferior pid socket version)
(inferior pid socket version packages table)
inferior?
(pid inferior-pid)
(socket inferior-socket)
(version inferior-version)) ;REPL protocol version
(version inferior-version) ;REPL protocol version
(packages inferior-package-promise) ;promise of inferior packages
(table inferior-package-table)) ;promise of vhash
(define (inferior-pipe directory command)
"Return an input/output pipe on the Guix instance in DIRECTORY. This runs
@ -96,9 +142,12 @@ (define pipe
(match (read pipe)
(('repl-version 0 rest ...)
(let ((result (inferior 'pipe pipe (cons 0 rest))))
(letrec ((result (inferior 'pipe pipe (cons 0 rest)
(delay (%inferior-packages result))
(delay (%inferior-package-table result)))))
(inferior-eval '(use-modules (guix)) result)
(inferior-eval '(use-modules (gnu)) result)
(inferior-eval '(use-modules (ice-9 match)) result)
(inferior-eval '(define %package-table (make-hash-table))
result)
result))
@ -123,8 +172,7 @@ (define (write-inferior-object object port)
(set-record-type-printer! <inferior-object> write-inferior-object)
(define (inferior-eval exp inferior)
"Evaluate EXP in INFERIOR."
(define (read-inferior-response inferior)
(define sexp->object
(match-lambda
(('value value)
@ -132,14 +180,21 @@ (define sexp->object
(('non-self-quoting address string)
(inferior-object address string))))
(write exp (inferior-socket inferior))
(newline (inferior-socket inferior))
(match (read (inferior-socket inferior))
(('values objects ...)
(apply values (map sexp->object objects)))
(('exception key objects ...)
(apply throw key (map sexp->object objects)))))
(define (send-inferior-request exp inferior)
(write exp (inferior-socket inferior))
(newline (inferior-socket inferior)))
(define (inferior-eval exp inferior)
"Evaluate EXP in INFERIOR."
(send-inferior-request exp inferior)
(read-inferior-response inferior))
;;;
;;; Inferior packages.
@ -162,8 +217,8 @@ (define (write-inferior-package package port)
(set-record-type-printer! <inferior-package> write-inferior-package)
(define (inferior-packages inferior)
"Return the list of packages known to INFERIOR."
(define (%inferior-packages inferior)
"Compute the list of inferior packages from INFERIOR."
(let ((result (inferior-eval
'(fold-packages (lambda (package result)
(let ((id (object-address package)))
@ -179,6 +234,33 @@ (define (inferior-packages inferior)
(inferior-package inferior name version id)))
result)))
(define (inferior-packages inferior)
"Return the list of packages known to INFERIOR."
(force (inferior-package-promise inferior)))
(define (%inferior-package-table inferior)
"Compute a package lookup table for INFERIOR."
(fold (lambda (package table)
(vhash-cons (inferior-package-name package) package
table))
vlist-null
(inferior-packages inferior)))
(define* (lookup-inferior-packages inferior name #:optional version)
"Return the sorted list of inferior packages matching NAME in INFERIOR, with
highest version numbers first. If VERSION is true, return only packages with
a version number prefixed by VERSION."
;; This is the counterpart of 'find-packages-by-name'.
(sort (filter (lambda (package)
(or (not version)
(version-prefix? version
(inferior-package-version package))))
(vhash-fold* cons '() name
(force (inferior-package-table inferior))))
(lambda (p1 p2)
(version>? (inferior-package-version p1)
(inferior-package-version p2)))))
(define (inferior-package-field package getter)
"Return the field of PACKAGE, an inferior package, accessed with GETTER."
(let ((inferior (inferior-package-inferior package))
@ -216,3 +298,261 @@ (define (inferior-package-location package)
(location->source-properties
loc)))
package-location))))
(define (inferior-package-input-field package field)
"Return the input field FIELD (e.g., 'native-inputs') of PACKAGE, an
inferior package."
(define field*
`(compose (lambda (inputs)
(map (match-lambda
;; XXX: Origins are not handled.
((label (? package? package) rest ...)
(let ((id (object-address package)))
(hashv-set! %package-table id package)
`(,label (package ,id
,(package-name package)
,(package-version package))
,@rest)))
(x
x))
inputs))
,field))
(define inputs
(inferior-package-field package field*))
(define inferior
(inferior-package-inferior package))
(map (match-lambda
((label ('package id name version) . rest)
;; XXX: eq?-ness of inferior packages is not preserved here.
`(,label ,(inferior-package inferior name version id)
,@rest))
(x x))
inputs))
(define inferior-package-inputs
(cut inferior-package-input-field <> 'package-inputs))
(define inferior-package-native-inputs
(cut inferior-package-input-field <> 'package-native-inputs))
(define inferior-package-propagated-inputs
(cut inferior-package-input-field <> 'package-propagated-inputs))
(define inferior-package-transitive-propagated-inputs
(cut inferior-package-input-field <> 'package-transitive-propagated-inputs))
(define (%inferior-package-search-paths package field)
"Return the list of search path specificiations of PACKAGE, an inferior
package."
(define paths
(inferior-package-field package
`(compose (lambda (paths)
(map (@ (guix search-paths)
search-path-specification->sexp)
paths))
,field)))
(map sexp->search-path-specification paths))
(define inferior-package-native-search-paths
(cut %inferior-package-search-paths <> 'package-native-search-paths))
(define inferior-package-search-paths
(cut %inferior-package-search-paths <> 'package-search-paths))
(define inferior-package-transitive-native-search-paths
(cut %inferior-package-search-paths <> 'package-transitive-native-search-paths))
(define (proxy client backend) ;adapted from (guix ssh)
"Proxy communication between CLIENT and BACKEND until CLIENT closes the
connection, at which point CLIENT is closed (both CLIENT and BACKEND must be
input/output ports.)"
(define (select* read write except)
;; This is a workaround for <https://bugs.gnu.org/30365> in Guile < 2.2.4:
;; since 'select' sometimes returns non-empty sets for no good reason,
;; call 'select' a second time with a zero timeout to filter out incorrect
;; replies.
(match (select read write except)
((read write except)
(select read write except 0))))
;; Use buffered ports so that 'get-bytevector-some' returns up to the
;; whole buffer like read(2) would--see <https://bugs.gnu.org/30066>.
(setvbuf client _IOFBF 65536)
(setvbuf backend _IOFBF 65536)
(let loop ()
(match (select* (list client backend) '() '())
((reads () ())
(when (memq client reads)
(match (get-bytevector-some client)
((? eof-object?)
(close-port client))
(bv
(put-bytevector backend bv)
(force-output backend))))
(when (memq backend reads)
(match (get-bytevector-some backend)
(bv
(put-bytevector client bv)
(force-output client))))
(unless (port-closed? client)
(loop))))))
(define* (inferior-package-derivation store package
#:optional
(system (%current-system))
#:key target)
"Return the derivation for PACKAGE, an inferior package, built for SYSTEM
and cross-built for TARGET if TARGET is true. The inferior corresponding to
PACKAGE must be live."
;; Create a named socket in /tmp and let the inferior of PACKAGE connect to
;; it and use it as its store. This ensures the inferior uses the same
;; store, with the same options, the same per-session GC roots, etc.
(call-with-temporary-directory
(lambda (directory)
(chmod directory #o700)
(let* ((name (string-append directory "/inferior"))
(socket (socket AF_UNIX SOCK_STREAM 0))
(inferior (inferior-package-inferior package))
(major (nix-server-major-version store))
(minor (nix-server-minor-version store))
(proto (logior major minor)))
(bind socket AF_UNIX name)
(listen socket 1024)
(send-inferior-request
`(let ((socket (socket AF_UNIX SOCK_STREAM 0)))
(connect socket AF_UNIX ,name)
;; 'port->connection' appeared in June 2018 and we can hardly
;; emulate it on older versions. Thus fall back to
;; 'open-connection', at the risk of talking to the wrong daemon or
;; having our build result reclaimed (XXX).
(let* ((store (if (defined? 'port->connection)
(port->connection socket #:version ,proto)
(open-connection)))
(package (hashv-ref %package-table
,(inferior-package-id package)))
(drv ,(if target
`(package-cross-derivation store package
,target
,system)
`(package-derivation store package
,system))))
(close-connection store)
(close-port socket)
(derivation-file-name drv)))
inferior)
(match (accept socket)
((client . address)
(proxy client (nix-server-socket store))))
(close-port socket)
(read-derivation-from-file (read-inferior-response inferior))))))
(define inferior-package->derivation
(store-lift inferior-package-derivation))
(define-gexp-compiler (package-compiler (package <inferior-package>) system
target)
;; Compile PACKAGE for SYSTEM, optionally cross-building for TARGET.
(inferior-package->derivation package system #:target target))
;;;
;;; Manifest entries.
;;;
(define* (inferior-package->manifest-entry package
#:optional (output "out")
#:key (parent (delay #f))
(properties '()))
"Return a manifest entry for the OUTPUT of package PACKAGE."
;; For each dependency, keep a promise pointing to its "parent" entry.
(letrec* ((deps (map (match-lambda
((label package)
(inferior-package->manifest-entry package
#:parent (delay entry)))
((label package output)
(inferior-package->manifest-entry package output
#:parent (delay entry))))
(inferior-package-propagated-inputs package)))
(entry (manifest-entry
(name (inferior-package-name package))
(version (inferior-package-version package))
(output output)
(item package)
(dependencies (delete-duplicates deps))
(search-paths
(inferior-package-transitive-native-search-paths package))
(parent parent)
(properties properties))))
entry))
;;;
;;; Cached inferiors.
;;;
(define %inferior-cache-directory
;; Directory for cached inferiors (GC roots).
(make-parameter (string-append (cache-directory #:ensure? #f)
"/inferiors")))
(define* (inferior-for-channels channels
#:key
(cache-directory (%inferior-cache-directory))
(ttl (* 3600 24 30)))
"Return an inferior for CHANNELS, a list of channels. Use the cache at
CACHE-DIRECTORY, where entries can be reclaimed after TTL seconds. This
procedure opens a new connection to the build daemon.
This is a convenience procedure that people may use in manifests passed to
'guix package -m', for instance."
(with-store store
(let ()
(define instances
(latest-channel-instances store channels))
(define key
(bytevector->base32-string
(sha256
(string->utf8
(string-concatenate (map channel-instance-commit instances))))))
(define cached
(string-append cache-directory "/" key))
(define (base32-encoded-sha256? str)
(= (string-length str) 52))
(define (cache-entries directory)
(map (lambda (file)
(string-append directory "/" file))
(scandir directory base32-encoded-sha256?)))
(define symlink*
(lift2 symlink %store-monad))
(define add-indirect-root*
(store-lift add-indirect-root))
(mkdir-p cache-directory)
(maybe-remove-expired-cache-entries cache-directory
cache-entries
#:entry-expiration
(file-expiration-time ttl))
(if (file-exists? cached)
(open-inferior cached)
(run-with-store store
(mlet %store-monad ((profile
(channel-instances->derivation instances)))
(mbegin %store-monad
(show-what-to-build* (list profile))
(built-derivations (list profile))
(symlink* (derivation->output-path profile) cached)
(add-indirect-root* cached)
(return (open-inferior cached)))))))))

27
guix/profiles.scm
View file

@ -314,12 +314,31 @@ (define (packages->manifest packages)
"Return a list of manifest entries, one for each item listed in PACKAGES.
Elements of PACKAGES can be either package objects or package/string tuples
denoting a specific output of a package."
(define inferiors-loaded?
;; This hack allows us to provide seamless integration for inferior
;; packages while not having a hard dependency on (guix inferior).
(resolve-module '(guix inferior) #f #f #:ensure #f))
(define (inferior->entry)
(module-ref (resolve-interface '(guix inferior))
'inferior-package->manifest-entry))
(manifest
(map (match-lambda
((package output)
(package->manifest-entry package output))
((? package? package)
(package->manifest-entry package)))
((package output)
(package->manifest-entry package output))
((? package? package)
(package->manifest-entry package))
((thing output)
(if inferiors-loaded?
((inferior->entry) thing output)
(throw 'wrong-type-arg 'packages->manifest
"Wrong package object: ~S" (list thing) (list thing))))
(thing
(if inferiors-loaded?
((inferior->entry) thing)
(throw 'wrong-type-arg 'packages->manifest
"Wrong package object: ~S" (list thing) (list thing)))))
packages)))
(define (manifest->gexp manifest)

4
guix/progress.scm
View file

@ -70,11 +70,11 @@ (define (start-progress-reporter! reporter)
(($ <progress-reporter> start report stop)
(start))))
(define (progress-reporter-report! reporter)
(define (progress-reporter-report! reporter . args)
"Low-level procedure to lead REPORTER to emit a report."
(match reporter
(($ <progress-reporter> start report stop)
(report))))
(apply report args))))
(define (stop-progress-reporter! reporter)
"Low-level procedure to stop REPORTER."

20
guix/scripts/pull.scm
View file

@ -180,9 +180,25 @@ (define (honor-lets-encrypt-certificates! store)
(define (honor-x509-certificates store)
"Use the right X.509 certificates for Git checkouts over HTTPS."
(let ((file (getenv "SSL_CERT_FILE"))
;; On distros such as CentOS 7, /etc/ssl/certs contains only a couple of
;; files (instead of all the certificates) among which "ca-bundle.crt". On
;; other distros /etc/ssl/certs usually contains the whole set of
;; certificates along with "ca-certificates.crt". Try to choose the right
;; one.
(let ((file (letrec-syntax ((choose
(syntax-rules ()
((_ file rest ...)
(let ((f file))
(if (and f (file-exists? f))
f
(choose rest ...))))
((_)
#f))))
(choose (getenv "SSL_CERT_FILE")
"/etc/ssl/certs/ca-certificates.crt"
"/etc/ssl/certs/ca-bundle.crt")))
(directory (or (getenv "SSL_CERT_DIR") "/etc/ssl/certs")))
(if (or (and file (file-exists? file))
(if (or file
(and=> (stat directory #f)
(lambda (st)
(> (stat:nlink st) 2))))

4
guix/scripts/substitute.scm
View file

@ -837,8 +837,8 @@ (define (progress-report-port reporter port)
(make-custom-binary-input-port "progress-port-proc"
read! #f #f
(lambda ()
(close-connection port)
(stop)))))))
(stop)
(close-port port)))))))
(define-syntax with-networking
(syntax-rules ()

3
guix/serialization.scm
View file

@ -301,8 +301,7 @@ (define basenames
(filter-map (lambda (base)
(let ((file (string-append directory
"/" base)))
(and (not (member base '("." "..")))
(select? file (lstat file))
(and (select? file (lstat file))
base)))
basenames))

44
guix/store/database.scm
View file

@ -23,6 +23,7 @@ (define-module (guix store database)
#:use-module (guix serialization)
#:use-module (guix store deduplication)
#:use-module (guix base16)
#:use-module (guix progress)
#:use-module (guix build syscalls)
#:use-module ((guix build utils)
#:select (mkdir-p executable-file?))
@ -234,7 +235,8 @@ (define* (register-path path
#:prefix prefix #:state-directory state-directory
#:deduplicate? deduplicate?
#:reset-timestamps? reset-timestamps?
#:schema schema))
#:schema schema
#:log-port (%make-void-port "w")))
(define %epoch
;; When it all began.
@ -245,12 +247,14 @@ (define* (register-items items
(deduplicate? #t)
(reset-timestamps? #t)
registration-time
(schema (sql-schema)))
(schema (sql-schema))
(log-port (current-error-port)))
"Register all of ITEMS, a list of <store-info> records as returned by
'read-reference-graph', in the database under PREFIX/STATE-DIRECTORY. ITEMS
must be in topological order (with leaves first.) If the database is
initially empty, apply SCHEMA to initialize it. REGISTRATION-TIME must be the
registration time to be recorded in the database; #f means \"now\"."
registration time to be recorded in the database; #f means \"now\".
Write a progress report to LOG-PORT."
;; Priority for options: first what is given, then environment variables,
;; then defaults. %state-directory, %store-directory, and
@ -286,20 +290,32 @@ (define to-register
(define real-file-name
(string-append store-dir "/" (basename (store-info-item item))))
(let-values (((hash nar-size) (nar-sha256 real-file-name)))
;; When TO-REGISTER is already registered, skip it. This makes a
;; significant differences when 'register-closures' is called
;; consecutively for overlapping closures such as 'system' and 'bootcfg'.
(unless (path-id db to-register)
(when reset-timestamps?
(reset-timestamps real-file-name))
(sqlite-register db #:path to-register
#:references (store-info-references item)
#:deriver (store-info-deriver item)
#:hash (string-append "sha256:"
(bytevector->base16-string hash))
#:nar-size nar-size
#:time registration-time)
(when deduplicate?
(deduplicate real-file-name hash #:store store-dir))))
(let-values (((hash nar-size) (nar-sha256 real-file-name)))
(sqlite-register db #:path to-register
#:references (store-info-references item)
#:deriver (store-info-deriver item)
#:hash (string-append "sha256:"
(bytevector->base16-string hash))
#:nar-size nar-size
#:time registration-time)
(when deduplicate?
(deduplicate real-file-name hash #:store store-dir)))))
(mkdir-p db-dir)
(parameterize ((sql-schema schema))
(with-database (string-append db-dir "/db.sqlite") db
(for-each (cut register db <>) items))))
(let* ((prefix (format #f "registering ~a items" (length items)))
(progress (progress-reporter/bar (length items)
prefix log-port)))
(call-with-progress-reporter progress
(lambda (report)
(for-each (lambda (item)
(register db item)
(report))
items)))))))

15
tests/guix-package.sh
View file

@ -358,6 +358,21 @@ EOF
guix package --bootstrap -m "$module_dir/manifest.scm"
guix package -I | grep guile
test `guix package -I | wc -l` -eq 1
guix package --rollback --bootstrap
# Applying a manifest file with inferior packages.
cat > "$module_dir/manifest.scm"<<EOF
(use-modules (guix inferior))
(define i
(open-inferior "$abs_top_srcdir" #:command "scripts/guix"))
(let ((guile (car (lookup-inferior-packages i "guile-bootstrap"))))
(packages->manifest (list guile)))
EOF
guix package --bootstrap -m "$module_dir/manifest.scm"
guix package -I | grep guile
test `guix package -I | wc -l` -eq 1
# Error reporting.
cat > "$module_dir/manifest.scm"<<EOF

123
tests/inferior.scm
View file

@ -17,11 +17,18 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (test-inferior)
#:use-module (guix tests)
#:use-module (guix inferior)
#:use-module (guix packages)
#:use-module (guix store)
#:use-module (guix profiles)
#:use-module (guix derivations)
#:use-module (gnu packages)
#:use-module (gnu packages bootstrap)
#:use-module (gnu packages guile)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-64))
#:use-module (srfi srfi-64)
#:use-module (ice-9 match))
(define %top-srcdir
(dirname (search-path %load-path "guix.scm")))
@ -29,6 +36,16 @@ (define %top-srcdir
(define %top-builddir
(dirname (search-path %load-compiled-path "guix.go")))
(define %store
(open-connection-for-tests))
(define (manifest-entry->list entry)
(list (manifest-entry-name entry)
(manifest-entry-version entry)
(manifest-entry-output entry)
(manifest-entry-search-paths entry)
(map manifest-entry->list (manifest-entry-dependencies entry))))
(test-begin "inferior")
@ -72,4 +89,108 @@ (define result
(close-inferior inferior)
result))))
(test-equal "lookup-inferior-packages"
(let ((->list (lambda (package)
(list (package-name package)
(package-version package)
(package-location package)))))
(list (map ->list (find-packages-by-name "guile" #f))
(map ->list (find-packages-by-name "guile" "2.2"))))
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(->list (lambda (package)
(list (inferior-package-name package)
(inferior-package-version package)
(inferior-package-location package))))
(lst1 (map ->list
(lookup-inferior-packages inferior "guile")))
(lst2 (map ->list
(lookup-inferior-packages inferior
"guile" "2.2"))))
(close-inferior inferior)
(list lst1 lst2)))
(test-assert "lookup-inferior-packages and eq?-ness"
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(lst1 (lookup-inferior-packages inferior "guile"))
(lst2 (lookup-inferior-packages inferior "guile")))
(close-inferior inferior)
(every eq? lst1 lst2)))
(test-equal "inferior-package-inputs"
(let ((->list (match-lambda
((label (? package? package) . rest)
`(,label
(package ,(package-name package)
,(package-version package)
,(package-location package))
,@rest)))))
(list (map ->list (package-inputs guile-2.2))
(map ->list (package-native-inputs guile-2.2))
(map ->list (package-propagated-inputs guile-2.2))))
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(guile (first (lookup-inferior-packages inferior "guile")))
(->list (match-lambda
((label (? inferior-package? package) . rest)
`(,label
(package ,(inferior-package-name package)
,(inferior-package-version package)
,(inferior-package-location package))
,@rest))))
(result (list (map ->list (inferior-package-inputs guile))
(map ->list
(inferior-package-native-inputs guile))
(map ->list
(inferior-package-propagated-inputs
guile)))))
(close-inferior inferior)
result))
(test-equal "inferior-package-search-paths"
(package-native-search-paths guile-2.2)
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(guile (first (lookup-inferior-packages inferior "guile")))
(result (inferior-package-native-search-paths guile)))
(close-inferior inferior)
result))
(test-equal "inferior-package-derivation"
(map derivation-file-name
(list (package-derivation %store %bootstrap-guile "x86_64-linux")
(package-derivation %store %bootstrap-guile "armhf-linux")))
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(packages (inferior-packages inferior))
(guile (find (lambda (package)
(string=? (package-name %bootstrap-guile)
(inferior-package-name package)))
packages)))
(map derivation-file-name
(list (inferior-package-derivation %store guile "x86_64-linux")
(inferior-package-derivation %store guile "armhf-linux")))))
(test-equal "inferior-package->manifest-entry"
(manifest-entry->list (package->manifest-entry
(first (find-best-packages-by-name "guile" #f))))
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(guile (first (lookup-inferior-packages inferior "guile")))
(entry (inferior-package->manifest-entry guile)))
(close-inferior inferior)
(manifest-entry->list entry)))
(test-equal "packages->manifest"
(map manifest-entry->list
(manifest-entries (packages->manifest
(find-best-packages-by-name "guile" #f))))
(let* ((inferior (open-inferior %top-builddir
#:command "scripts/guix"))
(guile (first (lookup-inferior-packages inferior "guile")))
(manifest (packages->manifest (list guile))))
(close-inferior inferior)
(map manifest-entry->list (manifest-entries manifest))))
(test-end "inferior")