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import: cran: Add support for git repositories.
* guix/import/cran.scm (vcs-file?): New procedure. (download): Support downloading from git. (fetch-description): Add a clause for the 'git repository type. (files-match-pattern?): New procedure. (tarball-files-match-pattern?): Implement in terms of FILES-MATCH-PATTERN?. (directory-needs-fortran?, directory-needs-zlib?, directory-needs-pkg-config?): New procedures. (needs-fortran?, needs-zlib?, needs-pkg-config?): Rename these procedures... (tarball-needs-fortran?, tarball-needs-zlib?, tarball-needs-pkg-config?): ...to this, and use them. (file-hash): New procedure. (description->package): Handle the 'git repository type. * guix/import/utils.scm (package->definition): Handle package expression inside of a let. * guix/scripts/import.scm (guix-import): Handle let expressions. * doc/guix.texi (Invoking guix import): Document it.
This commit is contained in:
Ricardo Wurmus
parent
ce82e8bf5b
commit
ad553ec4b1
4 changed files with 197 additions and 72 deletions
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@ -8638,6 +8638,14 @@ R package:
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guix import cran --archive=bioconductor GenomicRanges
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@end example
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Finally, you can also import R packages that have not yet been published on
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CRAN or Bioconductor as long as they are in a git repository. Use
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@code{--archive=git} followed by the URL of the git repository:
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@example
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guix import cran --archive=git https://github.com/immunogenomics/harmony
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@end example
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@item texlive
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@cindex TeX Live
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@cindex CTAN
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@ -24,6 +24,7 @@ (define-module (guix import cran)
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#:use-module ((ice-9 rdelim) #:select (read-string read-line))
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#:use-module (srfi srfi-1)
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#:use-module (srfi srfi-2)
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#:use-module (srfi srfi-11)
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#:use-module (srfi srfi-26)
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#:use-module (srfi srfi-34)
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#:use-module (ice-9 receive)
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@ -32,11 +33,13 @@ (define-module (guix import cran)
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#:use-module (guix http-client)
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#:use-module (gcrypt hash)
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#:use-module (guix store)
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#:use-module ((guix serialization) #:select (write-file))
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#:use-module (guix base32)
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#:use-module ((guix download) #:select (download-to-store))
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#:use-module (guix import utils)
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#:use-module ((guix build utils) #:select (find-files))
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#:use-module (guix utils)
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#:use-module (guix git)
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#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
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#:use-module (guix upstream)
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#:use-module (guix packages)
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@ -166,11 +169,25 @@ (define* (latest-bioconductor-package-version name #:optional type)
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(bioconductor-packages-list type))
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(cut assoc-ref <> "Version")))
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;; XXX taken from (guix scripts hash)
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(define (vcs-file? file stat)
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(case (stat:type stat)
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((directory)
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(member (basename file) '(".bzr" ".git" ".hg" ".svn" "CVS")))
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((regular)
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;; Git sub-modules have a '.git' file that is a regular text file.
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(string=? (basename file) ".git"))
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(else
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#f)))
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;; Little helper to download URLs only once.
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(define download
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(memoize
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(lambda (url)
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(with-store store (download-to-store store url)))))
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(lambda* (url #:optional git)
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(with-store store
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(if git
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(latest-repository-commit store url)
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(download-to-store store url))))))
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(define (fetch-description repository name)
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"Return an alist of the contents of the DESCRIPTION file for the R package
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@ -211,7 +228,18 @@ (define (fetch-description repository name)
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(string-append dir "/DESCRIPTION") read-string))
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(lambda (meta)
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(if (boolean? type) meta
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(cons `(bioconductor-type . ,type) meta))))))))))))
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(cons `(bioconductor-type . ,type) meta))))))))))
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((git)
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;; Download the git repository at "NAME"
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(call-with-values
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(lambda () (download name #t))
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(lambda (dir commit)
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(and=> (description->alist (with-input-from-file
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(string-append dir "/DESCRIPTION") read-string))
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(lambda (meta)
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(cons* `(git . ,name)
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`(git-commit . ,commit)
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meta))))))))
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(define (listify meta field)
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"Look up FIELD in the alist META. If FIELD contains a comma-separated
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@ -256,7 +284,7 @@ (define invalid-packages
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(define cran-guix-name (cut guix-name "r-" <>))
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(define (needs-fortran? tarball)
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(define (tarball-needs-fortran? tarball)
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"Check if the TARBALL contains Fortran source files."
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(define (check pattern)
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(parameterize ((current-error-port (%make-void-port "rw+"))
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@ -266,69 +294,127 @@ (define (check pattern)
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(check "*.f95")
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(check "*.f")))
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(define (directory-needs-fortran? dir)
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"Check if the directory DIR contains Fortran source files."
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(match (find-files dir "\\.f(90|95)?")
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(() #f)
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(_ #t)))
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(define (needs-fortran? thing tarball?)
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"Check if the THING contains Fortran source files."
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(if tarball?
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(tarball-needs-fortran? thing)
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(directory-needs-fortran? thing)))
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(define (files-match-pattern? directory regexp . file-patterns)
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"Return #T if any of the files matching FILE-PATTERNS in the DIRECTORY match
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the given REGEXP."
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(let ((pattern (make-regexp regexp)))
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(any (lambda (file)
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(call-with-input-file file
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(lambda (port)
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(let loop ()
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(let ((line (read-line port)))
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(cond
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((eof-object? line) #f)
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((regexp-exec pattern line) #t)
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(else (loop))))))))
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(apply find-files directory file-patterns))))
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(define (tarball-files-match-pattern? tarball regexp . file-patterns)
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"Return #T if any of the files represented by FILE-PATTERNS in the TARBALL
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match the given REGEXP."
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(call-with-temporary-directory
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(lambda (dir)
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(let ((pattern (make-regexp regexp)))
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(parameterize ((current-error-port (%make-void-port "rw+")))
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(apply system* "tar"
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"xf" tarball "-C" dir
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`("--wildcards" ,@file-patterns)))
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(any (lambda (file)
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(call-with-input-file file
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(lambda (port)
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(let loop ()
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(let ((line (read-line port)))
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(cond
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((eof-object? line) #f)
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((regexp-exec pattern line) #t)
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(else (loop))))))))
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(find-files dir))))))
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(parameterize ((current-error-port (%make-void-port "rw+")))
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(apply system* "tar"
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"xf" tarball "-C" dir
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`("--wildcards" ,@file-patterns)))
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(files-match-pattern? dir regexp))))
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(define (needs-zlib? tarball)
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(define (directory-needs-zlib? dir)
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"Return #T if any of the Makevars files in the src directory DIR contain a
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zlib linker flag."
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(files-match-pattern? dir "-lz" "(Makevars.*|configure.*)"))
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(define (tarball-needs-zlib? tarball)
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"Return #T if any of the Makevars files in the src directory of the TARBALL
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contain a zlib linker flag."
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(tarball-files-match-pattern?
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tarball "-lz"
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"*/src/Makevars*" "*/src/configure*" "*/configure*"))
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(define (needs-pkg-config? tarball)
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(define (needs-zlib? thing tarball?)
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"Check if the THING contains files indicating a dependency on zlib."
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(if tarball?
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(tarball-needs-zlib? thing)
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(directory-needs-zlib? thing)))
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(define (directory-needs-pkg-config? dir)
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"Return #T if any of the Makevars files in the src directory DIR reference
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the pkg-config tool."
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(files-match-pattern? dir "pkg-config"
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"(Makevars.*|configure.*)"))
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(define (tarball-needs-pkg-config? tarball)
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"Return #T if any of the Makevars files in the src directory of the TARBALL
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reference the pkg-config tool."
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(tarball-files-match-pattern?
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tarball "pkg-config"
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"*/src/Makevars*" "*/src/configure*" "*/configure*"))
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(define (needs-pkg-config? thing tarball?)
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"Check if the THING contains files indicating a dependency on pkg-config."
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(if tarball?
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(tarball-needs-pkg-config? thing)
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(directory-needs-pkg-config? thing)))
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;; XXX adapted from (guix scripts hash)
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(define (file-hash file select? recursive?)
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;; Compute the hash of FILE.
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(if recursive?
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(let-values (((port get-hash) (open-sha256-port)))
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(write-file file port #:select? select?)
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(force-output port)
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(get-hash))
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(call-with-input-file file port-sha256)))
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(define (description->package repository meta)
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"Return the `package' s-expression for an R package published on REPOSITORY
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from the alist META, which was derived from the R package's DESCRIPTION file."
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(let* ((base-url (case repository
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((cran) %cran-url)
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((bioconductor) %bioconductor-url)))
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((bioconductor) %bioconductor-url)
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((git) #f)))
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(uri-helper (case repository
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((cran) cran-uri)
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((bioconductor) bioconductor-uri)))
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((bioconductor) bioconductor-uri)
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((git) #f)))
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(name (assoc-ref meta "Package"))
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(synopsis (assoc-ref meta "Title"))
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(version (assoc-ref meta "Version"))
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(license (string->license (assoc-ref meta "License")))
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;; Some packages have multiple home pages. Some have none.
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(home-page (match (listify meta "URL")
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((url rest ...) url)
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(_ (string-append base-url name))))
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(source-url (match (apply uri-helper name version
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(case repository
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((bioconductor)
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(list (assoc-ref meta 'bioconductor-type)))
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(else '())))
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((url rest ...) url)
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((? string? url) url)
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(_ #f)))
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(tarball (download source-url))
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(home-page (case repository
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((git) (assoc-ref meta 'git))
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(else (match (listify meta "URL")
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((url rest ...) url)
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(_ (string-append base-url name))))))
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(source-url (case repository
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((git) (assoc-ref meta 'git))
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(else
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(match (apply uri-helper name version
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(case repository
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((bioconductor)
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(list (assoc-ref meta 'bioconductor-type)))
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(else '())))
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((url rest ...) url)
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((? string? url) url)
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(_ #f)))))
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(git? (assoc-ref meta 'git))
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(source (download source-url git?))
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(sysdepends (append
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(if (needs-zlib? tarball) '("zlib") '())
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(if (needs-zlib? source (not git?)) '("zlib") '())
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(filter (lambda (name)
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(not (member name invalid-packages)))
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(map string-downcase (listify meta "SystemRequirements")))))
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@ -339,41 +425,67 @@ (define (description->package repository meta)
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(listify meta "Imports")
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(listify meta "LinkingTo")
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(delete "R"
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(listify meta "Depends"))))))
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(listify meta "Depends")))))
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(package
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`(package
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(name ,(cran-guix-name name))
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(version ,(case repository
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((git)
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`(git-version ,version revision commit))
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(else version)))
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(source (origin
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(method ,(if git?
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'git-fetch
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'url-fetch))
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(uri ,(case repository
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((git)
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`(git-reference
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(url ,(assoc-ref meta 'git))
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(commit commit)))
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(else
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`(,(procedure-name uri-helper) ,name version
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,@(or (and=> (assoc-ref meta 'bioconductor-type)
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(lambda (type)
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(list (list 'quote type))))
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'())))))
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,@(if git?
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'((file-name (git-file-name name version)))
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'())
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(sha256
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(base32
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,(bytevector->nix-base32-string
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(case repository
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((git)
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(file-hash source (negate vcs-file?) #t))
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(else (file-sha256 source))))))))
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,@(if (not (and git?
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(equal? (string-append "r-" name)
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(cran-guix-name name))))
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`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
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'())
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs)
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,@(maybe-inputs
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`(,@(if (needs-fortran? source (not git?))
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'("gfortran") '())
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,@(if (needs-pkg-config? source (not git?))
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'("pkg-config") '()))
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'native-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append base-url name)
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home-page))
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(synopsis ,synopsis)
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(description ,(beautify-description (or (assoc-ref meta "Description")
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"")))
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(license ,license))))
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(values
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`(package
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(name ,(cran-guix-name name))
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(version ,version)
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(source (origin
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(method url-fetch)
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(uri (,(procedure-name uri-helper) ,name version
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,@(or (and=> (assoc-ref meta 'bioconductor-type)
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(lambda (type)
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(list (list 'quote type))))
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'())))
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(sha256
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(base32
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,(bytevector->nix-base32-string (file-sha256 tarball))))))
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,@(if (not (equal? (string-append "r-" name)
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(cran-guix-name name)))
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`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
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'())
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs)
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,@(maybe-inputs
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`(,@(if (needs-fortran? tarball)
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'("gfortran") '())
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,@(if (needs-pkg-config? tarball)
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'("pkg-config") '()))
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'native-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append base-url name)
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home-page))
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(synopsis ,synopsis)
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(description ,(beautify-description (or (assoc-ref meta "Description")
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"")))
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(license ,license))
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(case repository
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((git)
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`(let ((commit ,(assoc-ref meta 'git-commit))
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(revision "1"))
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,package))
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(else package))
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propagate)))
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(define cran->guix-package
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@ -2,7 +2,7 @@
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;;; Copyright © 2012, 2013, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
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;;; Copyright © 2016 David Craven <david@craven.ch>
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;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
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;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
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;;;
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@ -251,6 +251,9 @@ (define* (maybe-native-inputs package-names #:optional (output #f))
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(define (package->definition guix-package)
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(match guix-package
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(('package ('name (? string? name)) _ ...)
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`(define-public ,(string->symbol name)
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,guix-package))
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(('let anything ('package ('name (? string? name)) _ ...))
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`(define-public ,(string->symbol name)
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,guix-package))))
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|
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@ -2,6 +2,7 @@
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;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2014 David Thompson <davet@gnu.org>
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;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com>
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;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -113,7 +114,8 @@ (define (guix-import . args)
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(pretty-print expr (newline-rewriting-port
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(current-output-port))))))
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(match (apply (resolve-importer importer) args)
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((and expr ('package _ ...))
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((and expr (or ('package _ ...)
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('let _ ...)))
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(print expr))
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((? list? expressions)
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(for-each (lambda (expr)
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