From f2e791750be25b95540807c2e01c07625b65666c Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 20:13:42 +1000
Subject: [PATCH 01/22] gnu: r-s4vectors: Update to 0.10.2.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f6ff8811f..26e0f94b2d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4514,13 +4514,13 @@ (define-public r-dnacopy
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.10.0")
+    (version "0.10.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "1mi6lf6pnb9l657igy0vj4yz03yawbr2jhk22l757fzbjc7n9q3b"))))
+                "0cvq9yb97cka7lg5nimvzxbz8b2hxkscmjdqb5z23w5c7hrbjffp"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)

From 2a3e325f5e0a3ccb27ab6c1730d488e5ac0b536d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 20:52:50 +1000
Subject: [PATCH 02/22] gnu: r-genomeinfodb: Update to 1.8.3.

* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 26e0f94b2d..af9c6dbe23 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4594,13 +4594,13 @@ (define-public r-iranges
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.8.1")
+    (version "1.8.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0k4s6z5qj53zkfnyrmcbn3l2nzgm56bhv58rv321j22qa56cpz7d"))))
+                "03s2khhdwz06xr58cjpkil935y6p7f6ljqkbkkcai73qxl1k4ica"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)

From 5131e210644857217fdf9bf0e824d1f51b983f3d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:07:15 +1000
Subject: [PATCH 03/22] gnu: r-rtracklayer: Update to 1.32.2.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index af9c6dbe23..ad82f3191e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4994,13 +4994,13 @@ (define-public r-genomicalignments
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.32.0")
+    (version "1.32.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "0nrwk1g8b1ymvbgnqniimbvwfq13r01va9rx3b03xj4hpywzy5nv"))))
+                "190767zpwc7maqjpy0x5bpkm0jp1vfawy9991fifw0mc634cjkga"))))
     (build-system r-build-system)
     (arguments
      `(#:phases

From 29b0cc8ad57952e9f4dd30cd5966117f848a69b6 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:07:34 +1000
Subject: [PATCH 04/22] gnu: r-genomicalignments: Update to 1.8.4.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad82f3191e..501ccd0b55 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4961,13 +4961,13 @@ (define-public r-summarizedexperiment
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.8.0")
+    (version "1.8.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1y4qgqxq8dax9swgl59m6i7ggjpqrjllgx87b9vwls3z0nf1i6xj"))))
+                "1cccvalmm83ilk1kpq31ll8kdy9xclsr4pm4mlcc7bmp0rwkd2p2"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)

From 1864e051c9cf9bf58fee7800e99a692b25edaf69 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:07:44 +1000
Subject: [PATCH 05/22] gnu: r-summarizedexperiment: Update to 1.2.3.

* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 501ccd0b55..b70bd119b9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4932,13 +4932,13 @@ (define-public r-rsamtools
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.2.2")
+    (version "1.2.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1c81acgw3a0ha5fgapfh9xq8yhryqqf8k259n2dz0mgz1k2d9klg"))))
+                "0c43fsrha886sd0diislnlf8r5h5x7fbhphkzcm0rw3k2jz8wlyk"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)

From d104fc607d885c945a66b13255629c1fbffa14dc Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:08:33 +1000
Subject: [PATCH 06/22] gnu: r-biostrings: Update to 2.40.2.

* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b70bd119b9..02f507ce6d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4862,13 +4862,13 @@ (define-public r-biocparallel
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.40.0")
+    (version "2.40.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "03gyhiz14xy51nzg0glihk1rv19pq4p1aa3y5g23bzcshs67ggj9"))))
+                "153rfws5sdha324p1nv7jp75ip6ny0f62jzhqcvs46l85h3i8zgh"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)

From a22999f245a32b1e58fe8916392bc1b2712d1b3c Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:08:42 +1000
Subject: [PATCH 07/22] gnu: r-biocparallel: Update to 1.6.3.

* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 02f507ce6d..a95a0713fc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4838,13 +4838,13 @@ (define-public r-biomart
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.6.2")
+    (version "1.6.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0ki5xvb3cwjmlsx81gr8ylk1qy3imlj2dd04mzpvl28x42ay4dqj"))))
+                "1gb3lpafhx9wi7wbjdvczdf837qq1arpymcr438jwx39biv9dwb4"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)

From bab15ccec478d119ab197a2576422e6a08f2338f Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:09:06 +1000
Subject: [PATCH 08/22] gnu: r-annotationdbi: Update to 1.34.4.

* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a95a0713fc..287d9ec527 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4781,13 +4781,13 @@ (define-public r-biobase
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.34.2")
+    (version "1.34.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0nw6c23098gkjlwlrra4rh1m65azczb31qr01pq81cn5gya1zkr4"))))
+                "1k3gfsjrivc7467vg0h705hh4dvzgdhknz62j7zmfxm67qk9r8rq"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)

From a463055862e0b1e37bab41f76bb10537af5c42e8 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:09:16 +1000
Subject: [PATCH 09/22] gnu: r-genomicranges: Update to 1.24.2.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 287d9ec527..7d9b11d6b5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4732,13 +4732,13 @@ (define-public r-xvector
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.24.0")
+    (version "1.24.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "1iyzg1npl3rnnslwq3h759vf0xhshnn5v801rnlj6bnxzhn9yaqh"))))
+                "183kdz76rz93v69k6x684bpwa28xixp83bsyf6xfy182h6vh8x89"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)

From 2b2ff0bd917cad949a974dd0e584e2b1f7ad6a5d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:09:25 +1000
Subject: [PATCH 10/22] gnu: r-xvector: Update to 0.12.1.

* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7d9b11d6b5..5ddcac3023 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4696,13 +4696,13 @@ (define-public r-limma
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.12.0")
+    (version "0.12.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "0c9cqjcxxks3an4wiq167h2grxlfyazajn7bmxhbk42zifp8vmqp"))))
+                "1kydy9f5y0ihn2mbkamr1kh0g1d3g1k9d7s4i09qgw9ysr6j414v"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)

From f403941f811b54873511d0cd2c9da2c54cffb82f Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:09:41 +1000
Subject: [PATCH 11/22] gnu: r-limma: Update to 3.28.17.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5ddcac3023..46ac945095 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4677,13 +4677,13 @@ (define-public r-variantannotation
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.28.14")
+    (version "3.28.17")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1jgn66ajafhjlqpfcw2p85h6ah8mgmz66znmsw6pcapia7d34akw"))))
+                "124n8dbvl1yy8b1068kqmqszpfhaawk5xfyb73vixma2i66nrcyk"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")

From b0f0778a7c040b1f3f409681f24491d0610a3a21 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:10:05 +1000
Subject: [PATCH 12/22] gnu: r-iranges: Update to 2.6.1.

* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46ac945095..eb7151936b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4565,13 +4565,13 @@ (define-public r-seqinr
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.6.0")
+    (version "2.6.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "0dz7z0pk8hq79mcgylw920999s08h6j8xrl31rdxhssmi7l8v6vy"))))
+                "06pyam3bjjfw2m3l86rda503lsz2jcg645lcnhvrz6qi0nv359yg"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)

From 2c9f6251fc4e60ad84b3698e53879060ce50ee48 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:17:32 +1000
Subject: [PATCH 13/22] gnu: r-bsgenome: Update to 1.40.1.

* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb7151936b..d3ab72010d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5154,13 +5154,13 @@ (define-public r-topgo
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.40.0")
+    (version "1.40.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "08g3w47ysbmgj4hclb0x2wsn7pi9cnm3xkkfk4shgrka2g23qz44"))))
+                "0zmlzlcwairka59is5wmkh6knh6j4d328z9fsw3v91fx6gavjl2n"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)

From 6547708f718316dac79de845aabb7220122385a7 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 28 Jul 2016 21:54:44 +1000
Subject: [PATCH 14/22] gnu: r-genomicfeatures: Update to 1.24.5.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d3ab72010d..29fb3be0db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5039,13 +5039,13 @@ (define-public r-rtracklayer
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.24.2")
+    (version "1.24.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0ga5a7w8jnnq2k0kc07mshl6cggmbhzh42pzvhnilgl4x3kpbysl"))))
+                "17qpisdgqyjz2mnaiwc4dx7dg11pwq3mkvmkah9zn07g9rhh8f7p"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)

From 189b1543cbc2db50e6dd309e84bce4eb503f0493 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 28 Jul 2016 15:24:37 +0200
Subject: [PATCH 15/22] doc: Mention separate branch for packages with many
 dependents.

Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* doc/contributing.texi (Submitting Patches): Add note on packages with
more than 100 dependents.
---
 doc/contributing.texi | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/contributing.texi b/doc/contributing.texi
index c0755bb895..6496e10a14 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -300,6 +300,13 @@ For important changes, check that dependent package (if applicable) are
 not affected by the change; @code{guix refresh --list-dependent
 @var{package}} will help you do that (@pxref{Invoking guix refresh}).
 
+Packages with roughly 100 dependents or more usually have to be
+committed to a separate branch.  That branch can then be built
+separately by our build farm, and later merged into @code{master} once
+everything has been successfully built.  This allows us to fix issues
+before they hit users, and to reduce the window during which pre-built
+binaries are not available.
+
 @item
 @cindex determinism, of build processes
 @cindex reproducible builds, checking

From 3a78fab83dd5faa80d8eecd792f40dde6e334c7c Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Thu, 21 Jul 2016 18:05:30 +0000
Subject: [PATCH 16/22] doc: Send changes in your patch which are related.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/contributing.texi (Submitting Patches): New @item:
This gives information about sending related changes and examples on
what we view as related changes.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/contributing.texi | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/contributing.texi b/doc/contributing.texi
index 6496e10a14..a3684a5e1d 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -340,6 +340,13 @@ referring to people, such as
 @uref{https://en.wikipedia.org/wiki/Singular_they, singular
 ``they''@comma{} ``their''@comma{} ``them''}, and so forth.
 
+@item
+Verify that your patch contains only one set of related changes.
+Bundling unrelated changes together makes reviewing harder and slower.
+
+Examples of unrelated changes include the addition of several packages,
+or a package update along with fixes to that package.
+
 @end enumerate
 
 When posting a patch to the mailing list, use @samp{[PATCH] @dots{}} as

From d222522edf70cdac6cee7b4ab8fa1bfbf0a7ba9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 28 Jul 2016 15:41:00 +0200
Subject: [PATCH 17/22] doc: Discourage software bundling.

Fixes <http://bugs.gnu.org/24008>.
Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* doc/contributing.texi (Submitting Patches): Add item about bundling.
---
 doc/contributing.texi | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/doc/contributing.texi b/doc/contributing.texi
index a3684a5e1d..18d891db4e 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -288,6 +288,20 @@ name of the new or modified package, and fix any errors it reports
 Make sure the package builds on your platform, using @code{guix build
 @var{package}}.
 
+@item
+@cindex bundling
+Make sure the package does not use bundled copies of software already
+available as separate packages.
+
+Sometimes, packages include copies of the source code of their
+dependencies as a convenience for users.  However, as a distribution, we
+want to make sure that such packages end up using the copy we already
+have in the distribution, if there is one.  This improves resource usage
+(the dependency is built and stored only once), and allows the
+distribution to make transverse changes such as applying security
+updates for a given software package in a single place and have them
+affect the whole system---something that bundled copies prevent.
+
 @item
 Take a look at the profile reported by @command{guix size}
 (@pxref{Invoking guix size}).  This will allow you to notice references

From 71d9b98078e8c785ad57cf3ae2e70939e815a82f Mon Sep 17 00:00:00 2001
From: Alex Griffin <a@ajgrf.com>
Date: Wed, 27 Jul 2016 09:40:35 -0500
Subject: [PATCH 18/22] gnu: gnome: Propagate file-roller.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/gnome.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 318a04d403..b2f46959e6 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5014,6 +5015,7 @@ (define-public gnome
        ("eog"                       ,eog)
        ("epiphany"                  ,epiphany)
        ("evince"                    ,evince)
+       ("file-roller"               ,file-roller)
        ("gedit"                     ,gedit)
        ("glib-networking"           ,glib-networking)
        ("gnome-backgrounds"         ,gnome-backgrounds)

From cb55f9c652105d9ed4fc46cb902f0935fe7e35f8 Mon Sep 17 00:00:00 2001
From: Alex Griffin <a@ajgrf.com>
Date: Wed, 27 Jul 2016 16:22:32 -0500
Subject: [PATCH 19/22] gnu: Add asciinema.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/terminals.scm (asciinema): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/terminals.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index ee36f64354..98f0060c0d 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Mckinley Olsen <mck.olsen@gmail.com>
+;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +22,7 @@ (define-module (gnu packages terminals)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix packages)
@@ -30,6 +32,7 @@ (define-module (gnu packages terminals)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages wm)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages gtk)
@@ -121,3 +124,38 @@ (define-public termite
 
     ;; Files under util/ are under the Expat license; the rest is LGPLv2+.
     (license license:lgpl2.0+)))
+
+(define-public asciinema
+  (package
+    (name "asciinema")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/06/96/93947d9be78aebb7985014fdf"
+             "4d84896dd0f62514d922ee03f5bb55a21fb/asciinema-" version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1crdm9zfdbjflvz1gsqvy5zsbgwdfkj34z69kg6h5by70rrs1hdc"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'patch-exec-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((ncurses (assoc-ref inputs "ncurses")))
+               (substitute* "asciinema/recorder.py"
+                 (("'tput'")
+                  (string-append "'" ncurses "/bin/tput'"))))
+             #t)))))
+    (inputs `(("ncurses" ,ncurses)
+              ("python-setuptools" ,python-setuptools)))
+    (home-page "https://asciinema.org")
+    (synopsis "Terminal session recorder")
+    (description
+     "Use asciinema to record and share your terminal sessions, the right way.
+Forget screen recording apps and blurry video.  Enjoy a lightweight, purely
+text-based approach to terminal recording.")
+    (license license:gpl3)))

From 6980511b7391e65a307689f90e4ef5c1979e4541 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 28 Jul 2016 18:50:43 +0200
Subject: [PATCH 20/22] packages: Add 'hidden-package'.

* guix/packages.scm (hidden-package, hidden-package?): New procedures.
* gnu/packages.scm (fold-packages): Filter out 'hidden-package?'.
* tests/packages.scm ("hidden-package"): New test.
---
 gnu/packages.scm   |  3 ++-
 guix/packages.scm  | 15 +++++++++++++++
 tests/packages.scm |  4 ++++
 3 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/gnu/packages.scm b/gnu/packages.scm
index 9496a270eb..68a9eef2ad 100644
--- a/gnu/packages.scm
+++ b/gnu/packages.scm
@@ -200,7 +200,8 @@ (define (fold-packages proc init)
    (fold2 (lambda (module result seen)
             (fold2 (lambda (var result seen)
                      (if (and (package? var)
-                              (not (vhash-assq var seen)))
+                              (not (vhash-assq var seen))
+                              (not (hidden-package? var)))
                          (values (proc var result)
                                  (vhash-consq var #t seen))
                          (values result seen)))
diff --git a/guix/packages.scm b/guix/packages.scm
index bfb4c557ab..3646b9ba13 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -81,6 +81,8 @@ (define-module (guix packages)
             package-maintainers
             package-properties
             package-location
+            hidden-package
+            hidden-package?
             package-field-location
 
             package-direct-sources
@@ -290,6 +292,19 @@ (define-record-type* <package>
                                                        package)
                                                       16)))))
 
+(define (hidden-package p)
+  "Return a \"hidden\" version of P--i.e., one that 'fold-packages' and thus,
+user interfaces, ignores."
+  (package
+    (inherit p)
+    (properties `((hidden? . #t)
+                  ,@(package-properties p)))))
+
+(define (hidden-package? p)
+  "Return true if P is \"hidden\"--i.e., must not be visible to user
+interfaces."
+  (assoc-ref (package-properties p) 'hidden?))
+
 (define (package-field-location package field)
   "Return the source code location of the definition of FIELD for PACKAGE, or
 #f if it could not be determined."
diff --git a/tests/packages.scm b/tests/packages.scm
index fc75e38730..7c9ad05c21 100644
--- a/tests/packages.scm
+++ b/tests/packages.scm
@@ -79,6 +79,10 @@ (define %store
                     (write
                      (dummy-package "foo" (location #f)))))))
 
+(test-assert "hidden-package"
+  (and (hidden-package? (hidden-package (dummy-package "foo")))
+       (not (hidden-package? (dummy-package "foo")))))
+
 (test-assert "package-field-location"
   (let ()
     (define (goto port line column)

From 386b71d1b961a52201f64591076e51487a87bf0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 28 Jul 2016 18:53:13 +0200
Subject: [PATCH 21/22] gnu: commencement: 'guile-final' is now "hidden".

This way, we no longer have this annoying warning:

  $ guix build guile -n
  guix build: warning: ambiguous package specification `guile'
  guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2

* gnu/packages/commencement.scm (guile-final): Use 'hidden-package'.
* tests/packages.scm ("fold-packages, hidden package"): New test.
---
 gnu/packages/commencement.scm |  4 +++-
 tests/packages.scm            | 14 ++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index c52b6e8389..54b524aec7 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -685,8 +685,10 @@ (define %boot4-inputs
     ,@(alist-delete "bash" %boot3-inputs)))
 
 (define-public guile-final
+  ;; This package must be public because other modules refer to it.  However,
+  ;; mark it as hidden so that 'fold-packages' ignores it.
   (package-with-bootstrap-guile
-   (package-with-explicit-inputs guile-2.0/fixed
+   (package-with-explicit-inputs (hidden-package guile-2.0/fixed)
                                  %boot4-inputs
                                  (current-source-location)
                                  #:guile %bootstrap-guile)))
diff --git a/tests/packages.scm b/tests/packages.scm
index 7c9ad05c21..e9c8690730 100644
--- a/tests/packages.scm
+++ b/tests/packages.scm
@@ -749,6 +749,20 @@ (define read-at
                        r))
                  #f))
 
+(test-assert "fold-packages, hidden package"
+  ;; There are two public variables providing "guile@2.0" ('guile-final' in
+  ;; commencement.scm and 'guile-2.0/fixed' in guile.scm), but only the latter
+  ;; should show up.
+  (match (fold-packages (lambda (p r)
+                          (if (and (string=? (package-name p) "guile")
+                                   (string-prefix? "2.0"
+                                                   (package-version p)))
+                              (cons p r)
+                              r))
+                        '())
+    ((one)
+     (eq? one guile-2.0/fixed))))
+
 (test-assert "find-packages-by-name"
   (match (find-packages-by-name "hello")
     (((? (cut eq? hello <>))) #t)

From ae46cd0e4cfb1f06d099b2cda1f9e702e86c90e9 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 28 Jul 2016 13:47:25 -0400
Subject: [PATCH 22/22] gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].

* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
---
 gnu/local.mk                                  |   6 +-
 gnu/packages/gd.scm                           |  10 +-
 gnu/packages/patches/gd-CVE-2016-5766.patch   |  81 ------
 gnu/packages/patches/gd-CVE-2016-6128.patch   | 253 ------------------
 gnu/packages/patches/gd-CVE-2016-6132.patch   |  55 ----
 gnu/packages/patches/gd-CVE-2016-6214.patch   |  66 -----
 .../patches/gd-fix-test-on-i686.patch         |  34 ---
 .../patches/gd-fix-tests-on-i686.patch        |  61 +++++
 8 files changed, 65 insertions(+), 501 deletions(-)
 delete mode 100644 gnu/packages/patches/gd-CVE-2016-5766.patch
 delete mode 100644 gnu/packages/patches/gd-CVE-2016-6128.patch
 delete mode 100644 gnu/packages/patches/gd-CVE-2016-6132.patch
 delete mode 100644 gnu/packages/patches/gd-CVE-2016-6214.patch
 delete mode 100644 gnu/packages/patches/gd-fix-test-on-i686.patch
 create mode 100644 gnu/packages/patches/gd-fix-tests-on-i686.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index c143dd70a1..b0c4415f5b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -512,11 +512,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gcc-cross-environment-variables.patch	\
   %D%/packages/patches/gcc-libvtv-runpath.patch			\
   %D%/packages/patches/gcc-5.0-libvtv-runpath.patch		\
-  %D%/packages/patches/gd-CVE-2016-5766.patch			\
-  %D%/packages/patches/gd-CVE-2016-6128.patch			\
-  %D%/packages/patches/gd-CVE-2016-6132.patch			\
-  %D%/packages/patches/gd-CVE-2016-6214.patch			\
-  %D%/packages/patches/gd-fix-test-on-i686.patch		\
+  %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gegl-CVE-2012-4433.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghostscript-CVE-2015-3228.patch		\
diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm
index 3313ee68f2..153e1c7f8b 100644
--- a/gnu/packages/gd.scm
+++ b/gnu/packages/gd.scm
@@ -40,21 +40,17 @@ (define-public gd
     ;; Note: With libgd.org now pointing to github.com, genuine old
     ;; tarballs are no longer available.  Notably, versions 2.0.x are
     ;; missing.
-    (version "2.2.2")
+    (version "2.2.3")
 
     (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/libgd/libgd/releases/download/gd-"
                    version "/libgd-" version ".tar.xz"))
-             (patches (search-patches "gd-fix-test-on-i686.patch"
-                                      "gd-CVE-2016-5766.patch"
-                                      "gd-CVE-2016-6128.patch"
-                                      "gd-CVE-2016-6132.patch"
-                                      "gd-CVE-2016-6214.patch"))
              (sha256
               (base32
-               "1311g5mva2xlzqv3rjqjc4jjkn5lzls4skvr395h633zw1n7b7s8"))))
+               "0g3xz8jpz1pl2zzmssglrpa9nxiaa7rmcmvgpbrjz8k9cyynqsvl"))
+             (patches (search-patches "gd-fix-tests-on-i686.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/patches/gd-CVE-2016-5766.patch b/gnu/packages/patches/gd-CVE-2016-5766.patch
deleted file mode 100644
index 400cb0ab48..0000000000
--- a/gnu/packages/patches/gd-CVE-2016-5766.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-Fix CVE-2016-5766 (Integer Overflow in _gd2GetHeader() resulting in heap
-overflow).
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-5766
-
-Adapted from upstream commits:
-https://github.com/libgd/libgd/commit/aba3db8ba159465ecec1089027a24835a6da9cc0
-https://github.com/libgd/libgd/commit/a6a0e7feabb2a9738086a5dc96348f233c87fa79
-
-Since `patch` cannot apply Git binary diffs, we omit the addition of
-'tests/gd2/php_bug_72339.c' and its associated binary data.
-
-From aba3db8ba159465ecec1089027a24835a6da9cc0 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Tue, 28 Jun 2016 16:23:42 +0700
-Subject: [PATCH] fix php bug 72339 (CVE-2016-5766), Integer Overflow in
- _gd2GetHeader() resulting in heap overflow
-
----
- src/gd_gd2.c                    |   5 ++++-
- tests/gd2/CMakeLists.txt        |   1 +
- tests/gd2/Makemodule.am         |   6 ++++--
- tests/gd2/php_bug_72339.c       |  21 +++++++++++++++++++++
- tests/gd2/php_bug_72339_exp.gd2 | Bin 0 -> 67108882 bytes
- 5 files changed, 30 insertions(+), 3 deletions(-)
- create mode 100644 tests/gd2/php_bug_72339.c
- create mode 100644 tests/gd2/php_bug_72339_exp.gd2
-
-diff --git a/src/gd_gd2.c b/src/gd_gd2.c
-index fd1e0c9..bdbbecf 100644
---- a/src/gd_gd2.c
-+++ b/src/gd_gd2.c
-@@ -154,8 +154,11 @@ _gd2GetHeader (gdIOCtxPtr in, int *sx, int *sy,
- 		nc = (*ncx) * (*ncy);
- 		GD2_DBG (printf ("Reading %d chunk index entries\n", nc));
- 		sidx = sizeof (t_chunk_info) * nc;
-+		if (overflow2(sidx, nc)) {
-+			goto fail1;
-+		}
- 		cidx = gdCalloc (sidx, 1);
--		if (!cidx) {
-+		if (cidx == NULL) {
- 			goto fail1;
- 		}
- 		for (i = 0; i < nc; i++) {
-From a6a0e7feabb2a9738086a5dc96348f233c87fa79 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Wed, 29 Jun 2016 09:36:26 +0700
-Subject: [PATCH] fix php bug 72339 (CVE-2016-5766), Integer Overflow in
- _gd2GetHeader() resulting in heap overflow. Sync with php's sync
-
----
- src/gd_gd2.c              | 7 ++++++-
- tests/gd2/php_bug_72339.c | 2 +-
- 2 files changed, 7 insertions(+), 2 deletions(-)
-
-diff --git a/src/gd_gd2.c b/src/gd_gd2.c
-index bdbbecf..2837456 100644
---- a/src/gd_gd2.c
-+++ b/src/gd_gd2.c
-@@ -152,11 +152,16 @@ _gd2GetHeader (gdIOCtxPtr in, int *sx, int *sy,
- 
- 	if (gd2_compressed (*fmt)) {
- 		nc = (*ncx) * (*ncy);
-+
- 		GD2_DBG (printf ("Reading %d chunk index entries\n", nc));
-+		if (overflow2(sizeof(t_chunk_info), nc)) {
-+			goto fail1;
-+		}
- 		sidx = sizeof (t_chunk_info) * nc;
--		if (overflow2(sidx, nc)) {
-+		if (sidx <= 0) {
- 			goto fail1;
- 		}
-+
- 		cidx = gdCalloc (sidx, 1);
- 		if (cidx == NULL) {
- 			goto fail1;
--- 
-2.9.1
-
diff --git a/gnu/packages/patches/gd-CVE-2016-6128.patch b/gnu/packages/patches/gd-CVE-2016-6128.patch
deleted file mode 100644
index 45ee6b0cfa..0000000000
--- a/gnu/packages/patches/gd-CVE-2016-6128.patch
+++ /dev/null
@@ -1,253 +0,0 @@
-Fix CVE-2016-6128 (invalid color index is not properly handled leading
-to denial of service).
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=2016-6128
-
-Copied from upstream commits:
-https://github.com/libgd/libgd/compare/3fe0a7128bac5000fdcfab888bd2a75ec0c9447d...fd623025505e87bba7ec8555eeb72dae4fb0afd
-
-From 1ccfe21e14c4d18336f9da8515cd17db88c3de61 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:17:39 +0700
-Subject: [PATCH 1/8] fix php 72494, invalid color index not handled, can lead
- to crash
-
----
- src/gd_crop.c        | 4 ++++
- tests/CMakeLists.txt | 1 +
- tests/Makefile.am    | 1 +
- 3 files changed, 6 insertions(+)
-
-diff --git a/src/gd_crop.c b/src/gd_crop.c
-index 0296633..532b49b 100644
---- a/src/gd_crop.c
-+++ b/src/gd_crop.c
-@@ -136,6 +136,10 @@ BGD_DECLARE(gdImagePtr) gdImageCropThreshold(gdImagePtr im, const unsigned int c
- 		return NULL;
- 	}
- 
-+	if (color < 0 || (!gdImageTrueColor(im) && color >= gdImageColorsTotal(im))) {
-+		return NULL;
-+	}
-+
- 	/* TODO: Add gdImageGetRowPtr and works with ptr at the row level
- 	 * for the true color and palette images
- 	 * new formats will simply work with ptr
-diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
-index 6f5c786..5093d52 100644
---- a/tests/CMakeLists.txt
-+++ b/tests/CMakeLists.txt
-@@ -31,6 +31,7 @@ if (BUILD_TEST)
- 		gdimagecolortransparent
- 		gdimagecopy
- 		gdimagecopyrotated
-+        gdimagecrop
- 		gdimagefile
- 		gdimagefill
- 		gdimagefilledellipse
-diff --git a/tests/Makefile.am b/tests/Makefile.am
-index 4f6e756..5a0ebe8 100644
---- a/tests/Makefile.am
-+++ b/tests/Makefile.am
-@@ -25,6 +25,7 @@ include gdimagecolorresolve/Makemodule.am
- include gdimagecolortransparent/Makemodule.am
- include gdimagecopy/Makemodule.am
- include gdimagecopyrotated/Makemodule.am
-+include gdimagecrop/Makemodule.am
- include gdimagefile/Makemodule.am
- include gdimagefill/Makemodule.am
- include gdimagefilledellipse/Makemodule.am
--- 
-2.9.1
-
-From 8c9f39c7cb1f62ea00bc7a48aff64d3811c2d6d0 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:20:07 +0700
-Subject: [PATCH 2/8] fix php 72494, invalid color index not handled, can lead
- to crash
-
----
- tests/gdimagecrop/.gitignore | 1 +
- 1 file changed, 1 insertion(+)
- create mode 100644 tests/gdimagecrop/.gitignore
-
-diff --git a/tests/gdimagecrop/.gitignore b/tests/gdimagecrop/.gitignore
-new file mode 100644
-index 0000000..8e8c9c3
---- /dev/null
-+++ b/tests/gdimagecrop/.gitignore
-@@ -0,0 +1 @@
-+/php_bug_72494
--- 
-2.9.1
-
-From 8de370b7b6263a02268037a7cd13ddd991b43ea9 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:24:50 +0700
-Subject: [PATCH 3/8] fix php 72494, invalid color index not handled, can lead
- to crash
-
----
- tests/gdimagecrop/CMakeLists.txt | 5 +++++
- 1 file changed, 5 insertions(+)
- create mode 100644 tests/gdimagecrop/CMakeLists.txt
-
-diff --git a/tests/gdimagecrop/CMakeLists.txt b/tests/gdimagecrop/CMakeLists.txt
-new file mode 100644
-index 0000000..f7e4c7e
---- /dev/null
-+++ b/tests/gdimagecrop/CMakeLists.txt
-@@ -0,0 +1,5 @@
-+SET(TESTS_FILES
-+	php_bug_72494
-+)
-+
-+ADD_GD_TESTS()
--- 
-2.9.1
-
-From bca12e4e11ecda8a0ea719472700ad5c2b36a0d6 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:25:12 +0700
-Subject: [PATCH 4/8] fix php 72494, invalid color index not handled, can lead
- to crash
-
----
- tests/gdimagecrop/Makemodule.am | 5 +++++
- 1 file changed, 5 insertions(+)
- create mode 100644 tests/gdimagecrop/Makemodule.am
-
-diff --git a/tests/gdimagecrop/Makemodule.am b/tests/gdimagecrop/Makemodule.am
-new file mode 100644
-index 0000000..210888b
---- /dev/null
-+++ b/tests/gdimagecrop/Makemodule.am
-@@ -0,0 +1,5 @@
-+libgd_test_programs += \
-+	gdimagecrop/php_bug_72494
-+
-+EXTRA_DIST += \
-+	gdimagecrop/CMakeLists.txt
--- 
-2.9.1
-
-From 6ff72ae40c7c20ece939afb362d98cc37f4a1c96 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:25:40 +0700
-Subject: [PATCH 5/8] fix php 72494, invalid color index not handled, can lead
- to crash
-
----
- tests/gdimagecrop/php_bug_72494.c | 23 +++++++++++++++++++++++
- 1 file changed, 23 insertions(+)
- create mode 100644 tests/gdimagecrop/php_bug_72494.c
-
-diff --git a/tests/gdimagecrop/php_bug_72494.c b/tests/gdimagecrop/php_bug_72494.c
-new file mode 100644
-index 0000000..adaa379
---- /dev/null
-+++ b/tests/gdimagecrop/php_bug_72494.c
-@@ -0,0 +1,23 @@
-+#include <stdio.h>
-+#include <stdlib.h>
-+#include "gd.h"
-+
-+#include "gdtest.h"
-+
-+int main()
-+{
-+	gdImagePtr im, exp;
-+	int error = 0;
-+
-+	im = gdImageCreate(50, 50);
-+
-+	if (!im) {
-+		gdTestErrorMsg("gdImageCreate failed.\n");
-+		return 1;
-+	}
-+
-+	gdImageCropThreshold(im, 1337, 0);
-+	gdImageDestroy(im);
-+	/* this bug tests a crash, it never reaches this point if the bug exists*/
-+	return 0;
-+}
--- 
-2.9.1
-
-From a0f9f8f7bd0d3a6c6afd6d180b8e75d93aadddfa Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:38:07 +0700
-Subject: [PATCH 6/8] fix php 72494, CID 149753, color is unsigned int, remove
- useless <0 comparison
-
----
- src/gd_crop.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/gd_crop.c b/src/gd_crop.c
-index 532b49b..d51ad67 100644
---- a/src/gd_crop.c
-+++ b/src/gd_crop.c
-@@ -136,7 +136,7 @@ BGD_DECLARE(gdImagePtr) gdImageCropThreshold(gdImagePtr im, const unsigned int c
- 		return NULL;
- 	}
- 
--	if (color < 0 || (!gdImageTrueColor(im) && color >= gdImageColorsTotal(im))) {
-+	if (!gdImageTrueColor(im) && color >= gdImageColorsTotal(im)) {
- 		return NULL;
- 	}
- 
--- 
-2.9.1
-
-From 907115fbb980862934d0de91af4977a216745039 Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 11:51:40 +0700
-Subject: [PATCH 7/8] fix php 72494, CID 149753, color is unsigned int, remove
- useless <0 comparison
-
----
- tests/gdimagecrop/php_bug_72494.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/gdimagecrop/php_bug_72494.c b/tests/gdimagecrop/php_bug_72494.c
-index adaa379..5cb589b 100644
---- a/tests/gdimagecrop/php_bug_72494.c
-+++ b/tests/gdimagecrop/php_bug_72494.c
-@@ -6,7 +6,7 @@
- 
- int main()
- {
--	gdImagePtr im, exp;
-+	gdImagePtr im;
- 	int error = 0;
- 
- 	im = gdImageCreate(50, 50);
--- 
-2.9.1
-
-From fd623025505e87bba7ec8555eeb72dae4fb0afdc Mon Sep 17 00:00:00 2001
-From: Pierre Joye <pierre.php@gmail.com>
-Date: Mon, 27 Jun 2016 12:04:25 +0700
-Subject: [PATCH 8/8] fix php 72494, CID 149753, color is unsigned int, remove
- useless <0 comparison
-
----
- tests/gdimagecrop/php_bug_72494.c | 1 -
- 1 file changed, 1 deletion(-)
-
-diff --git a/tests/gdimagecrop/php_bug_72494.c b/tests/gdimagecrop/php_bug_72494.c
-index 5cb589b..3bd19be 100644
---- a/tests/gdimagecrop/php_bug_72494.c
-+++ b/tests/gdimagecrop/php_bug_72494.c
-@@ -7,7 +7,6 @@
- int main()
- {
- 	gdImagePtr im;
--	int error = 0;
- 
- 	im = gdImageCreate(50, 50);
- 
--- 
-2.9.1
-
diff --git a/gnu/packages/patches/gd-CVE-2016-6132.patch b/gnu/packages/patches/gd-CVE-2016-6132.patch
deleted file mode 100644
index 4c475b71b2..0000000000
--- a/gnu/packages/patches/gd-CVE-2016-6132.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-Fix CVE-2016-6132 (read out-of-bounds when parsing TGA files).
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=2016-6132
-
-Copied from upstream commit:
-https://github.com/libgd/libgd/commit/ead349e99868303b37f5e6e9d9d680c9dc71ff8d
-
-From ead349e99868303b37f5e6e9d9d680c9dc71ff8d Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Ond=C5=99ej=20Sur=C3=BD?= <ondrej@sury.org>
-Date: Tue, 12 Jul 2016 11:24:09 +0200
-Subject: [PATCH] Fix #247, A read out-of-bands was found in the parsing of TGA
- files (CVE-2016-6132)
-
----
- src/gd_tga.c | 13 +++++++++++--
- 1 file changed, 11 insertions(+), 2 deletions(-)
-
-diff --git a/src/gd_tga.c b/src/gd_tga.c
-index ef20f86..20fe2d2 100644
---- a/src/gd_tga.c
-+++ b/src/gd_tga.c
-@@ -237,7 +237,11 @@ int read_image_tga( gdIOCtx *ctx, oTga *tga )
- 			return -1;
- 		}
- 
--		gdGetBuf(conversion_buffer, image_block_size, ctx);
-+		if (gdGetBuf(conversion_buffer, image_block_size, ctx) != image_block_size) {
-+			gd_error("gd-tga: premature end of image data\n");
-+			gdFree(conversion_buffer);
-+			return -1;
-+		}
- 
- 		while (buffer_caret < image_block_size) {
- 			tga->bitmap[buffer_caret] = (int) conversion_buffer[buffer_caret];
-@@ -257,11 +261,16 @@ int read_image_tga( gdIOCtx *ctx, oTga *tga )
- 		}
- 		conversion_buffer = (unsigned char *) gdMalloc(image_block_size * sizeof(unsigned char));
- 		if (conversion_buffer == NULL) {
-+			gd_error("gd-tga: premature end of image data\n");
- 			gdFree( decompression_buffer );
- 			return -1;
- 		}
- 
--		gdGetBuf( conversion_buffer, image_block_size, ctx );
-+		if (gdGetBuf(conversion_buffer, image_block_size, ctx) != image_block_size) {
-+			gdFree(conversion_buffer);
-+			gdFree(decompression_buffer);
-+			return -1;
-+		}
- 
- 		buffer_caret = 0;
- 
--- 
-2.9.1
-
diff --git a/gnu/packages/patches/gd-CVE-2016-6214.patch b/gnu/packages/patches/gd-CVE-2016-6214.patch
deleted file mode 100644
index 7894a32bb1..0000000000
--- a/gnu/packages/patches/gd-CVE-2016-6214.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-Fix CVE-2016-6214 (read out-of-bounds when parsing TGA files).
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-6214
-
-Adapted from upstream commit:
-https://github.com/libgd/libgd/commit/341aa68843ceceae9ba6e083431f14a07bd92308
-
-Since `patch` cannot apply Git binary diffs, we omit the addition of
-'tests/tga/bug00247a.c' and its associated binary data.
-
-From 341aa68843ceceae9ba6e083431f14a07bd92308 Mon Sep 17 00:00:00 2001
-From: "Christoph M. Becker" <cmbecker69@gmx.de>
-Date: Tue, 12 Jul 2016 19:23:13 +0200
-Subject: [PATCH] Unsupported TGA bpp/alphabit combinations should error
- gracefully
-
-Currently, only 24bpp without alphabits and 32bpp with 8 alphabits are
-really supported. All other combinations will be rejected with a warning.
-
-(cherry picked from commit cb1a0b7e54e9aa118270c23a4a6fe560e4590dc9)
----
- src/gd_tga.c             |  16 ++++++----------
- tests/tga/.gitignore     |   1 +
- tests/tga/CMakeLists.txt |   1 +
- tests/tga/Makemodule.am  |   4 +++-
- tests/tga/bug00247a.c    |  19 +++++++++++++++++++
- tests/tga/bug00247a.tga  | Bin 0 -> 36 bytes
- 6 files changed, 30 insertions(+), 11 deletions(-)
- create mode 100644 tests/tga/bug00247a.c
- create mode 100644 tests/tga/bug00247a.tga
-
-diff --git a/src/gd_tga.c b/src/gd_tga.c
-index 20fe2d2..b4f8fa6 100644
---- a/src/gd_tga.c
-+++ b/src/gd_tga.c
-@@ -99,7 +99,7 @@ BGD_DECLARE(gdImagePtr) gdImageCreateFromTgaCtx(gdIOCtx* ctx)
- 			if (tga->bits == TGA_BPP_24) {
- 				*tpix = gdTrueColor(tga->bitmap[bitmap_caret + 2], tga->bitmap[bitmap_caret + 1], tga->bitmap[bitmap_caret]);
- 				bitmap_caret += 3;
--			} else if (tga->bits == TGA_BPP_32 || tga->alphabits) {
-+			} else if (tga->bits == TGA_BPP_32 && tga->alphabits) {
- 				register int a = tga->bitmap[bitmap_caret + 3];
- 
- 				*tpix = gdTrueColorAlpha(tga->bitmap[bitmap_caret + 2], tga->bitmap[bitmap_caret + 1], tga->bitmap[bitmap_caret], gdAlphaMax - (a >> 1));
-@@ -159,16 +159,12 @@ int read_header_tga(gdIOCtx *ctx, oTga *tga)
- 	printf("wxh: %i %i\n", tga->width, tga->height);
- #endif
- 
--	switch(tga->bits) {
--	case 8:
--	case 16:
--	case 24:
--	case 32:
--		break;
--	default:
--		gd_error("bps %i not supported", tga->bits);
-+	if (!((tga->bits == TGA_BPP_24 && tga->alphabits == 0)
-+		|| (tga->bits == TGA_BPP_32 && tga->alphabits == 8)))
-+	{
-+		gd_error_ex(GD_WARNING, "gd-tga: %u bits per pixel with %u alpha bits not supported\n",
-+			tga->bits, tga->alphabits);
- 		return -1;
--		break;
- 	}
- 
- 	tga->ident = NULL;
diff --git a/gnu/packages/patches/gd-fix-test-on-i686.patch b/gnu/packages/patches/gd-fix-test-on-i686.patch
deleted file mode 100644
index 6dd2e0fb03..0000000000
--- a/gnu/packages/patches/gd-fix-test-on-i686.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Disable part of the gdimagerotate test on architectures such as i686
-where intermediate floating-point operations are done with 80-bit long
-doubles, and typically later rounded to 64-bit doubles.  This double
-rounding causes small differences in the resulting pixel values
-compared with other architectures, causing the image comparison to
-fail.
-
-Patch by Mark H Weaver <mhw@netris.org>.
-
---- libgd-2.2.2/tests/gdimagerotate/bug00067.c	1969-12-31 19:00:00.000000000 -0500
-+++ libgd-2.2.2/tests/gdimagerotate/bug00067.c	2016-07-18 12:19:19.885423132 -0400
-@@ -1,5 +1,6 @@
- #include <stdio.h>
- #include <stdlib.h>
-+#include <float.h>
- #include "gd.h"
- 
- #include "gdtest.h"
-@@ -41,6 +42,7 @@
- 			return 1;
- 		}
- 
-+#if FLT_EVAL_METHOD != 2
- 		sprintf(filename, "bug00067_%03d_exp.png", angle);
- 		path = gdTestFilePath2("gdimagerotate", filename);
- 		if (!gdAssertImageEqualsToFile(path, exp)) {
-@@ -48,6 +50,7 @@
- 			error += 1;
- 		}
- 		free(path);
-+#endif
- 
- 		gdImageDestroy(exp);
- 	}
diff --git a/gnu/packages/patches/gd-fix-tests-on-i686.patch b/gnu/packages/patches/gd-fix-tests-on-i686.patch
new file mode 100644
index 0000000000..8db64e6aaf
--- /dev/null
+++ b/gnu/packages/patches/gd-fix-tests-on-i686.patch
@@ -0,0 +1,61 @@
+Disable some image comparison tests on architectures such as i686
+where intermediate floating-point operations are done with 80-bit long
+doubles, and typically later rounded to 64-bit doubles.  This double
+rounding causes small differences in the resulting pixel values
+compared with other architectures, causing the image comparisons to
+fail.
+
+Patch by Mark H Weaver <mhw@netris.org>.
+
+--- libgd-2.2.3/tests/gdimagerotate/bug00067.c	2016-06-18 05:42:16.000000000 -0400
++++ libgd-2.2.3/tests/gdimagerotate/bug00067.c	2016-07-28 13:43:48.470767178 -0400
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <float.h>
+ #include "gd.h"
+ 
+ #include "gdtest.h"
+@@ -43,7 +44,7 @@
+ 
+ 		sprintf(filename, "bug00067_%03d_exp.png", angle);
+ 		path = gdTestFilePath2("gdimagerotate", filename);
+-		if (!gdAssertImageEqualsToFile(path, exp)) {
++		if (FLT_EVAL_METHOD != 2 && !gdAssertImageEqualsToFile(path, exp)) {
+ 			gdTestErrorMsg("comparing rotated image to %s failed.\n", path);
+ 			error += 1;
+ 		}
+--- libgd-2.2.3/tests/gdimagecopyresampled/bug00201.c	2016-07-21 04:06:42.000000000 -0400
++++ libgd-2.2.3/tests/gdimagecopyresampled/bug00201.c	2016-07-28 13:56:46.021447064 -0400
+@@ -1,3 +1,4 @@
++#include <float.h>
+ #include "gd.h"
+ #include "gdtest.h"
+ 
+@@ -65,7 +66,7 @@
+     gdImageDestroy(background);
+     gdImageDestroy(scaled_logo);
+     
+-    gdAssertImageEqualsToFile("gdimagecopyresampled/bug00201_exp.png", img);
++    FLT_EVAL_METHOD != 2 && gdAssertImageEqualsToFile("gdimagecopyresampled/bug00201_exp.png", img);
+     gdImageDestroy(img);
+     return gdNumFailures();
+ }
+--- libgd-2.2.3/tests/gdimagecopyresampled/basic_alpha.c	2016-07-21 04:06:42.000000000 -0400
++++ libgd-2.2.3/tests/gdimagecopyresampled/basic_alpha.c	2016-07-28 13:57:18.857831608 -0400
+@@ -1,5 +1,6 @@
+ /* Testing basic gdImageCopyResampled() functionality with alpha channel */
+ 
++#include <float.h>
+ #include "gd.h"
+ #include "gdtest.h"
+ 
+@@ -33,7 +34,7 @@
+ 	gdImageCopyResampled(copy, im, 0,0, 0,0, 200,200, 400,300);
+ 	gdImageDestroy(im);
+ 
+-	gdAssertImageEqualsToFile("gdimagecopyresampled/basic_alpha_exp.png", copy);
++	FLT_EVAL_METHOD != 2 && gdAssertImageEqualsToFile("gdimagecopyresampled/basic_alpha_exp.png", copy);
+ 
+ 	gdImageDestroy(copy);
+ 	return gdNumFailures();