branch master updated: gnu: ytnef: Fix CVE-2021-3403 and CVE-2021-3404.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

lle_bout pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 090456d  gnu: ytnef: Fix CVE-2021-3403 and CVE-2021-3404.
090456d is described below

commit 090456dacb76160280a630d53f4f47b421281c66
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 04:47:10 2021 +0100

gnu: ytnef: Fix CVE-2021-3403 and CVE-2021-3404.

* gnu/packages/patches/ytnef-CVE-2021-3403.patch,
gnu/packages/patches/ytnef-CVE-2021-3404.patch: New patches.
* gnu/local.mk (dist_patch_DATA): Register them.
* gnu/packages/mail.scm (ytnef): Apply them.
---
 gnu/local.mk   |  2 ++
 gnu/packages/mail.scm  |  4 +++-
 gnu/packages/patches/ytnef-CVE-2021-3403.patch | 32 ++
 gnu/packages/patches/ytnef-CVE-2021-3404.patch | 30 
 4 files changed, 67 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 4900dab..fb3b395 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1755,6 +1755,8 @@ dist_patch_DATA = 
\
   %D%/packages/patches/xsane-support-ipv6.patch\
   %D%/packages/patches/xsane-tighten-default-umask.patch   \
   %D%/packages/patches/yggdrasil-extra-config.patch\
+  %D%/packages/patches/ytnef-CVE-2021-3403.patch   \
+  %D%/packages/patches/ytnef-CVE-2021-3404.patch   \
   %D%/packages/patches/zziplib-CVE-2018-16548.patch
 
 MISC_DISTRO_FILES =\
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 0e0934a..d90bfea 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3909,7 +3909,9 @@ It is a replacement for the @command{urlview} program.")
   (file-name (git-file-name name version))
   (sha256
(base32
-"07h48s5qf08503pp9kafqbwipdqghiif22ghki7z8j67gyp04l6l"
+"07h48s5qf08503pp9kafqbwipdqghiif22ghki7z8j67gyp04l6l"))
+  (patches (search-patches "ytnef-CVE-2021-3403.patch"
+   "ytnef-CVE-2021-3404.patch"
 (build-system gnu-build-system)
 (native-inputs
  `(("autoconf" ,autoconf)
diff --git a/gnu/packages/patches/ytnef-CVE-2021-3403.patch 
b/gnu/packages/patches/ytnef-CVE-2021-3403.patch
new file mode 100644
index 000..4b1c9d6
--- /dev/null
+++ b/gnu/packages/patches/ytnef-CVE-2021-3403.patch
@@ -0,0 +1,32 @@
+From f2380a53fb84d370eaf6e6c3473062c54c57fac7 Mon Sep 17 00:00:00 2001
+From: Oliver Giles 
+Date: Mon, 1 Feb 2021 10:12:16 +1300
+Subject: [PATCH] Prevent potential double-free in TNEFSubjectHandler
+
+If TNEFSubjectHandler is called multiple times, but the last time
+failed due to the PREALLOCCHECK, the subject.data member will be
+a freed, but invalid pointer. To prevent a double-free next time
+TNEFSubjectHandler is entered, set it to zero after freeing.
+
+Resolves: #85
+Reported-by: jasperla
+---
+ lib/ytnef.c | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/lib/ytnef.c b/lib/ytnef.c
+index b148719..b06c807 100644
+--- a/lib/ytnef.c
 b/lib/ytnef.c
+@@ -301,8 +301,10 @@ int TNEFFromHandler STD_ARGLIST {
+ }
+ // 
-
+ int TNEFSubjectHandler STD_ARGLIST {
+-  if (TNEF->subject.data)
++  if (TNEF->subject.data) {
+ free(TNEF->subject.data);
++TNEF->subject.data = NULL;
++  }
+ 
+   PREALLOCCHECK(size, 100);
+   TNEF->subject.data = calloc(size+1, sizeof(BYTE));
diff --git a/gnu/packages/patches/ytnef-CVE-2021-3404.patch 
b/gnu/packages/patches/ytnef-CVE-2021-3404.patch
new file mode 100644
index 000..e991d6a
--- /dev/null
+++ b/gnu/packages/patches/ytnef-CVE-2021-3404.patch
@@ -0,0 +1,30 @@
+From f9ff4a203b8c155d51a208cadadb62f224fba715 Mon Sep 17 00:00:00 2001
+From: Oliver Giles 
+Date: Mon, 1 Feb 2021 10:18:17 +1300
+Subject: [PATCH] Ensure the size of the version field is 4 bytes
+
+A corrupted version field size can cause TNEFVersion to access outside
+of allocated memory. Check the version is the expected size and raise
+an error if not.
+
+Resolves: #86
+Reported-by: jasperla
+---
+ lib/ytnef.c | 4 
+ 1 file changed, 4 insertions(+)
+
+diff --git a/lib/ytnef.c b/lib/ytnef.c
+index b148719..ffede44 100644
+--- a/lib/ytnef.c
 b/lib/ytnef.c
+@@ -335,6 +335,10 @@ int TNEFRendData STD_ARGLIST {
+ int TNEFVersion STD_ARGLIST {
+   WORD major;
+   WORD minor;
++  if (size != 2 * sizeof(WORD)) {
++printf("Incorrect size of version field, suspected corruption\n");
++return -1;
++  }
+   minor = SwapWord((BYTE*)data, size);
+   major = SwapWord((BYTE*)data + 2, size - 2);
+ 

branch master updated: gnu: zstd: Update to 1.4.9 [security fixes].

[guix-commits]

This is an automated email from the git hooks/post-receive script.

lle_bout pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 6f87373  gnu: zstd: Update to 1.4.9 [security fixes].
6f87373 is described below

commit 6f873731a030dd7ecbd8a5e756b38b26306f6966
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 02:42:34 2021 +0100

gnu: zstd: Update to 1.4.9 [security fixes].

Fixes CVE-2021-24031 and CVE-2021-24032.

* gnu/packages/compression.scm (zstd-1.4.9): New variable.
* gnu/packages/compression.scm (zstd): Update to 1.4.9.
[replacement]: Graft with 'zstd-1.4.9'.
---
 gnu/packages/compression.scm | 14 ++
 1 file changed, 14 insertions(+)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 3561dc6..ee7f607 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1442,6 +1442,7 @@ or junctions, and always follows hard links.")
"v" version "/zstd-" version ".tar.gz"))
(sha256
 (base32 "05ckxap00qvc0j51d3ci38150cxsw82w7s9zgd5fgzspnzmp1vsr"
+(replacement zstd-1.4.9)
 (build-system gnu-build-system)
 (outputs '("out";1.2MiB executables and documentation
"lib";1.2MiB shared library and headers
@@ -1501,6 +1502,19 @@ speed.")
license:public-domain ; zlibWrapper/examples/fitblk*
license:zlib  ; zlibWrapper/{gz*.c,gzguts.h}
 
+(define-public zstd-1.4.9
+  (package
+(inherit zstd)
+(name "zstd")
+(version "1.4.9")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append 
"https://github.com/facebook/zstd/releases/download/";
+   "v" version "/zstd-" version ".tar.gz"))
+   (sha256
+(base32 "14yj7309gsvg39rki4xqnd6w5idmqi0655v1fc0mk1m2kvhp9b19"))
+
 (define-public pzstd
   (package
 (name "pzstd")

branch core-updates updated: gnu: zstd: Update to 1.4.9.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

lle_bout pushed a commit to branch core-updates
in repository guix.

The following commit(s) were added to refs/heads/core-updates by this push:
 new cab3b57  gnu: zstd: Update to 1.4.9.
cab3b57 is described below

commit cab3b57543bf42247870e56ffb1acd685d854d97
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 02:30:40 2021 +0100

gnu: zstd: Update to 1.4.9.

* gnu/packages/compression.scm (zstd): Update to 1.4.9.
---
 gnu/packages/compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f96ed1f..f5f5887 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1434,14 +1434,14 @@ or junctions, and always follows hard links.")
 (define-public zstd
   (package
 (name "zstd")
-(version "1.4.8")
+(version "1.4.9")
 (source
  (origin
(method url-fetch)
(uri (string-append 
"https://github.com/facebook/zstd/releases/download/";
"v" version "/zstd-" version ".tar.gz"))
(sha256
-(base32 "094zqsj92iwz8glpgxjw96c43ib7adpjg5nm1082200mrabq4irj"
+(base32 "14yj7309gsvg39rki4xqnd6w5idmqi0655v1fc0mk1m2kvhp9b19"
 (build-system gnu-build-system)
 (outputs '("out";1.2MiB executables and documentation
"lib";1.2MiB shared library and headers

01/01: Merge branch 'master' into core-updates

[guix-commits]

cbaines pushed a commit to branch core-updates
in repository guix.

commit a8448da0f4a090818104e64dd79f90b0e50d5e77
Merge: 4f4b749 a714af3
Author: Christopher Baines 
AuthorDate: Fri Mar 5 22:56:40 2021 +

Merge branch 'master' into core-updates

 .guix-authorizations   | 2 +
 Makefile.am| 6 +
 doc/contributing.texi  |10 +-
 doc/guix.texi  |  1281 ++-
 etc/completion/fish/guix.fish  | 7 +-
 etc/completion/zsh/_guix   | 2 +-
 etc/news.scm   |80 +-
 gnu/build/file-systems.scm |45 +-
 gnu/image.scm  | 1 +
 gnu/local.mk   |26 +-
 gnu/machine/ssh.scm| 6 +-
 gnu/packages/admin.scm |   180 +-
 gnu/packages/algebra.scm   |28 +-
 gnu/packages/animation.scm | 6 +-
 gnu/packages/assembly.scm  |33 +-
 gnu/packages/astronomy.scm |   314 +-
 gnu/packages/audio.scm |   117 +-
 gnu/packages/authentication.scm| 4 +-
 gnu/packages/autotools.scm | 4 +-
 .../aux-files/chromium/master-preferences.json | 8 +-
 gnu/packages/aux-files/linux-libre/5.11-arm.conf   |  9944 +
 gnu/packages/aux-files/linux-libre/5.11-arm64.conf | 10140 +
 gnu/packages/aux-files/linux-libre/5.11-i686.conf  | 10792 ++
 .../aux-files/linux-libre/5.11-x86_64.conf | 10828 +++
 gnu/packages/batik.scm | 4 +-
 gnu/packages/benchmark.scm |28 +-
 gnu/packages/bioconductor.scm  |   347 +-
 gnu/packages/bioinformatics.scm|   354 +-
 gnu/packages/build-tools.scm   |50 +
 gnu/packages/calendar.scm  | 6 +-
 gnu/packages/cdrom.scm | 8 +-
 gnu/packages/check.scm | 2 +-
 gnu/packages/chromium.scm  | 8 +-
 gnu/packages/ci.scm|32 +-
 gnu/packages/cmake.scm |56 +-
 gnu/packages/compression.scm   |29 +-
 gnu/packages/compton.scm   | 2 +-
 gnu/packages/cpp.scm   |   114 +-
 gnu/packages/cran.scm  |   324 +-
 gnu/packages/crates-graphics.scm   |   344 +-
 gnu/packages/crates-gtk.scm|40 +-
 gnu/packages/crates-io.scm |  6813 ++--
 gnu/packages/crypto.scm|43 +-
 gnu/packages/cybersecurity.scm | 6 +-
 gnu/packages/databases.scm |62 +-
 gnu/packages/datastructures.scm|10 +-
 gnu/packages/dictionaries.scm  | 6 +-
 gnu/packages/diffoscope.scm| 5 +-
 gnu/packages/disk.scm  |19 +-
 gnu/packages/display-managers.scm  |31 +
 gnu/packages/distributed.scm   | 2 +-
 gnu/packages/dns.scm   |28 +-
 gnu/packages/documentation.scm | 2 +-
 gnu/packages/education.scm | 6 +-
 gnu/packages/electronics.scm   |52 +
 gnu/packages/emacs-xyz.scm |  1424 ++-
 gnu/packages/embedded.scm  |39 +-
 gnu/packages/emulators.scm |71 +-
 gnu/packages/engineering.scm   |   170 +-
 gnu/packages/file-systems.scm  |72 +-
 gnu/packages/fonts.scm |30 +-
 gnu/packages/fontutils.scm |26 +-
 gnu/packages/freedesktop.scm   |21 +-
 gnu/packages/freeipmi.scm  | 6 +-
 gnu/packages/game-development.scm  | 4 +-
 gnu/packages/games.scm |   164 +-
 gnu/packages/geo.scm   |14 +-
 gnu/packages/gimp.scm  | 2 +-
 gnu/packages/gl.scm| 4 +-
 gnu/packages/gnome.scm |91 +-
 gnu/packages/gnuzilla.scm  |14 +-
 gnu/packages/golang.scm|79 +
 gnu/packages/gps.scm   | 5 +-
 gnu/packages/graph.scm |31 +-
 gnu/packages/

branch core-updates updated (4f4b749 -> a8448da)

[guix-commits]

cbaines pushed a change to branch core-updates
in repository guix.

from 4f4b749  gnu: inetutils: Update to 2.0.
 add cf95ef7  gnu: Add gammastep.
 add 7f89105  gnu: Add wob.
 add a184921  gnu: OpenLDAP: Update to 2.4.57 [security fixes].
 add 61609fb  gnu: r-diffbind: Update to 3.0.13.
 add 669ea5a  gnu: r-matrixgenerics: Update to 1.2.1.
 add ebf9ad7  gnu: r-enrichplot: Update to 1.10.2.
 add 6d07092  gnu: r-clusterprofiler: Update to 3.18.1.
 add 691178d  gnu: r-multidataset: Update to 1.18.1.
 add 9470f90  gnu: r-cytolib: Update to 2.2.1.
 add 6f37c3e  gnu: r-gdsfmt: Update to 1.26.1.
 add da109ae  gnu: r-chemminer: Update to 3.42.1.
 add 18ebaca  gnu: r-preprocesscore: Update to 1.52.1.
 add f7947f8  gnu: r-hdf5array: Update to 1.18.1.
 add a135742  gnu: r-rhdf5lib: Update to 1.12.1.
 add 79d51ff  gnu: r-beachmat: Update to 2.6.4.
 add cf3e703  gnu: r-scuttle: Update to 1.0.4.
 add de4fc49  gnu: r-scran: Update to 1.18.5.
 add 8acfd9f  gnu: r-sparsematrixstats: Update to 1.2.1.
 add 311bb4b  gnu: r-delayedmatrixstats: Update to 1.12.3.
 add 074d142  gnu: r-genefilter: Update to 1.72.1.
 add d3ac91d  gnu: r-gseabase: Update to 1.52.1.
 add babb2dc  gnu: r-systempiper: Update to 1.24.3.
 add 88fd569  gnu: r-s4vectors: Update to 0.28.1.
 add 809f725  gnu: r-iranges: Update to 2.24.1.
 add 8e25b1a  gnu: r-edger: Update to 3.32.1.
 add 9b66b80  gnu: r-biomart: Update to 2.46.3.
 add 3f7e96a  gnu: r-delayedarray: Update to 0.16.1.
 add 2596200  gnu: r-methylkit: Update to 1.16.1.
 add 5103da0  gnu: r-msnbase: Update to 2.16.1.
 add 0e3e26c  gnu: r-gage: Update to 2.40.1.
 add 175bea0  doc: Try to improve the branching workflow.
 add 160e4a9  gnu: bowtie1: Update to 1.3.0.
 add b101d9f  gnu: emacs-consult: Update to 0.5.
 add af0e516  gnu: emacs-marginalia: Update to 0.3.
 add 6bf136c  gnu: opam: Update to 2.0.8.
 add f813750  gnu: diffoscope: Update to 166.
 add 8458d8d  gnu: zfs: Update to 2.0.3.
 add db6b9d2  services: Add transmission-daemon service.
 add 8cd181e  gnu: pianobar: Update to 2020.11.28.
 add c5f5b35  gnu: Add dwl.
 add 4e96ce4  gnu: dwl: Fix command name in description.
 add 18e7992  gnu: Add bpytop.
 add c84698e  gnu: Add xkeysnail.
 add 15903ea  gnu: bpytop: Don't propagated python-psutil.
 add b72444a  doc: Fix for 'guix pull'.
 add 84805ef  gnu: openjdk@9 : Add phase to hardcode libraries.
 add 44425e1  gnu: openjdk@11: Add phase to hardcode libraries.
 add fb3b4ff  gnu: Fix indentation in OpenJDK packages.
 add 9d22c0c  gnu: pari-gp: Update to 2.13.1.
 add adf6380  gnu: python-invoke: Patch reference to bash.
 add 512c6ea  gnu: python-invoke: Update to 1.5.0.
 add 5207c5e  pull: Create the "${XDG_CONFIG_HOME}/guix" directory when 
needed.
 add 65e9f13  gnu: fldigi: Use git repository.
 add 512459f  gnu: fldigi: Update to 4.1.18.
 add 9e54963  gnu: flrig: Use git repository.
 add 224582c  gnu: flamp: Use git repository.
 add 689b525  gnu: flwrap: Use git repository.
 add 66c31d5  services: cuirass: Add server argument for the remote-worker.
 add 8a8fb17  gnu: linux-libre: Update to 5.10.15.
 add 5953ec4  gnu: linux-libre 5.4: Update to 5.4.97.
 add 03fc596  gnu: linux-libre 4.19: Update to 4.19.175.
 add 21fdbb1  gnu: linux-libre 4.14: Update to 4.14.221.
 add 65812dd  gnu: linux-libre 4.9: Update to 4.9.257.
 add 044be2e  gnu: linux-libre 4.4: Update to 4.4.257.
 add 861e567  gnu: xterm: Update to 366 [fixes CVE-2021-27135].
 add ab512c2  import: crate: Use repository when home-page is unavailable
 add da4c7ba  gnu: ncmpc: Update to 0.45.
 add e69f2e9  gnu: emacs-selectrum: Update to 3.0.0-a2ba633.
 add d588cc8  gnu: diffoscope: Update to use python-magic.
 add bc7879c  gnu: Add swappy.
 add 0e3de2c  gnu: Add font-canada1500.
 add b4c6b9e  gnu: Git: Update to 2.30.1.
 add a2aacf1  gnu: xfce4-weather-plugin: Update to 0.11.0.
 add 2ebd74c  gnu: cheese: Add gst-plugins-good as an input.
 add 0d35619  gnu: guile-simple-zmq: Update to 0.0.0-6.b5f1aee.
 add dda2686  gnu: Add rust-codespan-reporting-0.11.
 add a91ac22  gnu: Add rust-html5ever-0.25.
 add 28e8df3  gnu: Add rust-nipper-0.1.
 add 97766bf  gnu: Add rust-sha2-asm-0.3.
 add 6e30a90  gnu: Add rust-byte-tools-0.2.
 add ea8fdfb  gnu: Add rust-block-buffer-0.2.
 add 3534187  gnu: Add rust-sha2-0.6.
 add 630c8a8  gnu: Add rust-rust-crypto-0.2.
 add 2912dc7  gnu: Add rust-quick-xml-0.12.
 add 04ddc64  gnu: Add rust-try-lock-0.1.
 add a0252a3  gnu: Add rust-want-0.0.
 add a280d81  gnu: Add rust-tokio-service-0.1.
 add 553d735  gnu: Add rust-take-0.1.
 add 5e314ea  gnu: Add rust-smallvec-0.2.
 add 1350817  gnu: Add rust-slab-0.3.
 add 034afd4  gnu: Add rust-tokio-proto-0.1.

06/06: gnu: verilator: Update to 4.110.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit 1462a11dbb3d2256c8693e56a583cfd100e27609
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 01:21:04 2021 +0100

gnu: verilator: Update to 4.110.

* gnu/packages/fpga.scm (verilator): Update to 4.110.
---
 gnu/packages/fpga.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm
index bee87d9..8c23258 100644
--- a/gnu/packages/fpga.scm
+++ b/gnu/packages/fpga.scm
@@ -502,7 +502,7 @@ using different abstraction levels.")
 (define-public verilator
   (package
 (name "verilator")
-(version "4.108")
+(version "4.110")
 (source
  (origin
(method git-fetch)
@@ -511,7 +511,7 @@ using different abstraction levels.")
  (commit (string-append "v" version
(file-name (git-file-name name version))
(sha256
-(base32 "0kcs0p8i2hiw348xqqh49pmllqspbzh2ljwmia03b42md5h4x5vf"
+(base32 "1lm2nyn7wzxj5y0ffwazhb4ygnmqf4d61sl937vmnmrpvdihsrrq"
 (native-inputs
  `(("autoconf" ,autoconf)
("automake" ,automake)

04/06: gnu: qtmips: Update to 0.7.5.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit cacab6853df6099fc7a3849fd4ebf93ce00a0bbb
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 01:16:08 2021 +0100

gnu: qtmips: Update to 0.7.5.

* gnu/packages/emulators.scm (qtmips): Update to 0.7.5.
---
 gnu/packages/emulators.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 057d78a..532ca60 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -285,7 +285,7 @@ older games.")
 (define-public qtmips
   (package
 (name "qtmips")
-(version "0.7.3")
+(version "0.7.5")
 (source (origin
   (method git-fetch)
   (uri (git-reference
@@ -294,7 +294,7 @@ older games.")
   (file-name (git-file-name name version))
   (sha256
(base32
-"1khvwgqz4h6q6mhbbq0yx43ajz8gx9wmwzs8784vmfrglndbxgax"
+"1fal7a8y5g0rqqjrk795jh1l50ihz01ppjnrfjrk9vkjbd59szbp"
 (build-system cmake-build-system)
 (arguments
  '(#:phases

05/06: gnu: fsarchiver: Update to 0.8.6.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit faaf7ef335f6ff49fcb4cc3bb86d2c047ca30f2b
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 01:17:34 2021 +0100

gnu: fsarchiver: Update to 0.8.6.

* gnu/packages/file-systems.scm (fsarchiver): Update to 0.8.6.
---
 gnu/packages/file-systems.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index 866e9e5..32f0db9 100644
--- a/gnu/packages/file-systems.scm
+++ b/gnu/packages/file-systems.scm
@@ -264,7 +264,7 @@ always possible.")
 (define-public fsarchiver
   (package
 (name "fsarchiver")
-(version "0.8.5")
+(version "0.8.6")
 (source
  (origin
(method git-fetch)
@@ -274,7 +274,7 @@ always possible.")
  (commit version)))
(file-name (git-file-name name version))
(sha256
-(base32 "1rvwq5v3rl14bqxjm1ibfapyicf0sa44nw7451v10kx39lp56ylp"
+(base32 "1ry2sdkfbg4bwcldk42g1i3wa3z4pr9yh9dil6ilhwcvhqiw41zc"
 (build-system gnu-build-system)
 (native-inputs
  `(("autoconf" ,autoconf)

branch master updated (373e5fc -> 1462a11)

[guix-commits]

nckx pushed a change to branch master
in repository guix.

from 373e5fc  gnu: Add gfeeds.
 new 1582f12  gnu: epson-inkjet-printer-escpr: Update to 1.7.9.
 new 170cf03  gnu: libmd: Update to 1.0.3.
 new c8cbd36  gnu: vim-full: Remove duplicate 'make-flags'.
 new cacab68  gnu: qtmips: Update to 0.7.5.
 new faaf7ef  gnu: fsarchiver: Update to 0.8.6.
 new 1462a11  gnu: verilator: Update to 4.110.

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/crypto.scm   |  4 ++--
 gnu/packages/cups.scm | 10 +-
 gnu/packages/emulators.scm|  4 ++--
 gnu/packages/file-systems.scm |  4 ++--
 gnu/packages/fpga.scm |  4 ++--
 gnu/packages/vim.scm  | 12 
 6 files changed, 21 insertions(+), 17 deletions(-)

03/06: gnu: vim-full: Remove duplicate 'make-flags'.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit c8cbd369eb512b0bc5cc0d5dfc2b5d35da50aa4f
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 01:07:24 2021 +0100

gnu: vim-full: Remove duplicate 'make-flags'.

Fixes .

Co-authored-by: Tobias Geerinckx-Rice 

* gnu/packages/vim.scm (vim-full)[arguments]: Remove duplicate
'make-flags'.

Signed-off-by: Tobias Geerinckx-Rice 
---
 gnu/packages/vim.scm | 12 
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index 372d470..d559364 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2019 Julien Lepiller 
 ;;; Copyright © 2019, 2020 Jakub Kądziołka 
 ;;; Copyright © 2020 Jack Hill 
+;;; Copyright © 2021 Simon Tournier 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -216,11 +217,14 @@ with the editor vim.")))
  "--enable-xim"
  "--disable-selinux"
  "--enable-gui")
-   ;; This flag fixes the following error:
-   ;; .../libpython3.7m.a(pyexpat.o): undefined reference to symbol 
'XML_FreeContentModel'
-   ;; .../libexpat.so.1: error adding symbols: DSO missing from command 
line
-   #:make-flags '("LDFLAGS=-lexpat")
,@(substitute-keyword-arguments (package-arguments vim)
+   ;; This flag fixes the following error:
+   ;; .../libpython3.7m.a(pyexpat.o): undefined reference to symbol 
'XML_FreeContentModel'
+   ;; .../libexpat.so.1: error adding symbols: DSO missing from 
command line
+   ((#:make-flags flags)
+`(append
+  (list "LDFLAGS=-lexpat")
+  (delete "CFLAGS=-D_REENTRANT" ,flags)))
((#:phases phases)
 `(modify-phases ,phases
(add-before 'check 'start-xserver

01/06: gnu: epson-inkjet-printer-escpr: Update to 1.7.9.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit 1582f12233b9de6faf7cb811b6736dac0774d867
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 00:47:35 2021 +0100

gnu: epson-inkjet-printer-escpr: Update to 1.7.9.

* gnu/packages/cups.scm (epson-inkjet-printer-escpr): Update to 1.7.9.
---
 gnu/packages/cups.scm | 10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index e12c1a0..2edd5d2 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -855,7 +855,7 @@ HP@tie{}LaserJet, and possibly other printers.  See 
@file{README} for details.")
 (define-public epson-inkjet-printer-escpr
   (package
 (name "epson-inkjet-printer-escpr")
-(version "1.7.8")
+(version "1.7.9")
 ;; XXX: This currently works.  But it will break as soon as a newer
 ;; version is available since the URLs for older versions are not
 ;; preserved.  An alternative source will be added as soon as
@@ -863,11 +863,11 @@ HP@tie{}LaserJet, and possibly other printers.  See 
@file{README} for details.")
 (source
  (origin
(method url-fetch)
-   (uri (string-append 
"https://download3.ebz.epson.net/dsc/f/03/00/12/04/32/";
-   "1a455ef8618def65700ca4e446311c2fb43cd839/"
-   "epson-inkjet-printer-escpr-1.7.8-1lsb3.2.tar.gz"))
+   (uri (string-append 
"https://download3.ebz.epson.net/dsc/f/03/00/12/50/95/";
+   "322b8d6b915ab85add33d41f04ba5130866aadbe/"
+   "epson-inkjet-printer-escpr-1.7.9-1lsb3.2.tar.gz"))
(sha256
-(base32 "1pygg2bd2gh27dc65h3dzwrpvi6bq5c87wl0ldchqlc2b3blsx6p"
+(base32 "136hhvhimxfnrdn3ksbiswjxgsifrwlp3zz8h0v63w4k1vkzpgc0"
 (build-system gnu-build-system)
 (arguments
  `(#:modules

02/06: gnu: libmd: Update to 1.0.3.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit 170cf035cece04fd2b9460451f5f66ba5c4485ca
Author: Tobias Geerinckx-Rice 
AuthorDate: Sat Mar 6 00:47:44 2021 +0100

gnu: libmd: Update to 1.0.3.

* gnu/packages/crypto.scm (libmd): Update to 1.0.3.
---
 gnu/packages/crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index e0fa744..5c8e4d6 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -114,7 +114,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public libmd
   (package
 (name "libmd")
-(version "1.0.1")
+(version "1.0.3")
 (source (origin
 (method url-fetch)
 (uri
@@ -125,7 +125,7 @@ communication, encryption, decryption, signatures, etc.")
  version ".tar.xz")))
 (sha256
  (base32
-  "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1"
+  "0jmga8y94h857ilra3qjaiax3wd5pd6mx1h120zhl9fcjmzhj0js"
 (build-system gnu-build-system)
 (synopsis "Message Digest functions from BSD systems")
 (description

03/03: gnu: Add gfeeds.

[guix-commits]

lle_bout pushed a commit to branch master
in repository guix.

commit 373e5fc96724fd38bb1263e4af90932ea36f596b
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 00:05:46 2021 +0100

gnu: Add gfeeds.

* gnu/packages/syndication.scm (gfeeds): New variable.
---
 gnu/packages/syndication.scm | 67 +++-
 1 file changed, 66 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index 89ef69f..79dbb77 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -24,10 +24,11 @@
   #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix build-system cargo)
-  #:use-module (guix build-system qt)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system qt)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
@@ -50,7 +51,9 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages web)
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages xml)
@@ -415,3 +418,65 @@ formats, including all versions of RSS and Atom.")
 (description "QuiteRSS is an RSS/Atom news feeds reader written on Qt/C++
 that aims to be quite fast and comfortable to it's user.")
 (license license:gpl3+)))
+
+(define-public gfeeds
+  (package
+(name "gfeeds")
+(version "0.16.2")
+(source (origin
+  (method url-fetch)
+  (uri
+   (string-append
+"https://gitlab.gnome.org/World/gfeeds/-/archive/"; version
+"/gfeeds-" version ".tar.bz2"))
+  (sha256
+   (base32
+"05gwwzqfz29m477imd5vh84jfla1wnklwpc2sdxnqli72wg08fli"
+(build-system meson-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-after 'unpack 'patch-mpv-path
+   (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "gfeeds/confManager.py"
+   (("mpv") (string-append (assoc-ref inputs "mpv") "/bin/mpv")))
+ #t))
+ (add-after 'install 'wrap-gfeeds
+   (lambda* (#:key outputs #:allow-other-keys)
+ (wrap-program (string-append
+(assoc-ref outputs "out") "/bin/gfeeds")
+   `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
+   `("GI_TYPELIB_PATH" ":" prefix (,(getenv "GI_TYPELIB_PATH")))
+   `("XDG_DATA_DIRS" ":" prefix (,(getenv "XDG_DATA_DIRS"
+ #t)
+(native-inputs
+ `(("glib:bin" ,glib "bin")
+   ("gobject-introspection" ,gobject-introspection)
+   ("gtk+:bin" ,gtk+ "bin")
+   ("pkg-config" ,pkg-config)))
+(inputs
+ `(("glib" ,glib)
+   ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+   ("gtk+" ,gtk+)
+   ("hicolor-icon-theme" ,hicolor-icon-theme)
+   ("libhandy" ,libhandy)
+   ("mpv" ,mpv)
+   ("python" ,python)
+   ("python-beautifulsoup4" ,python-beautifulsoup4)
+   ("python-dateutil" ,python-dateutil)
+   ("python-feedparser" ,python-feedparser)
+   ("python-html5lib" ,python-html5lib)
+   ("python-listparser" ,python-listparser)
+   ("python-lxml" ,python-lxml)
+   ("python-pillow" ,python-pillow)
+   ("python-pygments" ,python-pygments)
+   ("python-pytz" ,python-pytz)
+   ("python-readability" ,python-readability)
+   ("python-requests" ,python-requests)
+   ("webkitgtk" ,webkitgtk)
+   ("python-pygobject" ,python-pygobject)))
+(home-page "https://gfeeds.gabmus.org/";)
+(synopsis "Easy-to-use GTK+ RSS/Atom feed reader")
+(description "Feeds is an RSS/Atom feed reader made with GTK+
+and it has an easy-to-use graphical user interface.")
+(license license:gpl3+)))

02/03: gnu: Add python-listparser.

[guix-commits]

lle_bout pushed a commit to branch master
in repository guix.

commit 3218f02de4a95365e9e6eca83fd4c94dfd0b748c
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 00:02:28 2021 +0100

gnu: Add python-listparser.

* gnu/packages/python-xyz.scm (python-listparser): New variable.
---
 gnu/packages/python-xyz.scm | 21 +
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4e8a28e..aec5b5e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24040,3 +24040,24 @@ traditional readability measures based on simple 
surface
 characteristics. These measures are basically linear regressions based on the
 number of words, syllables, and sentences.")
 (license license:asl2.0)))
+
+(define-public python-listparser
+  (package
+(name "python-listparser")
+(version "0.18")
+(source
+ (origin
+   (method url-fetch)
+   (uri (pypi-uri "listparser" version))
+   (sha256
+(base32
+ "0hdqs1mmayw1r8yla43hgb4d9y3zqs5483vgf8j9ygczkd2wrq2b"
+(build-system python-build-system)
+(home-page
+ "https://github.com/kurtmckee/listparser";)
+(synopsis
+ "Parse subscription lists in Python")
+(description
+ "This package provides a Python library that can parse OPML, FOAF, and
+iGoogle subscription lists.")
+(license license:expat)))

branch master updated (ae22315 -> 373e5fc)

[guix-commits]

lle_bout pushed a change to branch master
in repository guix.

from ae22315  gnu: hplip: Update to 3.21.2.
 new db5a70c  gnu: Add python-readability.
 new 3218f02  gnu: Add python-listparser.
 new 373e5fc  gnu: Add gfeeds.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/python-xyz.scm  | 45 +
 gnu/packages/syndication.scm | 67 +++-
 2 files changed, 111 insertions(+), 1 deletion(-)

01/03: gnu: Add python-readability.

[guix-commits]

lle_bout pushed a commit to branch master
in repository guix.

commit db5a70c81dba2545d6114d5c41bfc7192ac27cd5
Author: Léo Le Bouter 
AuthorDate: Sat Mar 6 00:00:24 2021 +0100

gnu: Add python-readability.

* gnu/packages/python-xyz.scm (python-readability): New variable.
---
 gnu/packages/python-xyz.scm | 24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fbc9ad6..4e8a28e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24016,3 +24016,27 @@ and frame grabber interface.")
  "This package provides a command-line interface (CLI) to the Jinja2
 template engine.")
 (license license:bsd-3)))
+
+(define-public python-readability
+  (package
+(name "python-readability")
+(version "0.3.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (pypi-uri "readability" version))
+   (sha256
+(base32
+ "1b8gq3g2zwvx0aivvdg56cc0bn7xw6f2v6psmxdx9aiipkw0s0zr"
+(build-system python-build-system)
+(home-page
+ "https://github.com/andreasvc/readability/";)
+(synopsis
+ "Measure the readability of a given text using surface
+characteristics")
+(description
+ "This package provides a Python library that is an implementation of
+traditional readability measures based on simple surface
+characteristics. These measures are basically linear regressions based on the
+number of words, syllables, and sentences.")
+(license license:asl2.0)))

branch master updated: gnu: hplip: Update to 3.21.2.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

nckx pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new ae22315  gnu: hplip: Update to 3.21.2.
ae22315 is described below

commit ae2231559c8d33c222aa9a3b8cdb6aa5d49c8931
Author: Tobias Geerinckx-Rice 
AuthorDate: Fri Mar 5 23:56:15 2021 +0100

gnu: hplip: Update to 3.21.2.

* gnu/packages/cups.scm (hplip): Update to 3.21.2.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: Adapt.
---
 gnu/packages/cups.scm  |  6 ++--
 .../patches/hplip-remove-imageprocessor.patch  | 41 ++
 2 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 51efee5..e12c1a0 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Danny Milosavljevic 
 ;;; Copyright © 2017 Leo Famulari 
 ;;; Copyright © 2017 Mark H Weaver 
-;;; Copyright © 2017–2020 Tobias Geerinckx-Rice 
+;;; Copyright © 2017–2021 Tobias Geerinckx-Rice 
 ;;; Copyright © 2020 Marius Bakke 
 ;;;
 ;;; This file is part of GNU Guix.
@@ -484,14 +484,14 @@ should only be used as part of the Guix cups-pk-helper 
service.")
 (define-public hplip
   (package
 (name "hplip")
-(version "3.20.11")
+(version "3.21.2")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://sourceforge/hplip/hplip/" version
   "/hplip-" version ".tar.gz"))
   (sha256
(base32
-"04fvdyjyjbkviy3awgm7g43p3lrvrsmgaqz8bwra22g7v2rpa5hb"))
+"0hbwx9d4c8177vi0gavz9pxi7rc97jciacndp90ms8327shj2121"))
   (modules '((guix build utils)))
   (patches (search-patches "hplip-remove-imageprocessor.patch"))
   (snippet
diff --git a/gnu/packages/patches/hplip-remove-imageprocessor.patch 
b/gnu/packages/patches/hplip-remove-imageprocessor.patch
index cde3ecb..c9d27a4 100644
--- a/gnu/packages/patches/hplip-remove-imageprocessor.patch
+++ b/gnu/packages/patches/hplip-remove-imageprocessor.patch
@@ -1,4 +1,5 @@
-This patch is based heavily on the Debian patch.
+This patch is based heavily on the Debian patch, but was updated to
+apply to subsequent upstream changes not yet in Debian.
 
 
https://salsa.debian.org/printing-team/hplip/raw/debian/3.18.10+dfsg0-1/debian/patches/0025-Remove-all-ImageProcessor-functionality-which-is-clo.patch
 
@@ -175,55 +176,67 @@ index 5b282d8..0bacfaf 100644
  
  #include 
  #include 
-@@ -637,16 +636,10 @@ int HPCupsFilter::processRasterData(cups_raster_t 
*cups_raster)
- 
+@@ -651,21 +650,8 @@
  
  sprintf(hpPreProcessedRasterFile, 
"%s/hp_%s_cups_SwapedPagesXX",CUPS_TMP_DIR, m_JA.user_name);
--image_processor_t* imageProcessor = imageProcessorCreate();
- 
+  
+-image_processor_t* imageProcessor=NULL;
+-IMAGE_PROCESSOR_ERROR result;
+-//added if condition to check if pinter language is "ljzjstream"
+-//If so, then bypass imageprocessing functions while running HPCUPS 
filter.
+-if(strncmp(m_JA.printer_platform, "ljzjstream",10) == 0){
+-imageProcessor = imageProcessorCreate();
+-}
  while (cupsRasterReadHeader2(cups_raster, &cups_header))
  {
- 
--IMAGE_PROCESSOR_ERROR result = 
imageProcessorStartPage(imageProcessor, &cups_header);
+-   if(strncmp(m_JA.printer_platform, "ljzjstream",10) == 0){
+-result = imageProcessorStartPage(imageProcessor, &cups_header);
 -if (result != IPE_SUCCESS){
 -dbglog("DEBUG: imageProcessorStartPage failed result = %d\n", 
result);
 -}
--
+- }
  current_page_number++;
  
  if (current_page_number == 1) {
-@@ -745,12 +738,6 @@ int HPCupsFilter::processRasterData(cups_raster_t 
*cups_raster)
+@@ -764,14 +750,6 @@
  color_raster = rgbRaster;
  black_raster = kRaster;
  
+-  if(strncmp(m_JA.printer_platform, "ljzjstream",10) == 0)
+-  {
 -result = imageProcessorProcessLine(imageProcessor, 
m_pPrinterBuffer, cups_header.cupsBytesPerLine);
 -if (result != IPE_SUCCESS){
 -dbglog("DEBUG: imageProcessorProcessLine failed result = 
%d\n", result);
 -}
--
+-  }
 -
  if ((y == 0) && !is_ljmono) {
  //For ljmono, make sure that first line is not a blankRaster 
line.Otherwise printer
  //may not skip blank lines before actual data
-@@ -780,12 +767,6 @@ int HPCupsFilter::processRasterData(cups_raster_t 
*cups_raster)
+@@ -801,14 +779,6 @@
  }
  }  // for() loop end
  
+-  if(strncmp(m_JA.printer_platform, "ljzjstream",10) == 0)
+-  {
 -result = imageProcessorEndPage(imageProcessor);
 -if (result != IPE_SUCCESS){
 -dbglog("DEBUG: imageProcessorEndPage failed result

02/02: gnu: openscad: Disable failing tests with cgal@5.2 input.

[guix-commits]

lle_bout pushed a commit to branch master
in repository guix.

commit 04d780b5c64c0e1aed08b33936f1e3b2789f784d
Author: Léo Le Bouter 
AuthorDate: Fri Mar 5 23:48:31 2021 +0100

gnu: openscad: Disable failing tests with cgal@5.2 input.

* gnu/packages/engineering.scm (openscad)[arguments]: Add more disable 
tests in
'check phase.
---
 gnu/packages/engineering.scm | 13 -
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 66331d7..f560a15 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2553,7 +2553,18 @@ specification can be downloaded at 
@url{http://3mf.io/specification/}.";)
  "echotest_allexpressions"
  "lazyunion-*"
  "pdfexporttest_centered"
- "pdfexporttest_simple-pdf")
+ "pdfexporttest_simple-pdf"
+
+ ;; Broken due since cgal@5.2 +
+ ;; https://github.com/CGAL/cgal/pull/5371 (security)
+ ;; FIXME: Investigate or wait for future releases to
+ ;; fix it.
+ ;; Unsure if wrong test-suite or wrong security
+ ;; patch.
+ "cgalpngtest_nef3_broken"
+ "opencsgtest_nef3_broken"
+ "csgpngtest_nef3_broken"
+ "throwntogethertest_nef3_broken")
 "|")))
  ;; strip python test files since lib dir ends up in out/share
  (for-each delete-file

01/02: gnu: cgal: Update to 5.2 [security fixes].

[guix-commits]

lle_bout pushed a commit to branch master
in repository guix.

commit fc193b6518ad8df0cc92cb50b88217430dea47e3
Author: Léo Le Bouter 
AuthorDate: Fri Mar 5 23:31:15 2021 +0100

gnu: cgal: Update to 5.2 [security fixes].

* gnu/packages/patches/cgal-security-pr-5371.patch: New patch. Downloaded 
from
, 
with
hunks on files matching pattern "*Convex_decomposition_3*" removed because
they don't exist in cgal's released sources.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/graphics.scm (cgal): Update to 5.2.
[source]: Apply patch.
---
 gnu/local.mk |1 +
 gnu/packages/graphics.scm|   10 +-
 gnu/packages/patches/cgal-security-pr-5371.patch | 1611 ++
 3 files changed, 1618 insertions(+), 4 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 25afb99..4900dab 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -879,6 +879,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/cdparanoia-fpic.patch   \
   %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch \
   %D%/packages/patches/ceph-disable-cpu-optimizations.patch\
+  %D%/packages/patches/cgal-security-pr-5371.patch \
   %D%/packages/patches/chmlib-inttypes.patch   \
   %D%/packages/patches/cl-asdf-config-directories.patch\
   %D%/packages/patches/clamav-config-llvm-libs.patch   \
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 7e83c7e..db04b93 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -718,15 +718,17 @@ more.")
 (define-public cgal
   (package
 (name "cgal")
-(version "4.14.2")
+(version "5.2")
 (source (origin
   (method url-fetch)
   (uri (string-append
-"https://github.com/CGAL/cgal/releases/download/releases/";
-"CGAL-" version "/CGAL-" version ".tar.xz"))
+"https://github.com/CGAL/cgal/releases/download/v"; version
+"/CGAL-" version ".tar.xz"))
   (sha256
(base32
-"08lrp3hfwdypggz4138bnkh6bjxn441zg2y9xnq5mrjfc5ini6w1"
+"08sr2k2dm4zasfbvisqpvs6djqw3rywzwpzr701an870nvnqck3l"))
+  (patches (search-patches "cgal-security-pr-5371.patch"))
+  (patch-flags '("-p2"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f)); no test target
diff --git a/gnu/packages/patches/cgal-security-pr-5371.patch 
b/gnu/packages/patches/cgal-security-pr-5371.patch
new file mode 100644
index 000..dea53dc
--- /dev/null
+++ b/gnu/packages/patches/cgal-security-pr-5371.patch
@@ -0,0 +1,1611 @@
+From 618b409b0fbcef7cb536a4134ae3a424ef5aae45 Mon Sep 17 00:00:00 2001
+From: Maxime Gimeno 
+Date: Mon, 18 Jan 2021 15:40:40 +0100
+Subject: [PATCH 1/8] Fix Nef_2 and Nef_S2 IO
+
+---
+ Nef_2/include/CGAL/Nef_2/PM_io_parser.h   |  74 ---
+ Nef_2/include/CGAL/Nef_polyhedron_2.h |   2 +
+ Nef_S2/include/CGAL/Nef_S2/SM_io_parser.h | 106 --
+ 3 files changed, 142 insertions(+), 40 deletions(-)
+
+diff --git a/Nef_2/include/CGAL/Nef_2/PM_io_parser.h 
b/Nef_2/include/CGAL/Nef_2/PM_io_parser.h
+index 85295f3d85a..9b84dd37fbe 100644
+--- a/Nef_2/include/CGAL/Nef_2/PM_io_parser.h
 b/Nef_2/include/CGAL/Nef_2/PM_io_parser.h
+@@ -200,6 +200,11 @@ bool PM_io_parser::read_vertex(Vertex_handle v)
+!(in >> p) ||
+!check_sep("}") ) return false;
+ 
++  if(!(f >= 0 && ((iso && f < fn) || (!iso && f < en
++  {
++in.clear(std::ios_base::badbit);
++return false;
++  }
+   if (iso) v->set_face(Face_of[f]);
+   else v->set_halfedge(Halfedge_of[f]);
+   mark(v) = m; point(v) = p;
+@@ -229,10 +234,14 @@ bool PM_io_parser::read_hedge(Halfedge_handle e)
+!(in >> f) || !check_sep(",") ||
+!(in >> m) || !check_sep("}") )
+ return false;
+-  CGAL_assertion_msg
+- (eo >= 0 || (std::size_t) eo < en || epr >= 0 || (std::size_t) epr < en 
|| ene >= 0 || (std::size_t) ene < en ||
+-  v >= 0 || (std::size_t) v < vn || f >= 0 || (std::size_t) f < fn ,
+-  "wrong index in read_hedge");
++
++  if(!(eo >= 0 && (std::size_t) eo < en && epr >= 0 && (std::size_t) epr < en 
&& ene >= 0 && (std::size_t) ene < en &&
++   v >= 0 && (std::size_t) v < vn && f >= 0 && (std::size_t) f < fn ))
++  {
++in.clear(std::ios_base::badbit);
++std::cerr<<"wrong index in read_hedge"> n) || !check_sep("{") ) return false;
+   if ( !(in >> ei) || !check_sep(",") ) return false;
+-  if (ei >= 0) f->set_halfedge(Halfedge_of[ei]);
++  if (ei >= 0 && ei < en)
++  {
++f->set_halfedge(Hal

branch master updated (a714af3 -> 04d780b)

[guix-commits]

lle_bout pushed a change to branch master
in repository guix.

from a714af3  gnu: guix: Update to 112692c.
 new fc193b6  gnu: cgal: Update to 5.2 [security fixes].
 new 04d780b  gnu: openscad: Disable failing tests with cgal@5.2 input.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk |1 +
 gnu/packages/engineering.scm |   13 +-
 gnu/packages/graphics.scm|   10 +-
 gnu/packages/patches/cgal-security-pr-5371.patch | 1611 ++
 4 files changed, 1630 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/cgal-security-pr-5371.patch

branch master updated: gnu: guix: Update to 112692c.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

cbaines pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new a714af3  gnu: guix: Update to 112692c.
a714af3 is described below

commit a714af38d5d1046081524d859cde4cd8fd12a923
Author: Christopher Baines 
AuthorDate: Fri Mar 5 21:54:12 2021 +

gnu: guix: Update to 112692c.

* gnu/packages/package-management.scm (guix): Update to 112692c.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm 
b/gnu/packages/package-management.scm
index 776867e..4c12e85 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -132,8 +132,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.2.0")
-(commit "a53f711422f63d7e32b8639b968cf00bcc69ffea")
-(revision 13))
+(commit "112692c0d546d35cd67c5dc70dbd1dc609b18f64")
+(revision 14))
 (package
   (name "guix")
 
@@ -149,7 +149,7 @@
   (commit commit)))
 (sha256
  (base32
-  "01sky036v6dh8zwvrzl08pj4r6vkz7mjadkqbrwhak4nvds5frq8"))
+  "081m6zcgscmh3xbz1wrm7bjwj5d1fnwd8w89qbmd8z44a1iknf49"))
 (file-name (string-append "guix-" version "-checkout"
   (build-system gnu-build-system)
   (arguments

branch master updated: gnu: camlboot: Fix typo in properties.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

roptat pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new c6ada49  gnu: camlboot: Fix typo in properties.
c6ada49 is described below

commit c6ada4914d9ed1a8424c4b3953bd7dcf47fdf73c
Author: Julien Lepiller 
AuthorDate: Fri Mar 5 22:38:19 2021 +0100

gnu: camlboot: Fix typo in properties.

* gnu/packages/ocaml.scm (camlboot)[properties]: Add missing pair of
parenthesis.
---
 gnu/packages/ocaml.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index eb09747..086f3b0 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -156,7 +156,7 @@
   (native-inputs
`(("guile" ,guile-3.0)))
   (properties
-   `(max-silent-time . 14400)) ; 4 hours, expected even on x86_64
+   `((max-silent-time . 14400))) ; 4 hours, expected even on x86_64
   (home-page "https://github.com/Ekdohibs/camlboot";)
   (synopsis "OCaml souce bootstrap")
   (description "OCaml is written in OCaml.  Its sources contain a 
pre-compiled

branch master updated: guix: Split (guix substitutes) from (guix scripts substitute).

[guix-commits]

This is an automated email from the git hooks/post-receive script.

cbaines pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 112692c  guix: Split (guix substitutes) from (guix scripts substitute).
112692c is described below

commit 112692c0d546d35cd67c5dc70dbd1dc609b18f64
Author: Christopher Baines 
AuthorDate: Mon Feb 22 22:42:03 2021 +

guix: Split (guix substitutes) from (guix scripts substitute).

This means there's a module for working with substitutes, rather than all 
the
code sitting in the script. The need for this can be seen with the weather 
and
challenge scripts, that now don't have to use code from the substitute 
script,
but can instead use the substitute module.

The separation here between the actual functionality of the substitute 
script
and the underlying functionality used both there and elsewhere should make
maintenance easier moving forward.

This commit just moves code, none of the code should have been changed
significantly.

* guix/scripts/substitute.scm (%narinfo-cache-directory, %narinfo-ttl,
%narinfo-negative-ttl, %narinfo-transient-error-ttl, %unreachable-hosts): 
Move
variables to guix/substitutes.scm.
(narinfo-cache-file, cached-narinfo, cache-narinfo!, narinfo-request,
read-to-eof, call-with-connection-error-handling, fetch-narinfos,
lookup-narinfos, lookup-narinfos/diverse): Move procedures to
guix/substitutes.scm.
* guix/substitutes.scm: New file.
* Makefile.am: Add it.
* guix/narinfo.scm: Remove redundant module.
* guix/scripts/challenge.scm: Change (guix scripts substitute) to (guix
substitutes).
* guix/scripts/weather.scm: Change (guix scripts substitute) to (guix
substitutes).
---
 Makefile.am |   1 +
 guix/narinfo.scm|   1 -
 guix/scripts/challenge.scm  |   2 +-
 guix/scripts/substitute.scm | 312 +
 guix/scripts/weather.scm|   2 +-
 guix/substitutes.scm| 366 
 6 files changed, 376 insertions(+), 308 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 394d2ef..bb27297 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -114,6 +114,7 @@ MODULES =   \
   guix/channels.scm\
   guix/gnu-maintenance.scm \
   guix/self.scm\
+  guix/substitutes.scm \
   guix/upstream.scm\
   guix/licenses.scm\
   guix/lint.scm\
diff --git a/guix/narinfo.scm b/guix/narinfo.scm
index d3deba2..2d06124 100644
--- a/guix/narinfo.scm
+++ b/guix/narinfo.scm
@@ -25,7 +25,6 @@
   #:use-module (guix base64)
   #:use-module (guix records)
   #:use-module (guix diagnostics)
-  #:use-module (guix scripts substitute)
   #:use-module (gcrypt hash)
   #:use-module (gcrypt pk-crypto)
   #:use-module (rnrs bytevectors)
diff --git a/guix/scripts/challenge.scm b/guix/scripts/challenge.scm
index cc9cbe6..4ec3be9 100644
--- a/guix/scripts/challenge.scm
+++ b/guix/scripts/challenge.scm
@@ -27,7 +27,7 @@
   #:use-module (guix packages)
   #:use-module ((guix progress) #:hide (dump-port*))
   #:use-module (guix serialization)
-  #:use-module (guix scripts substitute)
+  #:use-module (guix substitutes)
   #:use-module (guix narinfo)
   #:use-module (rnrs bytevectors)
   #:autoload   (guix http-client) (http-fetch)
diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index fcb462b..5866b8b 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -24,6 +24,7 @@
   #:use-module (guix scripts)
   #:use-module (guix narinfo)
   #:use-module (guix store)
+  #:use-module (guix substitutes)
   #:use-module (guix utils)
   #:use-module (guix combinators)
   #:use-module (guix config)
@@ -39,40 +40,28 @@
   #:use-module (guix cache)
   #:use-module (gcrypt pk-crypto)
   #:use-module (guix pki)
-  #:use-module ((guix build utils) #:select (mkdir-p dump-port))
+  #:use-module ((guix build utils) #:select (mkdir-p))
   #:use-module ((guix build download)
 #:select (uri-abbreviation nar-uri-abbreviation
   (open-connection-for-uri
-   . guix:open-connection-for-uri)
-  store-path-abbreviation byte-count->string))
-  #:autoload   (gnutls) (error/invalid-session)
+   . guix:open-connection-for-uri)))
   #:use-module (guix progress)
   #:use-module ((guix build syscalls)
 #:select (set-thread-name))
   #:use-module (ice-9 rdelim)
-  #:use-module (ice-9 regex)
   #:use-module (ice-9 match)
   #:use-module (ice-9 format)
   #:use-module (ice-9 ftw)
-  #:use-module (ice-9 binary-ports)
-  #:use-module (ice-9 vlist)
   #:use-module

01/02: gnu: network-manager-applet: Activate support for libappindicator.

[guix-commits]

bricewge pushed a commit to branch master
in repository guix.

commit 0055f6a8a3913634f1615ca6f14f1eeb9824a17d
Author: Sébastien Lerique 
AuthorDate: Fri Mar 5 23:26:57 2021 +0900

gnu: network-manager-applet: Activate support for libappindicator.

* gnu/packages/gnome.scm (network-manager-applet): Activate support for
libappindicator.
[arguments]: Add #:configure-flags.
[inputs]: Add "libappindicator".

Signed-off-by: Brice Waegeneire 
---
 gnu/packages/gnome.scm | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 32cecb7..a8f921d 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -57,6 +57,7 @@
 ;;; Copyright © 2020 Michael Rohleder 
 ;;; Copyright © 2020 Tim Gesthuizen 
 ;;; Copyright © 2020, 2021 Andy Tai 
+;;; Copyright © 2020, 2021 Sébastien Lerique 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7978,7 +7979,9 @@ Cisco's AnyConnect SSL VPN.")
 "1rf3nm0hjcy9f8ajb4vmvwy503w8yj8d4daxkcb7w7i7b92qmyfn"
 (build-system meson-build-system)
 (arguments
- '(#:glib-or-gtk? #t))
+ '(#:glib-or-gtk? #t
+   #:configure-flags
+   '("-Dappindicator=yes")))
 (native-inputs
  `(("intltool" ,intltool)
("glib:bin" ,glib "bin") ; for glib-compile-resources, etc.
@@ -7994,6 +7997,7 @@ Cisco's AnyConnect SSL VPN.")
("libnma" ,libnma)))
 (inputs
  `(("gcr" ,gcr)
+   ("libappindicator" ,libappindicator)
("libgudev" ,libgudev)
("libnotify" ,libnotify)
("libsecret" ,libsecret)

02/02: gnu: network-manager-applet: Update to 1.20.0.

[guix-commits]

bricewge pushed a commit to branch master
in repository guix.

commit 23c6be1d3dfb4c6fa6170d7fff348e82f379a0ba
Author: Brice Waegeneire 
AuthorDate: Fri Mar 5 21:44:51 2021 +0100

gnu: network-manager-applet: Update to 1.20.0.

* gnu/packages/gnome.scm (network-manager-applet): Update to 1.20.0.
---
 gnu/packages/gnome.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index a8f921d..1aaffe0 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -52,7 +52,7 @@
 ;;; Copyright © 2020 Naga Malleswari 
 ;;; Copyright © 2020 Ryan Prior 
 ;;; Copyright © 2020, 2021 Vinicius Monego 
-;;; Copyright © 2020 Brice Waegeneire 
+;;; Copyright © 2020, 2021 Brice Waegeneire 
 ;;; Copyright © 2020 Arun Isaac 
 ;;; Copyright © 2020 Michael Rohleder 
 ;;; Copyright © 2020 Tim Gesthuizen 
@@ -7968,7 +7968,7 @@ Cisco's AnyConnect SSL VPN.")
 (define-public network-manager-applet
   (package
 (name "network-manager-applet")
-(version "1.16.0")
+(version "1.20.0")
 (source (origin
   (method url-fetch)
   (uri (string-append 
"mirror://gnome/sources/network-manager-applet/"
@@ -7976,7 +7976,7 @@ Cisco's AnyConnect SSL VPN.")
   "network-manager-applet-" version ".tar.xz"))
   (sha256
(base32
-"1rf3nm0hjcy9f8ajb4vmvwy503w8yj8d4daxkcb7w7i7b92qmyfn"
+"0lsjkbv66hn7acl2pg9h6hz4b700zzv4cjwrwjvy7043blw0bcla"
 (build-system meson-build-system)
 (arguments
  '(#:glib-or-gtk? #t

branch master updated (fa7f478 -> 23c6be1)

[guix-commits]

bricewge pushed a change to branch master
in repository guix.

from fa7f478  gnu: Audacity: Fix a crash on foreign distros.
 new 0055f6a  gnu: network-manager-applet: Activate support for 
libappindicator.
 new 23c6be1  gnu: network-manager-applet: Update to 1.20.0.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/gnome.scm | 12 
 1 file changed, 8 insertions(+), 4 deletions(-)

04/05: gnu: Python: Absorb grafted replacement.

[guix-commits]

lfam pushed a commit to branch wip-next-release
in repository guix.

commit 5cebf32a00fc4f24afce847009940881ba553fd3
Author: Leo Famulari 
AuthorDate: Fri Mar 5 15:13:20 2021 -0500

gnu: Python: Absorb grafted replacement.

* gnu/packages/python.scm (python-3.8)[source]: Add
'python-3.8-CVE-2021-3177.patch'.
[replacement]: Remove field.
(python-3.8/fixed): Remove variable.
---
 gnu/packages/python.scm | 10 +-
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e05c91b..95eae60 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -374,7 +374,6 @@ data types.")
 (define-public python-3.8
   (package (inherit python-2)
 (name "python")
-(replacement python-3.8/fixed)
 (version "3.8.2")
 (source (origin
   (method url-fetch)
@@ -382,6 +381,7 @@ data types.")
   version "/Python-" version ".tar.xz"))
   (patches (search-patches
 "python-CVE-2020-26116.patch"
+"python-3.8-CVE-2021-3177.patch"
 "python-3-fix-tests.patch"
 "python-3.8-fix-tests.patch"
 "python-3-deterministic-build-info.patch"
@@ -532,14 +532,6 @@ data types.")
 (version-major+minor version)
 "/site-packages"
 
-(define python-3.8/fixed
-  (package
-(inherit python-3.8)
-(source (origin
-  (inherit (package-source python-3.8))
-  (patches (append (search-patches 
"python-3.8-CVE-2021-3177.patch")
-   (origin-patches (package-source 
python-3.8
-
 (define-public python-3.9
   (package (inherit python-3.8)
 (name "python-next")

03/05: gnu: OpenLDAP: Absorb grafted replacement.

[guix-commits]

lfam pushed a commit to branch wip-next-release
in repository guix.

commit f2976ccd4b3079b065656f88fd142134b10375c8
Author: Leo Famulari 
AuthorDate: Fri Mar 5 15:08:43 2021 -0500

gnu: OpenLDAP: Absorb grafted replacement.

* gnu/packages/openldap.scm (openldap): Update to 2.4.57.
[replacement]: Remove field.
(openldap-2.4.57): Remove variable.
---
 gnu/packages/openldap.scm | 26 ++
 1 file changed, 2 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index 400f106..062d646 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -61,8 +61,7 @@
 (define-public openldap
   (package
(name "openldap")
-   (replacement openldap-2.4.57)
-   (version "2.4.50")
+   (version "2.4.57")
(source (origin
  (method url-fetch)
  ;; See  for a list of
@@ -78,7 +77,7 @@
  "openldap-release/openldap-" version ".tgz")))
  (sha256
   (base32
-   "1f46nlfwmys110j36sifm7ah8m8f3s10c3vaiikmmigmifapvdaw"
+   "0nmlyqhc52v24b4awh914sczmvxbazgq2cnlycvb9dgcwvhlgfn7"
(build-system gnu-build-system)
(inputs `(("bdb" ,bdb-5.3)
  ("cyrus-sasl" ,cyrus-sasl)
@@ -126,27 +125,6 @@
(license openldap2.8)
(home-page "https://www.openldap.org/";)))
 
-(define-public openldap-2.4.57
-  (package
-(inherit openldap)
-(version "2.4.57")
-(source (origin
-  (method url-fetch)
-  ;; See  for a list of
-  ;; mirrors.
-  (uri (list (string-append
-  "ftp://mirror.switch.ch/mirror/OpenLDAP/";
-  "openldap-release/openldap-" version ".tgz")
- (string-append
-  
"https://www.openldap.org/software/download/OpenLDAP/";
-  "openldap-release/openldap-" version ".tgz")
- (string-append
-  "ftp://ftp.dti.ad.jp/pub/net/OpenLDAP/";
-  "openldap-release/openldap-" version ".tgz")))
-  (sha256
-   (base32
-"0nmlyqhc52v24b4awh914sczmvxbazgq2cnlycvb9dgcwvhlgfn7"))
-
 (define-public nss-pam-ldapd
   (package
 (name "nss-pam-ldapd")

branch wip-next-release created (now 08f0330)

[guix-commits]

lfam pushed a change to branch wip-next-release
in repository guix.

  at 08f0330  gnu: Python 2: Absorb grafted replacement.

This branch includes the following new commits:

 new dbc51a9  gnu: tzdata: Update to 2021a.
 new e460db1  gnu: postgresql: Absorb grafted replacement.
 new f2976cc  gnu: OpenLDAP: Absorb grafted replacement.
 new 5cebf32  gnu: Python: Absorb grafted replacement.
 new 08f0330  gnu: Python 2: Absorb grafted replacement.

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.

02/05: gnu: postgresql: Absorb grafted replacement.

[guix-commits]

lfam pushed a commit to branch wip-next-release
in repository guix.

commit e460db1eec2c72ccc09cf4492ec7a459f4065aab
Author: Leo Famulari 
AuthorDate: Fri Mar 5 15:06:16 2021 -0500

gnu: postgresql: Absorb grafted replacement.

* gnu/packages/databases.scm (postgresql-13): Update to 13.2.
[replacement]: Remove field.
(postgresql-13.2): Remove variable.
---
 gnu/packages/databases.scm | 19 ++-
 1 file changed, 2 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 261d239..fd9bdf1 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1196,15 +1196,14 @@ developed in C/C++ to MariaDB and MySQL databases.")
 (define-public postgresql-13
   (package
 (name "postgresql")
-(replacement postgresql-13.2)
-(version "13.1")
+(version "13.2")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://ftp.postgresql.org/pub/source/v";
   version "/postgresql-" version ".tar.bz2"))
   (sha256
(base32
-"07z6zwr58dckaa97yl9ml240z83d1lhgaxw9aq49i8lsp21mqd0j"))
+"1z5d847jnajcfr3wa6jn52a8xjhamvwzmz18xlm5nvxqip8grmsz"))
   (patches (search-patches 
"postgresql-disable-resolve_symlinks.patch"
 (build-system gnu-build-system)
 (arguments
@@ -1245,20 +1244,6 @@ TIMESTAMP.  It also supports storage of binary large 
objects, including
 pictures, sounds, or video.")
 (license (license:x11-style "file://COPYRIGHT"
 
-(define-public postgresql-13.2
-  (package
-(inherit postgresql-13)
-(name "postgresql")
-(version "13.2")
-(source (origin
-  (method url-fetch)
-  (uri (string-append "https://ftp.postgresql.org/pub/source/v";
-  version "/postgresql-" version ".tar.bz2"))
-  (sha256
-   (base32
-"1z5d847jnajcfr3wa6jn52a8xjhamvwzmz18xlm5nvxqip8grmsz"))
-  (patches (search-patches 
"postgresql-disable-resolve_symlinks.patch"))
-
 (define-public postgresql-11
   (package
 (inherit postgresql-13)

05/05: gnu: Python 2: Absorb grafted replacement.

[guix-commits]

lfam pushed a commit to branch wip-next-release
in repository guix.

commit 08f0330c7b74cb735041fb154c3174127c3e47a5
Author: Leo Famulari 
AuthorDate: Fri Mar 5 15:15:01 2021 -0500

gnu: Python 2: Absorb grafted replacement.

* gnu/packages/python.scm (python-2.7)[source]: Add
'python-2.7-CVE-2021-3177.patch'.
[replacement]: Remove field.
(python-2.7/fixed): Remove variable.
---
 gnu/packages/python.scm | 12 ++--
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 95eae60..6c416fd 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -107,7 +107,6 @@
 (define-public python-2.7
   (package
 (name "python2")
-(replacement python-2.7/fixed)
 (version "2.7.17")
 (source
  (origin
@@ -122,7 +121,8 @@
"python-2.7-site-prefixes.patch"
"python-2.7-source-date-epoch.patch"
"python-2.7-adjust-tests.patch"
-   "python-cross-compile.patch"))
+   "python-cross-compile.patch"
+   "python-2.7-CVE-2021-3177.patch"))
   (modules '((guix build utils)))
   (snippet
'(begin
@@ -351,14 +351,6 @@ data types.")
 (properties '((cpe-name . "python")))
 (license license:psfl)))
 
-(define python-2.7/fixed
-  (package
-(inherit python-2.7)
-(source (origin
-  (inherit (package-source python-2.7))
-  (patches (append (search-patches 
"python-2.7-CVE-2021-3177.patch")
-   (origin-patches (package-source 
python-2.7
-
 ;; Current 2.x version.
 (define-public python-2 python-2.7)
 

01/05: gnu: tzdata: Update to 2021a.

[guix-commits]

lfam pushed a commit to branch wip-next-release
in repository guix.

commit dbc51a98494261eb40c080501ca5a7edb940038b
Author: Leo Famulari 
AuthorDate: Fri Mar 5 15:03:07 2021 -0500

gnu: tzdata: Update to 2021a.

* gnu/packages/base.scm (tzdata): Update to 2021a.
[inputs]: Update tzcode.
---
 gnu/packages/base.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 9aa69cf..5733edb 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -1244,7 +1244,7 @@ command.")
 (define-public tzdata
   (package
 (name "tzdata")
-(version "2020f")
+(version "2021a")
 (source (origin
  (method url-fetch)
  (uri (string-append
@@ -1252,7 +1252,7 @@ command.")
version ".tar.gz"))
  (sha256
   (base32
-   "10b8cr55x6ji14n3kqkn3avj1s9b79b8gszh81fxrrisij8k248j"
+   "022fn6gkmp7pamlgab04x0dm5hnyn2m2fcnyr3pvm36612xd5rrr"
 (build-system gnu-build-system)
 (arguments
  `(#:tests? #f
@@ -1312,7 +1312,7 @@ command.")
 version ".tar.gz"))
   (sha256
(base32
-
"1i998crd9fxdfhv4jd241j1arx0ng7j7cvczpmj4y5j5fwmfmvng"))
+
"1l02b0jiwp3fl0xd6227i69d26rmx3yrnq0ssq9vvdmm4jhvyipb"))
 (home-page "https://www.iana.org/time-zones";)
 (synopsis "Database of current and historical time zones")
 (description "The Time Zone Database (often called tz or zoneinfo)

branch master updated: gnu: Audacity: Fix a crash on foreign distros.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

lfam pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new fa7f478  gnu: Audacity: Fix a crash on foreign distros.
fa7f478 is described below

commit fa7f4781ca79ba55ce923bc6b3f57fb806dfe900
Author: Leo Famulari 
AuthorDate: Fri Mar 5 14:14:30 2021 -0500

gnu: Audacity: Fix a crash on foreign distros.

Without the wrap phase, Audacity crashes like this when trying to use the 
"Open
file" dialog:

(audacity:28276): GLib-GIO-ERROR **: 14:14:55.211: Settings schema 
'org.gtk.Settings.FileChooser' is not installed

* gnu/packages/audio.scm (audacity)[arguments]: Add (guix build
glib-or-gtk-build-system) to #:imported-modules. Adjust #:modules 
accordingly.
Add phases 'glib-or-gtk-wrap'.
---
 gnu/packages/audio.scm | 10 +-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 052360d..2440fed 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -750,6 +750,12 @@ engineers, musicians, soundtrack editors and composers.")
 "-Daudacity_use_ffmpeg=linked"
 "-Daudacity_use_lame=system"
 "-Daudacity_use_portsmf=system")
+   #:imported-modules ((guix build glib-or-gtk-build-system)
+   ,@%cmake-build-system-modules)
+   #:modules
+   ((guix build utils)
+(guix build cmake-build-system)
+((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:))
#:phases
(modify-phases %standard-phases
  (add-after 'unpack 'comment-out-revision-ident
@@ -766,7 +772,9 @@ engineers, musicians, soundtrack editors and composers.")
(("../lib-src/portmidi/pm_common/portmidi.h") "portmidi.h")
(("../lib-src/portmidi/porttime/porttime.h") "porttime.h"))
  (substitute* "src/prefs/MidiIOPrefs.cpp"
-   (("../../lib-src/portmidi/pm_common/portmidi.h") 
"portmidi.h")
+   (("../../lib-src/portmidi/pm_common/portmidi.h") 
"portmidi.h"
+ (add-after 'wrap-program 'glib-or-gtk-wrap
+   (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))
  ;; The test suite is not "well exercised" according to the developers,
  ;; and fails with various errors.  See
  ;; .

02/03: gnu: libburn: Update to 1.5.4.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit b9610b242027b2f7fb7d32f805f637842331ea11
Author: Tobias Geerinckx-Rice 
AuthorDate: Fri Mar 5 19:06:48 2021 +0100

gnu: libburn: Update to 1.5.4.

* gnu/packages/cdrom.scm (libburn): Update to 1.5.4.
---
 gnu/packages/cdrom.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 905103e..d93c673 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -862,14 +862,14 @@ laid out on the image.")
 (define-public libburn
   (package
 (name "libburn")
-(version "1.5.2")
+(version "1.5.4")
 (source (origin
  (method url-fetch)
  (uri (string-append "http://files.libburnia-project.org/releases/";
  "libburn-" version ".tar.gz"))
  (sha256
   (base32
-   "09sjrvq8xsj1gnl2wwyv4lbmicyzzl6x1ac2rrn53xnp34bxnckv"
+   "0m1vyry6pi115nysfgb0cg313qqhnlxqdg7f920wpiar0z8mjl2j"
 (build-system gnu-build-system)
 (native-inputs
  `(("pkg-config" ,pkg-config)))

branch master updated (e539449 -> 41b984c)

[guix-commits]

nckx pushed a change to branch master
in repository guix.

from e539449  gnu: denemo: Update to 2.5.0.
 new d0f4283  pull: Expand help text for --{url,commit,branch}.
 new b9610b2  gnu: libburn: Update to 1.5.4.
 new 41b984c  gnu: pencil2d: Update to 0.6.6.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/animation.scm | 6 +++---
 gnu/packages/cdrom.scm | 4 ++--
 guix/scripts/pull.scm  | 8 
 3 files changed, 9 insertions(+), 9 deletions(-)

03/03: gnu: pencil2d: Update to 0.6.6.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit 41b984ccfceb5fb088d03a6306a8e02becab9ab3
Author: Tobias Geerinckx-Rice 
AuthorDate: Fri Mar 5 19:07:05 2021 +0100

gnu: pencil2d: Update to 0.6.6.

* gnu/packages/animation.scm (pencil2d): Update to 0.6.6.
---
 gnu/packages/animation.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index c92c4ae..3a915c7 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2017 Ricardo Wurmus 
-;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice 
+;;; Copyright © 2018–2021 Tobias Geerinckx-Rice 
 ;;; Copyright © 2019 Pkill -9 
 ;;; Copyright © 2020 Vinicius Monego 
 ;;;
@@ -392,7 +392,7 @@ waveform until they line up with the proper sounds.")
 (define-public pencil2d
   (package
 (name "pencil2d")
-(version "0.6.5")
+(version "0.6.6")
 (source (origin
   (method git-fetch)
   (uri (git-reference
@@ -401,7 +401,7 @@ waveform until they line up with the proper sounds.")
   (file-name (git-file-name name version))
   (sha256
(base32
-"06l60wawkhb3wrsj79p5f7ka5cgcyly36pbvm95fvwbkmlvmjzf1"
+"0b1nwiwyg01087q318vymg4si76dw41ykxbn2zwd6dqbxzbpr1dh"
 (build-system gnu-build-system)
 (inputs
  `(("qtbase" ,qtbase)

01/03: pull: Expand help text for --{url,commit,branch}.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit d0f4283c449173df9561691453b8462c9e9f99ef
Author: Tobias Geerinckx-Rice 
AuthorDate: Fri Mar 5 17:25:00 2021 +0100

pull: Expand help text for --{url,commit,branch}.

* guix/scripts/pull.scm (show-help): Document that ‘--url’, ‘--commit’,
and ‘--branch’ affect only the ‘guix’ channel (for now?).
---
 guix/scripts/pull.scm | 8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 13d5ece..0761324 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2017, 2018, 2019, 2020 Ludovic Courtès 

 ;;; Copyright © 2017 Marius Bakke 
-;;; Copyright © 2020 Tobias Geerinckx-Rice 
+;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -91,11 +91,11 @@ Download and deploy the latest version of Guix.\n"))
   (display (G_ "
   -C, --channels=FILEdeploy the channels defined in FILE"))
   (display (G_ "
-  --url=URL  download from the Git repository at URL"))
+  --url=URL  download \"guix\" channel from the Git repository at 
URL"))
   (display (G_ "
-  --commit=COMMITdownload the specified COMMIT"))
+  --commit=COMMITdownload the specified \"guix\" channel COMMIT"))
   (display (G_ "
-  --branch=BRANCHdownload the tip of the specified BRANCH"))
+  --branch=BRANCHdownload the tip of the specified \"guix\" channel 
BRANCH"))
   (display (G_ "
   --allow-downgrades allow downgrades to earlier channel revisions"))
   (display (G_ "

branch master updated: gnu: denemo: Update to 2.5.0.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new e539449  gnu: denemo: Update to 2.5.0.
e539449 is described below

commit e5394493979bc63f65fd64cd36890fcb5f2a84b3
Author: Nicolas Goaziou 
AuthorDate: Fri Mar 5 17:44:07 2021 +0100

gnu: denemo: Update to 2.5.0.

* gnu/packages/music.scm (denemo): Update to 2.5.0.
---
 gnu/packages/music.scm | 7 +++
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 415005c..40780ab 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -599,14 +599,13 @@ many input formats and provides a customisable Vi-style 
user interface.")
 (define-public denemo
   (package
 (name "denemo")
-(version "2.4.0")
+(version "2.5.0")
 (source
  (origin
(method url-fetch)
-   (uri (string-append "mirror://gnu/denemo/"
-   "denemo-" version ".tar.gz"))
+   (uri (string-append "mirror://gnu/denemo/denemo-" version ".tar.gz"))
(sha256
-(base32 "145kq0zfgdadykl3i6na221i4s5wzdrcqq48amzyfarnrqk2rmpd"
+(base32 "05kwy8894hsxr6123hc854j2qq2sxyjw721zk4g3vzz8pw29p887"
 (build-system gnu-build-system)
 (arguments
  `(#:phases

branch master updated: gnu: Add emacs-envrc.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new be2b2e8  gnu: Add emacs-envrc.
be2b2e8 is described below

commit be2b2e884b1061c0509e962e80bb477e31bd2acb
Author: Xinglu Chen 
AuthorDate: Fri Mar 5 13:33:10 2021 +0100

gnu: Add emacs-envrc.

* gnu/packages/emacs-xyz.scm (emacs-envrc): New variable.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/emacs-xyz.scm | 27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index c312b7c..cfd1fde 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -93,6 +93,7 @@
 ;;; Copyright © 2021 Alexandr Vityazev 
 ;;; Copyright © 2021 Yurii Kholodkov 
 ;;; Copyright © 2021 Alexey Abramov 
+;;; Copyright © 2021 Xinglu Chen 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -13667,6 +13668,32 @@ query them from the comfort of your editor.")
 (home-page "https://github.com/hrs/engine-mode";)
 (license license:gpl3+)))
 
+(define-public emacs-envrc
+  (package
+(name "emacs-envrc")
+(version "0.2")
+(source
+ (origin
+   (method git-fetch)
+   (uri (git-reference
+ (url "https://github.com/purcell/envrc";)
+ (commit version)))
+   (file-name (git-file-name name version))
+   (sha256
+(base32
+ "0ssf9i6iym2rb530k2w5aj392qa73i6p5y0vwrs5qhkv9lagqq7p"
+(build-system emacs-build-system)
+(home-page "https://github.com/purcell/envrc";)
+(synopsis "Support for Direnv which operates buffer-locally")
+(description
+ "This is library which uses Direnv to set environment variables on
+a per-buffer basis.  This means that when you work across multiple projects
+which have @file{.envrc} files, all processes launched from the buffers ``in''
+those projects will be executed with the environment variables specified in
+those files.  This allows different versions of linters and other tools to be
+used in each project if desired.")
+(license license:gpl3+)))
+
 (define-public emacs-prop-menu
   (package
 (name "emacs-prop-menu")

branch master updated: gnu: youtube-dl: Update to 2021-03-03.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 3aa65ce  gnu: youtube-dl: Update to 2021-03-03.
3aa65ce is described below

commit 3aa65ce266878ddf558b7553185ef7ffb9eb0bdb
Author: Daniel Brooks 
AuthorDate: Fri Mar 5 05:28:11 2021 -0800

gnu: youtube-dl: Update to 2021-03-03.

gnu/packages/video.scm (youtube-dl): Update to 2021-03-03.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 564c465..4cc1f0b 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2197,14 +2197,14 @@ To load this plugin, specify the following option when 
starting mpv:
 (define-public youtube-dl
   (package
 (name "youtube-dl")
-(version "2021.02.22")
+(version "2021.03.03")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://youtube-dl.org/downloads/latest/";
   "youtube-dl-" version ".tar.gz"))
   (sha256
(base32
-"19j4kfqln1yk47dpid9j4z3zvgxy6xar1mpfsadifikfdgbmsq7x"))
+"11z2v8mdii0bl13850mc6hgz80d0kgzb4hdxyikc3wa4jqfwrq7f"))
   (snippet
'(begin
   ;; Delete the pre-generated files, except for the man page

branch master updated: gnu: Add lr.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new e693927  gnu: Add lr.
e693927 is described below

commit e693927a747e36a8c7bef042f7be92f15304cc8b
Author: Stefan Reichör 
AuthorDate: Thu Mar 4 21:58:28 2021 +0100

gnu: Add lr.

* gnu/packages/admin.scm (lr): New variable.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/admin.scm | 27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c24e8d1..b0fee13 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2130,6 +2130,33 @@ environment variable is set and output is to tty.")
 (home-page "http://mama.indstate.edu/users/ice/tree/";)
 (license license:gpl2+)))
 
+(define-public lr
+  (package
+(name "lr")
+(version "1.5.1")
+(source
+ (origin
+   (method git-fetch)
+   (uri (git-reference
+ (url "https://git.vuxu.org/lr/";)
+ (commit (string-append "v" version
+   (file-name (git-file-name name version))
+   (sha256
+(base32 "1wv2acm4r5y5gg6f64v2hiwpg1f3lnr4fy1a9zssw77fmdc7ys3j"
+(build-system gnu-build-system)
+(arguments
+ `(#:tests? #f
+   #:make-flags (list (string-append "CC=" ,(cc-for-target))
+  (string-append "PREFIX=" %output))
+   #:phases (modify-phases %standard-phases
+  (delete 'configure
+(synopsis "Tool to generate customized file listings")
+(description
+ "lr is a tool for generating file listings, which includes the best
+features of ls(1), find(1), stat(1) and du(1).")
+(home-page "https://git.vuxu.org/lr/about";)
+(license license:expat)))
+
 (define-public direvent
   (package
 (name "direvent")

branch master updated: gnu: Add emacs-springboard.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 697a4c4  gnu: Add emacs-springboard.
697a4c4 is described below

commit 697a4c464d4911ba5f32352db863aba1a64d562b
Author: Stefan Reichör 
AuthorDate: Thu Mar 4 21:15:33 2021 +0100

gnu: Add emacs-springboard.

* gnu/packages/emacs-xyz.scm (emacs-springboard): New variable.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/emacs-xyz.scm | 30 ++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 3af56ef..c312b7c 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -22484,6 +22484,36 @@ functions for Fish shell scripts.")
 parent directory using @code{Eshell}.")
   (license license:gpl3+
 
+(define-public emacs-springboard
+  ;; Upstream provides no tag.  Using the latest commit.  Version is extracted
+  ;; from "Version:" keyword.
+  (let ((commit "687d1e5898a880878995dc9bffe93b4598366203")
+(version "1.0")
+(revision "1"))
+(package
+  (name "emacs-springboard")
+  (version (git-version version revision commit))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/jwiegley/springboard";)
+   (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+  (base32 "0fn8c4hqblfjvcpg68kj2dmdjqsdnxddqbzgvakl43zckjg8pi01"
+  (build-system emacs-build-system)
+  (propagated-inputs
+   `(("emacs-helm" ,emacs-helm)
+ ("emacs-ivy" ,emacs-ivy)))
+  (home-page "https://github.com/jwiegley/springboard";)
+  (synopsis "Change the Emacs default directory quickly")
+  (description
+   "This Emacs package provides a quick way to change the default
+directory for only the next invoked command.  The directory selection can be
+done using Helm, Ido or Ivy.")
+  (license license:gpl2+
+
 (define-public emacs-tco-el
   (let ((commit "482db5313f090b17ed22ccd856f0e141dc75afe6")
 (revision "1"))

branch master updated: gnu: Add emacs-multifiles.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

ngz pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 1fe75f8  gnu: Add emacs-multifiles.
1fe75f8 is described below

commit 1fe75f8397670afb409922ed44fb4152eda3c8f3
Author: Stefan Reichör 
AuthorDate: Thu Mar 4 20:57:42 2021 +0100

gnu: Add emacs-multifiles.

* gnu/packages/emacs-xyz.scm (emacs-multifiles): New variable.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/emacs-xyz.scm | 27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 6b1edae..3af56ef 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -5781,6 +5781,33 @@ interactive searches to move multiple fake cursors.")
 simultaneous cursors.")
 (license license:gpl3+)))
 
+(define-public emacs-multifiles
+  ;; There is no tag and no "Version:" keyword.  Using the latest release
+  ;; instead.
+  (let ((commit "dddfe64b8e1c1cd1f9ccc1f03405477fc0d53897")
+(revision "1"))
+(package
+  (name "emacs-multifiles")
+  (version (git-version "0" revision commit))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/magnars/multifiles.el";)
+   (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+  (base32 "065l04ylplng1vgykkbn2vnkcs3sn1k2cikx1ha2q8wmgx6bkvai"
+  (build-system emacs-build-system)
+  (propagated-inputs
+   `(("emacs-dash" ,emacs-dash)))
+  (home-page "https://github.com/magnars/multifiles.el";)
+  (synopsis "Edit multiple files in a single Emacs buffer")
+  (description
+   "This package allows one to view and edit parts of multiple files in
+one Emacs buffer.")
+  (license license:gpl3+
+
 (define-public emacs-mc-extras
   (let ((commit "053abc52181b8718559d7361a587bbb795faf164")
 (revision "1"))

02/02: gnu: emacs-eglot: Add missing dependency.

[guix-commits]

ngz pushed a commit to branch master
in repository guix.

commit 92894e64a00cf4b907a1045905032c53d52c8202
Author: John Soo 
AuthorDate: Wed Mar 3 10:42:13 2021 -0800

gnu: emacs-eglot: Add missing dependency.

* gnu/packages/emacs-xyz.scm (emacs-eglot):[arguments] Add dependency.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/emacs-xyz.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 2bd37b9..6b1edae 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -12876,7 +12876,8 @@ Emacs.")
 (base32 "1zvs144hxq2mmq1h0ynx9hy7yyccb46f3pjg9mgq8v9cw5y678vk"
 (build-system emacs-build-system)
 (propagated-inputs
- `(("emacs-jsonrpc" ,emacs-jsonrpc)
+ `(("emacs-eldoc" ,emacs-eldoc)
+   ("emacs-jsonrpc" ,emacs-jsonrpc)
("emacs-project" ,emacs-project)))
 (home-page "https://github.com/joaotavora/eglot";)
 (synopsis "Client for Language Server Protocol (LSP) servers")

branch master updated (81aa2fa -> 92894e6)

[guix-commits]

ngz pushed a change to branch master
in repository guix.

from 81aa2fa  gnu: php: Update to 7.4.16 [security fixes].
 new ad0c8f7  gnu: Add emacs-eldoc.
 new 92894e6  gnu: emacs-eglot: Add missing dependency.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/emacs-xyz.scm | 27 ++-
 1 file changed, 26 insertions(+), 1 deletion(-)

01/02: gnu: Add emacs-eldoc.

[guix-commits]

ngz pushed a commit to branch master
in repository guix.

commit ad0c8f7eaa5217fa51a6c02790d094fe16bb880d
Author: John Soo 
AuthorDate: Wed Mar 3 10:40:39 2021 -0800

gnu: Add emacs-eldoc.

* gnu/packages/emacs-xyz.scm (emacs-eldoc): New variable.

Signed-off-by: Nicolas Goaziou 
---
 gnu/packages/emacs-xyz.scm | 24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 93dc4f8..2bd37b9 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -12887,6 +12887,30 @@ for the current file, using the major mode as a hint.  
It prompts you to enter
 one if it fails.")
 (license license:gpl3+)))
 
+(define-public emacs-eldoc
+  (package
+(name "emacs-eldoc")
+(version "1.11.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "https://elpa.gnu.org/packages/eldoc-"; version ".el"))
+   (sha256
+(base32 "1py9l1vl7s90y5kfpglhy11jswam2gcrqap09h6wb5ldnyb8cgq2"
+(build-system emacs-build-system)
+(home-page "http://elpa.gnu.org/packages/eldoc.html";)
+(synopsis "Show function arglist or variable docstring in echo area")
+(description
+ "This program was inspired by the behavior of the ``mouse documentation
+window'' on many Lisp Machine systems; as you type a function's symbol name as
+part of a sexp, it will print the argument list for that function.  Behavior
+is not identical; for example, you need not actually type the function name,
+you need only move point around in a sexp that calls it.  Also, if point is
+over a documented variable, it will print the one-line documentation for that
+variable instead, to remind you of that variable's meaning.")
+(license license:gpl3+)))
+
 ;; Tests for ert-runner have a circular dependency with ecukes, and therefore
 ;; cannot be run
 (define-public emacs-ert-runner

01/03: gnu: Add r-rcppthread.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit dfbbc736708851d7156ee86428eea40e56e356c0
Author: Mădălin Ionel Patrașcu 
AuthorDate: Fri Mar 5 02:20:37 2021 +0100

gnu: Add r-rcppthread.

* gnu/packages/cran.scm (r-rcppthread): New variable.
---
 gnu/packages/cran.scm | 23 ++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 60d5d11..0943a89 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Sandeep Subramanian 
 ;;; Copyright © 2018 Charlie Ritter 
 ;;; Copyright © 2018 Konrad Hinsen 
-;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu 

+;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu 

 ;;; Copyright © 2018 Laura Lazzati 
 ;;; Copyright © 2018 Leo Famulari 
 ;;; Copyright © 2018 Marius Bakke 
@@ -2691,6 +2691,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel 
(2013, Springer); see
 @code{citation(\"Rcpp\")} for details on these last two.")
 (license license:gpl2+)))
 
+(define-public r-rcppthread
+  (package
+(name "r-rcppthread")
+(version "1.0.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "RcppThread" version))
+   (sha256
+(base32
+ "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"
+(properties `((upstream-name . "RcppThread")))
+(build-system r-build-system)
+(home-page
+ "https://github.com/tnagler/RcppThread";)
+(synopsis "R threading in C++")
+(description
+ "This package provides a C++11-style thread class and thread pool that can
+safely be interrupted from R.")
+(license license:expat)))
+
 (define-public r-bindr
   (package
 (name "r-bindr")

branch master updated (58277e6 -> 297531e)

[guix-commits]

rekado pushed a change to branch master
in repository guix.

from 58277e6  gnu: camlboot: Raise max-silent-time timeout value to 4 hours.
 new dfbbc73  gnu: Add r-rcppthread.
 new 1353e53  gnu: Add r-universalmotif.
 new 297531e  gnu: Add r-circrnaprofiler.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioconductor.scm | 105 +-
 gnu/packages/cran.scm |  23 -
 2 files changed, 126 insertions(+), 2 deletions(-)

branch master updated: gnu: php: Update to 7.4.16 [security fixes].

[guix-commits]

This is an automated email from the git hooks/post-receive script.

nckx pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 81aa2fa  gnu: php: Update to 7.4.16 [security fixes].
81aa2fa is described below

commit 81aa2fa4ae8fda14dd900ca07559f809ab3354b9
Author: Tobias Geerinckx-Rice 
AuthorDate: Thu Mar 4 21:31:50 2021 +0100

gnu: php: Update to 7.4.16 [security fixes].

* gnu/packages/php.scm (php): Update to 7.4.16.
[arguments]: Patch failing new test.
---
 gnu/packages/php.scm | 14 +++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 46062fa..e93d112 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016-2020 Julien Lepiller 
 ;;; Copyright © 2016 Marius Bakke 
-;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice 
+;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice 
 ;;; Copyright © 2018 Ricardo Wurmus 
 ;;; Copyright © 2019 Oleg Pykhalov 
 ;;; Copyright © 2020 Maxim Cournoyer 
@@ -60,7 +60,7 @@
 (define-public php
   (package
 (name "php")
-(version "7.4.15")
+(version "7.4.16")
 (home-page "https://secure.php.net/";)
 (source (origin
   (method url-fetch)
@@ -68,7 +68,7 @@
   "php-" version ".tar.xz"))
   (sha256
(base32
-"1f1wsi2frdbr9a3hvhmk3mmd7cwzf6mwya2akpzkwyygy1jrr1cv"))
+"12xr7w2mk8ab3igvbpi94ks2xfw2nqga9a6nxs94rvcdz3xcw5hw"))
   (modules '((guix build utils)))
   (snippet
'(with-directory-excursion "ext"
@@ -327,6 +327,14 @@
  ;; Expects an empty Array; gets one with " " in it.
  "ext/pcre/tests/bug80118.phpt"))
 
+ ;; Accomodate two extra openssl errors flanking the expected one:
+ ;; random number generator:RAND_{load,write}_file:Cannot open file
+ ;; This is due to an invalid $HOME, but changing it in the test
+ ;; still prints the first one & changing it globally is overkill.
+ (substitute* "ext/openssl/tests/bug80747.phpt"
+   ((".*error:%s:key size too small.*" match)
+(string-append "%s\n" match "%s\n")))
+
  ;; Skip tests requiring network access.
  (setenv "SKIP_ONLINE_TESTS" "1")
  ;; Without this variable, 'make test' passes regardless of 
failures.

02/03: gnu: Add r-universalmotif.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 1353e536054c3f7375d784885014add9b9ea990b
Author: Mădălin Ionel Patrașcu 
AuthorDate: Fri Mar 5 02:20:38 2021 +0100

gnu: Add r-universalmotif.

* gnu/packages/bioconductor.scm (r-universalmotif): New variable.
---
 gnu/packages/bioconductor.scm | 52 ++-
 1 file changed, 51 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4d97fa..9e426df 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice 
 ;;; Copyright © 2019, 2020 Simon Tournier 
 ;;; Copyright © 2020 Peter Lo 
-;;; Copyright © 2020 Mădălin Ionel Patrașcu 

+;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu 

 ;;; Copyright © 2020 Jakub Kądziołka 
 ;;;
 ;;; This file is part of GNU Guix.
@@ -7435,6 +7435,56 @@ data.  This modified test allows for testing 
differential expression in qPCR
 data.")
 (license license:gpl2+)))
 
+(define-public r-universalmotif
+  (package
+(name "r-universalmotif")
+(version "1.8.3")
+(source
+ (origin
+   (method url-fetch)
+   (uri (bioconductor-uri "universalmotif" version))
+   (sha256
+(base32
+ "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"
+(properties
+ `((upstream-name . "universalmotif")))
+(build-system r-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-after 'unpack 'fix-reference-to-strip
+   (lambda _
+ (substitute* "src/Makevars"
+   (("/usr/bin/strip") (which "strip"
+(propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+   ("r-biostrings" ,r-biostrings)
+   ("r-ggplot2" ,r-ggplot2)
+   ("r-ggseqlogo" ,r-ggseqlogo)
+   ("r-iranges" ,r-iranges)
+   ("r-mass" ,r-mass)
+   ("r-rcpp" ,r-rcpp)
+   ("r-rcppthread" ,r-rcppthread)
+   ("r-rdpack" ,r-rdpack)
+   ("r-rlang" ,r-rlang)
+   ("r-s4vectors" ,r-s4vectors)
+   ("r-yaml" ,r-yaml)))
+(native-inputs
+ `(("r-knitr" ,r-knitr)))
+(home-page
+ "https://bioconductor.org/packages/universalmotif/";)
+(synopsis
+ "Specific structures importer, modifier, and exporter for R")
+(description
+ "This package allows importing most common @dfn{specific structure}
+(motif) types into R for use by functions provided by other Bioconductor
+motif-related packages.  Motifs can be exported into most major motif formats
+from various classes as defined by other Bioconductor packages.  A suite of
+motif and sequence manipulation and analysis functions are included, including
+enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
+motifs, and others.")
+(license license:gpl3)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs

03/03: gnu: Add r-circrnaprofiler.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 297531ef58ea91d167dac0474d02a538e8e6bc74
Author: Mădălin Ionel Patrașcu 
AuthorDate: Fri Mar 5 02:20:39 2021 +0100

gnu: Add r-circrnaprofiler.

* gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.
---
 gnu/packages/bioconductor.scm | 53 +++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e426df..89b1915 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6810,6 +6810,59 @@ accessibility data.")
  ,@(alist-delete "r-monocle"
  (package-propagated-inputs r-cicero)))
 
+(define-public r-circrnaprofiler
+  (package
+(name "r-circrnaprofiler")
+(version "1.4.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (bioconductor-uri "circRNAprofiler" version))
+   (sha256
+(base32
+ "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn"
+(properties
+ `((upstream-name . "circRNAprofiler")))
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-annotationhub" ,r-annotationhub)
+   ("r-biostrings" ,r-biostrings)
+   ("r-bsgenome" ,r-bsgenome)
+   ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+   ("r-deseq2" ,r-deseq2)
+   ("r-dplyr" ,r-dplyr)
+   ("r-edger" ,r-edger)
+   ("r-genomeinfodb" ,r-genomeinfodb)
+   ("r-genomicranges" ,r-genomicranges)
+   ("r-ggplot2" ,r-ggplot2)
+   ("r-gwascat" ,r-gwascat)
+   ("r-iranges" ,r-iranges)
+   ("r-magrittr" ,r-magrittr)
+   ("r-r-utils" ,r-r-utils)
+   ("r-readr" ,r-readr)
+   ("r-reshape2" ,r-reshape2)
+   ("r-rlang" ,r-rlang)
+   ("r-rtracklayer" ,r-rtracklayer)
+   ("r-s4vectors" ,r-s4vectors)
+   ("r-seqinr" ,r-seqinr)
+   ("r-stringi" ,r-stringi)
+   ("r-stringr" ,r-stringr)
+   ("r-universalmotif" ,r-universalmotif)))
+(native-inputs
+ `(("r-knitr" ,r-knitr)))
+(home-page
+ "https://github.com/Aufiero/circRNAprofiler";)
+(synopsis
+ "Computational framework for the downstream analysis of circular RNA's")
+(description
+ "@code{r-circrnaprofiler} is a computational framework for a comprehensive
+in silico analysis of @dfn{circular RNA} (circRNAs).  This computational
+framework allows to combine and analyze circRNAs previously detected by
+multiple publicly available annotation-based circRNA detection tools.  It
+covers different aspects of circRNAs analysis from differential expression
+analysis, evolutionary conservation, biogenesis to functional analysis.")
+(license license:gpl3)))
+
 (define-public r-cistopic
   (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
 (revision "0"))

branch master updated: gnu: camlboot: Raise max-silent-time timeout value to 4 hours.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

roptat pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new 58277e6  gnu: camlboot: Raise max-silent-time timeout value to 4 hours.
58277e6 is described below

commit 58277e68d4427e110c07fca7bce931be31e6a266
Author: Julien Lepiller 
AuthorDate: Fri Mar 5 15:51:52 2021 +0100

gnu: camlboot: Raise max-silent-time timeout value to 4 hours.

* gnu/packages/ocaml.scm (camlboot)[properties]: Add a 'max-silent-time'
property, with a value of 4 hours.
---
 gnu/packages/ocaml.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 3eb14c7..eb09747 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -155,6 +155,8 @@
  (install-file "ocamllex" bin)))
   (native-inputs
`(("guile" ,guile-3.0)))
+  (properties
+   `(max-silent-time . 14400)) ; 4 hours, expected even on x86_64
   (home-page "https://github.com/Ekdohibs/camlboot";)
   (synopsis "OCaml souce bootstrap")
   (description "OCaml is written in OCaml.  Its sources contain a 
pre-compiled

02/02: gnu: Add r-cellchat.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit f5c3e8e2ec9ab9e105c0b53afa0c2f5d5fa11065
Author: Ricardo Wurmus 
AuthorDate: Fri Mar 5 15:02:31 2021 +0100

gnu: Add r-cellchat.

* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
---
 gnu/packages/bioinformatics.scm | 66 +
 1 file changed, 66 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d617736..6d21e14 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10859,6 +10859,72 @@ explore and perform basic analysis of single cell 
sequencing data coming from
 droplet sequencing.  It has been particularly tailored for Drop-seq.")
   (license license:gpl3
 
+(define-public r-cellchat
+  (let ((commit
+ "21edd226ca408e4c413408f98562d71ee0b54e5d")
+(revision "1"))
+(package
+  (name "r-cellchat")
+  (version (git-version "1.0.0" revision commit))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/sqjin/CellChat";)
+   (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+  (base32
+   "0cvzl9mi8jjznpql2gv67swnk1dndn3a2h22z5l84h7lwpwjmh53"))
+ (snippet
+  '(for-each delete-file '("src/CellChat.so"
+   "src/CellChat_Rcpp.o"
+   "src/RcppExports.o")
+  (properties `((upstream-name . "CellChat")))
+  (build-system r-build-system)
+  (propagated-inputs
+   `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-circlize" ,r-circlize)
+ ("r-colorspace" ,r-colorspace)
+ ("r-complexheatmap" ,r-complexheatmap)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-expm" ,r-expm)
+ ("r-fnn" ,r-fnn)
+ ("r-forcats" ,r-forcats)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-gg-gap" ,r-gg-gap)
+ ("r-ggalluvial" ,r-ggalluvial)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-nmf" ,r-nmf)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-reshape2" ,r-reshape2)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rspectra" ,r-rspectra)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-shape" ,r-shape)
+ ("r-sna" ,r-sna)
+ ("r-stringr" ,r-stringr)
+ ("r-svglite" ,r-svglite)))
+  (native-inputs `(("r-knitr" ,r-knitr)))
+  (home-page "https://github.com/sqjin/CellChat";)
+  (synopsis "Analysis of cell-cell communication from single-cell 
transcriptomics data")
+  (description
+   "This package infers, visualizes and analyzes the cell-cell
+communication networks from scRNA-seq data.")
+  (license license:gpl3
+
 (define-public sambamba
   (package
 (name "sambamba")

branch master updated (b2a94e5 -> f5c3e8e)

[guix-commits]

rekado pushed a change to branch master
in repository guix.

from b2a94e5  gnu: virtualpg: Update to 2.0.1.
 new c0c3f74  gnu: Add r-gg-gap.
 new f5c3e8e  gnu: Add r-cellchat.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm | 66 +
 gnu/packages/cran.scm   | 23 ++
 2 files changed, 89 insertions(+)

01/02: gnu: Add r-gg-gap.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit c0c3f7466c733ba8abcde9cc3bd436f435faaf33
Author: Ricardo Wurmus 
AuthorDate: Fri Mar 5 15:02:18 2021 +0100

gnu: Add r-gg-gap.

* gnu/packages/cran.scm (r-gg-gap): New variable.
---
 gnu/packages/cran.scm | 23 +++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1d574b9..60d5d11 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1954,6 +1954,29 @@ in R and Shiny via the D3 visualization library.")
 from Wes Anderson movies.")
 (license license:expat)))
 
+(define-public r-gg-gap
+  (package
+(name "r-gg-gap")
+(version "1.3")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "gg.gap" version))
+   (sha256
+(base32
+ "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"
+(properties `((upstream-name . "gg.gap")))
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-cowplot" ,r-cowplot)
+   ("r-ggplot2" ,r-ggplot2)))
+(home-page "https://github.com/ChrisLou-bioinfo/gg.gap";)
+(synopsis "Define segments on the y-axis for ggplot2")
+(description
+ "The @code{gg.gap} function enables you to define segments for the y-axis
+in a ggplot2 plot.")
+(license license:gpl3)))
+
 (define-public r-tablerdash
   (package
 (name "r-tablerdash")

branch master updated: gnu: virtualpg: Update to 2.0.1.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

glv pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new b2a94e5  gnu: virtualpg: Update to 2.0.1.
b2a94e5 is described below

commit b2a94e59b8fba2f43fbefc45c2f1c4caeabdedb1
Author: Felix Gruber 
AuthorDate: Fri Mar 5 10:23:11 2021 +0100

gnu: virtualpg: Update to 2.0.1.

* gnu/packages/geo.scm (virtualpg): Update to 2.0.1.

Signed-off-by: Guillaume Le Vaillant 
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index bd8dd6b..ae37c8f 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1756,14 +1756,14 @@ tools supporting SpatiaLite.")
 (define-public virtualpg
   (package
 (name "virtualpg")
-(version "1.0.2")
+(version "2.0.1")
 (source
  (origin
(method url-fetch)
(uri (string-append "https://www.gaia-gis.it/gaia-sins/";
"virtualpg-" version ".tar.gz"))
(sha256
-(base32 "0kjipcd08vvn188xmwbs7sw41xcs06x47n2hbqshpjcr51mxbarp"
+(base32 "12z0l7368r4116ljzg7nljy5hf425r11vxc540w79wlzikmynamy"
 (build-system gnu-build-system)
 (inputs
  `(("postgresql" ,postgresql)

branch master updated: evaluation: Add doc strings.

[Mathieu Othacehe]

This is an automated email from the git hooks/post-receive script.

mothacehe pushed a commit to branch master
in repository guix-cuirass.

The following commit(s) were added to refs/heads/master by this push:
 new 9a2f597  evaluation: Add doc strings.
9a2f597 is described below

commit 9a2f59740a97fc5c69f64a0ee13d719f3c5a4b76
Author: Mathieu Othacehe 
AuthorDate: Fri Mar 5 13:13:24 2021 +0100

evaluation: Add doc strings.

* bin/evaluate.in: Add doc strings.
---
 bin/evaluate.in | 18 +++---
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/bin/evaluate.in b/bin/evaluate.in
index 0e38703..67db3e7 100644
--- a/bin/evaluate.in
+++ b/bin/evaluate.in
@@ -52,10 +52,9 @@ CHECKOUTS."
   #:key
   eval-id channels
   spec build systems)
-  "Spawn an inferior on INSTANCES that uses the given STORE.  Withing that
-inferior, call PROC with PROC-ARGS arguments from MODULE.  Pass PROC a
-register procedure that writes its arguments on a socket.  Listen that socket
-for new jobs and register them using REGISTER-JOB procedure."
+  "Spawn an inferior on INSTANCES that uses the given STORE and PROFILE.
+Withing that inferior, call EVAL-PROC from the EVAL-MODULE.  Register the
+returned jobs in database."
   ;; The module where the below procedure is defined.
   (define eval-module '(gnu ci))
 
@@ -75,6 +74,8 @@ for new jobs and register them using REGISTER-JOB procedure."
   (db-register-builds jobs eval-id spec
 
 (define (instances->cached-profile* instances)
+  "Call INSTANCES->CACHED-PROFILE on an opened store with disable
+substitutes."
   (with-store store
 (set-build-options store
#:use-substitutes? #f
@@ -83,9 +84,8 @@ for new jobs and register them using REGISTER-JOB procedure."
 
 (define* (main #:optional (args (command-line)))
   "This procedure spawns an inferior on the given channels.  An evaluation
-procedure is called within that inferior.  The evaluation procedure is passed
-a job registration callback.  The registered jobs are then read on a socket
-nd registered in database."
+procedure is called within that inferior, it returns a list of jobs that are
+registered in database."
   (match args
 ((command database eval-str)
  (parameterize ((%package-database database))
@@ -102,6 +102,10 @@ nd registered in database."
 (instances->cached-profile* instances))
(channels
 (map channel-instance->sexp instances)))
+   ;; Evaluate jobs on a per-system basis for two reasons.  It
+   ;; speeds up the evaluation speed as the evaluations can be
+   ;; performed concurrently.  It also decreases the amount of
+   ;; memory needed per evaluation process.
(par-for-each
 (lambda (system)
   (with-store store

branch master updated: evaluation: Build the cached profile only once.

[Mathieu Othacehe]

This is an automated email from the git hooks/post-receive script.

mothacehe pushed a commit to branch master
in repository guix-cuirass.

The following commit(s) were added to refs/heads/master by this push:
 new 943577b  evaluation: Build the cached profile only once.
943577b is described below

commit 943577bd90613982ea016e55ae253831c53fb0f2
Author: Mathieu Othacehe 
AuthorDate: Fri Mar 5 13:01:22 2021 +0100

evaluation: Build the cached profile only once.

* bin/evaluate.in (inferior-evaluation): Move profile building to ...
(main): ... here.
---
 bin/evaluate.in | 42 +-
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/bin/evaluate.in b/bin/evaluate.in
index aa87ddc..0e38703 100644
--- a/bin/evaluate.in
+++ b/bin/evaluate.in
@@ -48,9 +48,10 @@ CHECKOUTS."
#:commit commit)))
checkouts))
 
-(define* (inferior-evaluation store instances
+(define* (inferior-evaluation store profile
   #:key
-  eval-id spec build systems)
+  eval-id channels
+  spec build systems)
   "Spawn an inferior on INSTANCES that uses the given STORE.  Withing that
 inferior, call PROC with PROC-ARGS arguments from MODULE.  Pass PROC a
 register procedure that writes its arguments on a socket.  Listen that socket
@@ -61,9 +62,7 @@ for new jobs and register them using REGISTER-JOB procedure."
   ;; The Guix procedure for job evaluation.
   (define eval-proc 'cuirass-jobs)
 
-  (let* ((cached (cached-channel-instance store instances))
- (inferior (open-inferior cached))
- (channels (map channel-instance->sexp instances))
+  (let* ((inferior (open-inferior profile))
  (args `((channels . ,channels)
  (systems . ,systems)
  (subset . ,build
@@ -75,6 +74,13 @@ for new jobs and register them using REGISTER-JOB procedure."
(,eval-proc store ',args)
   (db-register-builds jobs eval-id spec
 
+(define (instances->cached-profile* instances)
+  (with-store store
+(set-build-options store
+   #:use-substitutes? #f
+   #:substitute-urls '())
+(instances->cached-profile store instances)))
+
 (define* (main #:optional (args (command-line)))
   "This procedure spawns an inferior on the given channels.  An evaluation
 procedure is called within that inferior.  The evaluation procedure is passed
@@ -92,18 +98,20 @@ nd registered in database."
   (build (specification-build spec))
   (systems (specification-systems spec)))
 
- (par-for-each
-  (lambda (system)
-(with-store store
-  (set-build-options store
-   #:use-substitutes? #f
-   #:substitute-urls '())
-  (inferior-evaluation store instances
-   #:eval-id eval-id
-   #:spec spec
-   #:build build
-   #:systems (list system
-  systems)
+ (let ((profile
+(instances->cached-profile* instances))
+   (channels
+(map channel-instance->sexp instances)))
+   (par-for-each
+(lambda (system)
+  (with-store store
+(inferior-evaluation store profile
+ #:eval-id eval-id
+ #:channels channels
+ #:spec spec
+ #:build build
+ #:systems (list system
+systems))
  (display 'done)
 (x
  (format (current-error-port) "Wrong command: ~a~%." x)

04/06: download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer to native tools.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 9d349afaa1dbcad85511ce6e6a1f2bdd6f43d385
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 09:41:40 2021 +0100

download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer to native tools.

* guix/download.scm (url-fetch/tarbomb, url-fetch/zipbomb): Use
'ungexp-native' instead of 'ungexp' when referring to the decompression
tools.
---
 guix/download.scm | 8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/guix/download.scm b/guix/download.scm
index 4948258..579996f 100644
--- a/guix/download.scm
+++ b/guix/download.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic 
Courtès 
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 
Ludovic Courtès 
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge 
 ;;; Copyright © 2015 Federico Beffa 
 ;;; Copyright © 2016 Alex Griffin 
@@ -535,9 +535,9 @@ own.  This helper makes it easier to deal with \"tar 
bombs\"."
 #~(begin
 (use-modules (guix build utils))
 (mkdir #$output)
-(setenv "PATH" (string-append #$gzip "/bin"))
+(setenv "PATH" (string-append #+gzip "/bin"))
 (chdir #$output)
-(invoke (string-append #$tar "/bin/tar")
+(invoke (string-append #+tar "/bin/tar")
 "xf" #$drv)))
   #:system system
   #:guile-for-build guile
@@ -574,7 +574,7 @@ own.  This helper makes it easier to deal with \"zip 
bombs\"."
 (use-modules (guix build utils))
 (mkdir #$output)
 (chdir #$output)
-(invoke (string-append #$unzip "/bin/unzip")
+(invoke (string-append #+unzip "/bin/unzip")
 #$drv)))
   #:system system
   #:guile-for-build guile

branch master updated (c9d42d6 -> d2278be)

[guix-commits]

civodul pushed a change to branch master
in repository guix.

from c9d42d6  gnu: hamlib: Update to 4.1.
 new 90ea8b1  profiles: 'package->manifest-entry' preserves transformations 
by default.
 new c19304d  doc: Refer to the right node for '--keep-failed'.
 new 6de3ef0  gexp: Honor #:target in 'compiled-modules'.
 new 9d349af  download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer 
to native tools.
 new b124801  tests: Refer to '%derivation-cache' in the right module.
 new d2278be  gnu: racket: Update to 8.0.

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 doc/guix.texi |  4 +-
 gnu/packages/scheme.scm   | 98 ++-
 guix/download.scm |  8 ++--
 guix/gexp.scm |  1 +
 guix/profiles.scm |  9 -
 guix/scripts/pack.scm | 31 +++
 guix/scripts/package.scm  |  6 +--
 guix/tests.scm|  4 +-
 tests/guix-package.sh | 15 
 tests/transformations.scm | 10 +
 10 files changed, 128 insertions(+), 58 deletions(-)

01/06: profiles: 'package->manifest-entry' preserves transformations by default.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 90ea8b16eb519a88d8f739fea5a416c0b99de19f
Author: Ludovic Courtès 
AuthorDate: Thu Mar 4 10:57:46 2021 +0100

profiles: 'package->manifest-entry' preserves transformations by default.

Previously, transformations applied from a manifest (rather than via
"guix install") would be lost.  This change fixes that and simplifies
things.

Reported by zimoun at
.

* guix/profiles.scm (default-properties): New procedure.
(package->manifest-entry): Use it for #:properties.
* guix/scripts/pack.scm (guix-pack)[with-transformations]: Remove.
Remove caller.
* guix/scripts/package.scm (transaction-upgrade-entry): Remove calls to
'manifest-entry-with-transformations'.
* tests/guix-package.sh: Add test.
* tests/transformations.scm ("options->transformation + 
package->manifest-entry"):
New test.
---
 guix/profiles.scm |  9 -
 guix/scripts/pack.scm | 31 +--
 guix/scripts/package.scm  |  6 ++
 tests/guix-package.sh | 15 +++
 tests/transformations.scm | 10 ++
 5 files changed, 48 insertions(+), 23 deletions(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index ea8bc6e..67d9053 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -362,9 +362,16 @@ file name."
#t
lst)))
 
+(define (default-properties package)
+  "Return the default properties of a manifest entry for PACKAGE."
+  ;; Preserve transformation options by default.
+  (match (assq-ref (package-properties package) 'transformations)
+(#f '())
+(transformations `((transformations . ,transformations)
+
 (define* (package->manifest-entry package #:optional (output "out")
   #:key (parent (delay #f))
-  (properties '()))
+  (properties (default-properties package)))
   "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
diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index 8ecdcb8..b653138 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2017, 2018, 2019, 2020 Ludovic Courtès 
+;;; Copyright © 2015, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès 

 ;;; Copyright © 2017, 2018 Ricardo Wurmus 
 ;;; Copyright © 2018 Konrad Hinsen 
 ;;; Copyright © 2018 Chris Marusich 
@@ -1170,24 +1170,19 @@ Create a bundle of PACKAGE.\n"))
manifest))
 identity))
 
-  (define (with-transformations manifest)
-(map-manifest-entries manifest-entry-with-transformations
-  manifest))
-
   (with-provenance
-   (with-transformations
-(cond
- ((and (not (null? manifests)) (not (null? packages)))
-  (leave (G_ "both a manifest and a package list were given~%")))
- ((not (null? manifests))
-  (concatenate-manifests
-   (map (lambda (file)
-  (let ((user-module (make-user-module
-  '((guix profiles) (gnu)
-(load* file user-module)))
-manifests)))
- (else
-  (packages->manifest packages)))
+   (cond
+((and (not (null? manifests)) (not (null? packages)))
+ (leave (G_ "both a manifest and a package list were given~%")))
+((not (null? manifests))
+ (concatenate-manifests
+  (map (lambda (file)
+ (let ((user-module (make-user-module
+ '((guix profiles) (gnu)
+   (load* file user-module)))
+   manifests)))
+(else
+ (packages->manifest packages))
 
   (with-error-handling
 (with-store store
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index 8234a17..fc5bf81 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -235,14 +235,12 @@ non-zero relevance score."
(case (version-compare candidate-version version)
  ((>)
   (manifest-transaction-install-entry
-   (manifest-entry-with-transformations
-(package->manifest-entry* pkg output))
+   (package->manifest-entry* pkg output)
transaction))
  ((<)
   transaction)
  ((=)
-  (let* ((new (manifest-entry-with-transformations
-   (package->manifest-entry* pkg output
+  (let* ((new (package->manifest-entry* pkg output)))
 ;; Here we want to determine whet

03/06: gexp: Honor #:target in 'compiled-modules'.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 6de3ef0d5e74e18e82292617c424cf30f932e699
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 09:29:24 2021 +0100

gexp: Honor #:target in 'compiled-modules'.

* guix/gexp.scm (compiled-modules): Pass #:target to 'gexp->derivation'.
---
 guix/gexp.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/guix/gexp.scm b/guix/gexp.scm
index b72b8f4..b9a2483 100644
--- a/guix/gexp.scm
+++ b/guix/gexp.scm
@@ -1708,6 +1708,7 @@ TARGET, a GNU triplet."
 ;; TODO: Pass MODULES as an environment variable.
 (gexp->derivation name build
   #:system system
+  #:target target
   #:guile-for-build guile
   #:local-build? #t
   #:env-vars

06/06: gnu: racket: Update to 8.0.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit d2278beb103871ea469dcc55deafe7d687c75149
Author: Philip McGrath 
AuthorDate: Mon Mar 1 19:43:18 2021 -0500

gnu: racket: Update to 8.0.

* gnu/packages/scheme.scm (racket): Update to 8.0.
[arguments]: Add #:configure-flags.  Add 'patch-chez-configure' phase.
[inputs]: Add "zlib", "zlib:static", "lz4", and "lz4:static".
[synopsis, description]: Tweak.
(racket-minimal): Update to 8.0.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/scheme.scm | 98 +++--
 1 file changed, 71 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index 6c30ed8..10be0aa 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -398,22 +398,26 @@ implementation techniques and as an expository tool.")
 (define-public racket
   (package
 (name "racket")
-(version "7.9"); note: remember to also update racket-minimal!
+(version "8.0"); note: remember to also update racket-minimal!
 (source (origin
   (method url-fetch)
-  (uri (list (string-append 
"http://mirror.racket-lang.org/installers/";
-version "/racket-" version "-src.tgz")
+  (uri (list (string-append 
"https://mirror.racket-lang.org/installers/";
+version "/racket-src.tgz")
+ ;; this mirror seems to have broken HTTPS:
  (string-append
   
"http://mirror.informatik.uni-tuebingen.de/mirror/racket/";
-  version "/racket-" version "-src.tgz")))
+  version "/racket-src.tgz")))
   (sha256
(base32
-"0gmp2ahmfd97nn9bwpfx9lznjmjkd042slnrrbdmyh59cqh98y2m"))
+"047wpjblfzmf1msz7snrp2c2h0zxyzlmbsqr9bwsyvz3frcg0888"))
   (patches (search-patches
 "racket-store-checksum-override.patch"
 (build-system gnu-build-system)
 (arguments
- '(#:phases
+ '(#:configure-flags
+   '("--enable-libz"
+ "--enable-liblz4")
+   #:phases
(modify-phases %standard-phases
  (add-before 'configure 'pre-configure-minimal
(lambda* (#:key inputs #:allow-other-keys)
@@ -493,13 +497,45 @@ implementation techniques and as an expository tool.")
(lambda _
  (substitute* "collects/racket/system.rkt"
(("/bin/sh") (which "sh")))
- #t)))
+ #t))
+ (add-after 'patch-/bin/sh 'patch-chez-configure
+   (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "src/cs/c/Makefile.in"
+   (("/bin/sh") (which "sh")))
+ ;; TODO: Racket CS uses a fork of Chez Scheme.
+ ;; Most of this is copy-pasted from the "chez.scm",
+ ;; but maybe there's a way to reuse more directly.
+ (with-directory-excursion "src/ChezScheme"
+   (substitute* (find-files "mats" "Mf-.*")
+ (("^[[:space:]]+(cc ) *") "\tgcc "))
+   (substitute*
+   (find-files "." (string-append
+"("
+"Mf-[a-zA-Z0-9.]+"
+"|Makefile[a-zA-Z0-9.]*"
+"|checkin"
+"|stex\\.stex"
+"|newrelease"
+"|workarea"
+"|unix\\.ms"
+"|^6\\.ms"
+;;"|[a-zA-Z0-9.]+\\.ms" ; guile can't read
+")"))
+ (("/bin/rm") (which "rm"))
+ (("/bin/ln") (which "ln"))
+ (("/bin/cp") (which "cp"))
+ (("/bin/echo") (which "echo")))
+   (substitute* "makefiles/installsh"
+ (("/bin/true") (which "true")))
;; XXX: how to run them?
#:tests? #f))
 (inputs
- `(("libffi" ,libffi)
-   ;; Hardcode dynamically loaded libraries for better functionality.
+ `(;; Hardcode dynamically loaded libraries for better functionality.
;; sqlite and libraries for `racket/draw' are needed to build the doc.
+   ("zlib" ,zlib)
+   ("zlib:static" ,zlib "static")
+   ("lz4" ,lz4)
+   ("lz4:static" ,lz4 "static")
("cairo" ,cairo)
("fontconfig" ,fontconfig)
("glib" ,glib)
@@ -519,10 +555,14 @@ implementation techniques and as an expository tool.")
 (home-page "https://racket-lang.org";)
 (synopsis "Implementation of Scheme and related languages")
 (description
- "Racket is an implementation of the Scheme programming language (R5RS 

02/06: doc: Refer to the right node for '--keep-failed'.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit c19304d2d20ded7db1eb5c898ca9528deda1c02c
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 10:58:42 2021 +0100

doc: Refer to the right node for '--keep-failed'.

* doc/guix.texi (Invoking guix-daemon, Debugging Build Failures): Refer
to "Common Build Options" for '--keep-failed'.
---
 doc/guix.texi | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 763603b..464c114 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -1492,7 +1492,7 @@ the build tree is always called 
@file{/tmp/guix-build-@var{name}.drv-0}.
 
 The build directory is automatically deleted upon completion, unless the
 build failed and the client specified @option{--keep-failed}
-(@pxref{Invoking guix build, @option{--keep-failed}}).
+(@pxref{Common Build Options, @option{--keep-failed}}).
 
 The daemon listens for connections and spawns one sub-process for each session
 started by a client (one of the @command{guix} sub-commands).  The
@@ -10817,7 +10817,7 @@ build daemon uses.
 To that end, the first thing to do is to use the @option{--keep-failed}
 or @option{-K} option of @command{guix build}, which will keep the
 failed build tree in @file{/tmp} or whatever directory you specified as
-@env{TMPDIR} (@pxref{Invoking guix build, @option{--keep-failed}}).
+@env{TMPDIR} (@pxref{Common Build Options, @option{--keep-failed}}).
 
 From there on, you can @command{cd} to the failed build tree and source
 the @file{environment-variables} file, which contains all the

05/06: tests: Refer to '%derivation-cache' in the right module.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit b1248016e0492e1897f4d1127ccb07736c9bb6a5
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 11:37:53 2021 +0100

tests: Refer to '%derivation-cache' in the right module.

* guix/tests.scm (call-with-external-store): Fix module name for
'%derivation-cache'.
---
 guix/tests.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/tests.scm b/guix/tests.scm
index fc3d521..af6f34e 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès 

+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic 
Courtès 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -140,7 +140,7 @@ no external store to talk to."
   (lambda ()
 ;; Since we're using a different store we must clear the
 ;; package-derivation cache.
-(hash-clear! (@@ (guix packages) %derivation-cache))
+(hash-clear! (@@ (guix derivations) %derivation-cache))
 
 (proc store))
   (lambda ()

04/06: squash! packages: Core procedures are written in monadic style.

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit 02bdf5c8248b6eb2e3ef612d55da1851395808bd
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 11:18:18 2021 +0100

squash! packages: Core procedures are written in monadic style.

(%graft-cache): Remove.
---
 guix/packages.scm | 22 +-
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/guix/packages.scm b/guix/packages.scm
index 22e792e..54a33c6 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -1277,11 +1277,6 @@ and return it."
  (&package-error
   (package package
 
-(define %graft-cache
-  ;; 'eq?' cache mapping package objects to a graft corresponding to their
-  ;; replacement package.
-  (make-weak-key-hash-table 200))
-
 (define (input-graft system)
   "Return a monadic procedure that, given a package with a graft, returns a
 graft, and #f otherwise."
@@ -1290,17 +1285,18 @@ graft, and #f otherwise."
   (((? package? package) output)
(let ((replacement (package-replacement package)))
  (if replacement
- (return
-  (cached (=> %graft-cache) package (cons output system)
-  (mlet %store-monad ((orig (package->derivation package 
system
+ ;; XXX: We should use a separate cache instead of abusing the
+ ;; object cache.
+ (mcached (mlet %store-monad ((orig (package->derivation package 
system
  #:graft? 
#f))
   (new  (package->derivation 
replacement system
  #:graft? 
#t)))
-(graft
-  (origin orig)
-  (origin-output output)
-  (replacement new)
-  (replacement-output output)
+(return (graft
+  (origin orig)
+  (origin-output output)
+  (replacement new)
+  (replacement-output output
+  package 'graft output system)
  (return #f
   (_
(return #f)

05/06: squash! build-system: Rewrite using gexps

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit b81655a970f3660722d21ac455c7bec57b3fa7c9
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 11:32:03 2021 +0100

squash! build-system: Rewrite using gexps

* tests/packages.scm ("package->bag, sensitivity to
%current-target-system"): Change 'build' to match the new build system
signature.
---
 tests/builders.scm | 18 --
 tests/packages.scm | 10 +-
 2 files changed, 5 insertions(+), 23 deletions(-)

diff --git a/tests/builders.scm b/tests/builders.scm
index 62ff991..f36a8c9 100644
--- a/tests/builders.scm
+++ b/tests/builders.scm
@@ -190,23 +190,5 @@ setup(
  python-dummy-fail-requirements
  python-dummy-fail-import
  python-dummy-fail-console-script)))
-(when (or (not (network-reachable?)) (shebang-too-long?))
-  (test-skip 1))
-
-(test-assert "gnu-build"
-  (let* ((url  "http://ftp.gnu.org/gnu/hello/hello-2.8.tar.gz";)
- (hash (nix-base32-string->bytevector
-"0wqd8sjmxfskrflaxywc7gqw7sfawrfvdxd9skxawzfgyy0pzdz6"))
- (tarball  (url-fetch* %store url 'sha256 hash
-   #:guile %bootstrap-guile))
- (build((store-lower gnu-build) %store "hello-2.8"
-(%bootstrap-inputs)
-#:source tarball
-#:guile %bootstrap-guile
-#:search-paths %bootstrap-search-paths))
- (out  (derivation->output-path build)))
-(and (build-derivations %store (list (pk 'hello-drv build)))
- (valid-path? %store out)
- (file-exists? (string-append out "/bin/hello")
 
 (test-end "builders")
diff --git a/tests/packages.scm b/tests/packages.scm
index 747f844..f68b078 100644
--- a/tests/packages.scm
+++ b/tests/packages.scm
@@ -1170,11 +1170,11 @@
(bag (name name) (system system) (target target)
 (build-inputs native-inputs)
 (host-inputs inputs)
-(build (lambda* (store name inputs
-   #:key system target
-   #:allow-other-keys)
- (build-expression->derivation
-  store "foo" '(mkdir %output
+(build (lambda* (name inputs
+  #:key system target
+  #:allow-other-keys)
+ (gexp->derivation "foo"
+   #~(mkdir 
#$output
  (bs(build-system
   (name 'build-system-without-cross-compilation)
   (description "Does not support cross compilation.")

03/06: download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer to native tools.

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit 0ac434a083dc7f3b33e5a4e84ebb53914b3a3355
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 09:41:40 2021 +0100

download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer to native tools.

* guix/download.scm (url-fetch/tarbomb, url-fetch/zipbomb): Use
'ungexp-native' instead of 'ungexp' when referring to the decompression
tools.
---
 guix/download.scm | 8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/guix/download.scm b/guix/download.scm
index 4948258..579996f 100644
--- a/guix/download.scm
+++ b/guix/download.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic 
Courtès 
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 
Ludovic Courtès 
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge 
 ;;; Copyright © 2015 Federico Beffa 
 ;;; Copyright © 2016 Alex Griffin 
@@ -535,9 +535,9 @@ own.  This helper makes it easier to deal with \"tar 
bombs\"."
 #~(begin
 (use-modules (guix build utils))
 (mkdir #$output)
-(setenv "PATH" (string-append #$gzip "/bin"))
+(setenv "PATH" (string-append #+gzip "/bin"))
 (chdir #$output)
-(invoke (string-append #$tar "/bin/tar")
+(invoke (string-append #+tar "/bin/tar")
 "xf" #$drv)))
   #:system system
   #:guile-for-build guile
@@ -574,7 +574,7 @@ own.  This helper makes it easier to deal with \"zip 
bombs\"."
 (use-modules (guix build utils))
 (mkdir #$output)
 (chdir #$output)
-(invoke (string-append #$unzip "/bin/unzip")
+(invoke (string-append #+unzip "/bin/unzip")
 #$drv)))
   #:system system
   #:guile-for-build guile

06/06: tests: Refer to '%derivation-cache' in the right module.

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit 063beaa8a762c9f3b1213f3308514a03b95f8aae
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 11:37:53 2021 +0100

tests: Refer to '%derivation-cache' in the right module.

* guix/tests.scm (call-with-external-store): Fix module name for
'%derivation-cache'.
---
 guix/tests.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/tests.scm b/guix/tests.scm
index da75835..4c6c7d9 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès 

+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic 
Courtès 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -143,7 +143,7 @@ no external store to talk to."
   (lambda ()
 ;; Since we're using a different store we must clear the
 ;; package-derivation cache.
-(hash-clear! (@@ (guix packages) %derivation-cache))
+(hash-clear! (@@ (guix derivations) %derivation-cache))
 
 (proc store))
   (lambda ()

branch wip-build-systems-gexp updated (b1da83b -> 063beaa)

[guix-commits]

civodul pushed a change to branch wip-build-systems-gexp
in repository guix.

from b1da83b  build-system: Use 'input-tuples->gexp' and 'outputs->gexp'.
 new 7e9bb0f  gexp: Honor #:target in 'compiled-modules'.
 new c58a4f6  packages: '%standard-patch-inputs' is not influenced by 
'%current-target-system'.
 new 0ac434a  download: 'url-fetch/tarbomb' and 'url-fetch/zipbomb' refer 
to native tools.
 new 02bdf5c  squash! packages: Core procedures are written in monadic 
style.
 new b81655a  squash! build-system: Rewrite using gexps
 new 063beaa  tests: Refer to '%derivation-cache' in the right module.

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 guix/download.scm  |  8 
 guix/gexp.scm  |  1 +
 guix/packages.scm  | 30 +++---
 guix/tests.scm |  4 ++--
 tests/builders.scm | 18 --
 tests/packages.scm | 10 +-
 6 files changed, 27 insertions(+), 44 deletions(-)

01/06: gexp: Honor #:target in 'compiled-modules'.

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit 7e9bb0f400031842acc7f891bff666e4184cbe2f
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 09:29:24 2021 +0100

gexp: Honor #:target in 'compiled-modules'.

* guix/gexp.scm (compiled-modules): Pass #:target to 'gexp->derivation'.
---
 guix/gexp.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/guix/gexp.scm b/guix/gexp.scm
index 73eb79b..ded205f 100644
--- a/guix/gexp.scm
+++ b/guix/gexp.scm
@@ -1719,6 +1719,7 @@ TARGET, a GNU triplet."
 ;; TODO: Pass MODULES as an environment variable.
 (gexp->derivation name build
   #:system system
+  #:target target
   #:guile-for-build guile
   #:local-build? #t
   #:env-vars

02/06: packages: '%standard-patch-inputs' is not influenced by '%current-target-system'.

[guix-commits]

civodul pushed a commit to branch wip-build-systems-gexp
in repository guix.

commit c58a4f628dd7f1bcd175fbdebcca0a8c8ff02ab2
Author: Ludovic Courtès 
AuthorDate: Fri Mar 5 09:30:55 2021 +0100

packages: '%standard-patch-inputs' is not influenced by 
'%current-target-system'.

* guix/packages.scm (%standard-patch-inputs): Parameterize
%CURRENT-TARGET-SYSTEM around call to CANONICAL.
---
 guix/packages.scm | 8 ++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/guix/packages.scm b/guix/packages.scm
index e182e0b..22e792e 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -556,8 +556,12 @@ identifiers.  The result is inferred from the file names 
of patches."
   (let* ((canonical (module-ref (resolve-interface '(gnu packages base))
 'canonical-package))
  (ref   (lambda (module var)
-  (canonical
-   (module-ref (resolve-interface module) var)
+  ;; Make sure 'canonical-package' is not influenced by
+  ;; '%current-target-system' since we're going to use the
+  ;; native package anyway.
+  (parameterize ((%current-target-system #f))
+(canonical
+ (module-ref (resolve-interface module) var))
 `(("tar"   ,(ref '(gnu packages base) 'tar))
   ("xz",(ref '(gnu packages compression) 'xz))
   ("bzip2" ,(ref '(gnu packages compression) 'bzip2))

branch master updated: gnu: hamlib: Update to 4.1.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

glv pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new c9d42d6  gnu: hamlib: Update to 4.1.
c9d42d6 is described below

commit c9d42d611c43e485fe39ef0adc2b032a4aec8fae
Author: Guillaume Le Vaillant 
AuthorDate: Fri Mar 5 10:40:18 2021 +0100

gnu: hamlib: Update to 4.1.

* gnu/packages/radio.scm (hamlib): Update to 4.1.
---
 gnu/packages/radio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index af6d852..6a48e87 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -773,7 +773,7 @@ you must extend 'udev-service-type' with this package.  
E.g.:
 (define-public hamlib
   (package
 (name "hamlib")
-(version "3.3")
+(version "4.1")
 (source
  (origin
(method url-fetch)
@@ -781,7 +781,7 @@ you must extend 'udev-service-type' with this package.  
E.g.:
  "https://github.com/Hamlib/Hamlib/releases/download/";
  version "/hamlib-" version ".tar.gz"))
(sha256
-(base32 "10788mgrhbc57zpzakcxv5aqnr2819pcshml6fbh8zvnkja562y9"
+(base32 "0hi3nc1k55mxff05amdv5iwryaz6r3205l24q0bg7l84f53bkm5l"
 (build-system gnu-build-system)
 (native-inputs
  `(("doxygen" ,doxygen)

branch master updated: services: guix-build-coordinator: Add dynamic auth with file record.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

cbaines pushed a commit to branch master
in repository guix.

The following commit(s) were added to refs/heads/master by this push:
 new c6c4849  services: guix-build-coordinator: Add dynamic auth with file 
record.
c6c4849 is described below

commit c6c48494e318defbe28bcc6d37f28d59c30dbf32
Author: Christopher Baines 
AuthorDate: Fri Mar 5 09:29:58 2021 +

services: guix-build-coordinator: Add dynamic auth with file record.

* gnu/services/guix.scm 
(guix-build-coordinator-agent-dynamic-auth-with-file,
guix-build-coordinator-agent-dynamic-auth-with-filen?,
guix-build-coordinator-agent-dynamic-auth-with-file-agent-name,
guix-build-coordinator-agent-dynamic-auth-with-file-token-file): New 
procedures.
(guix-build-coordinator-agent-shepherd-services): Handle new dynamic auth 
with
file record.
* doc/guix.texi (Guix Build Coordinator): Document the new dynamic auth with
file record.
---
 doc/guix.texi | 17 +
 gnu/services/guix.scm | 20 +++-
 2 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index e8fb346..763603b 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -31034,6 +31034,23 @@ database, and is used by the agent to authenticate.
 @end table
 @end deftp
 
+@deftp {Data Type} guix-build-coordinator-agent-dynamic-auth-with-file
+Data type representing an agent authenticating with a coordinator via a
+dyanmic auth token read from a file and agent name.
+
+@table @asis
+@item @code{agent-name}
+Name of an agent, this is used to match up to an existing entry in the
+database if there is one.  When no existing entry is found, a new entry
+is automatically added.
+
+@item @code{token-file}
+File containing the dynamic auth token, this is created and stored in
+the coordinator database, and is used by the agent to authenticate.
+
+@end table
+@end deftp
+
 The Guix Build Coordinator package contains a script to query an
 instance of the Guix Data Service for derivations to build, and then
 submit builds for those derivations to the coordinator.  The service
diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm
index b0d2c05..d1d31fe 100644
--- a/gnu/services/guix.scm
+++ b/gnu/services/guix.scm
@@ -76,6 +76,11 @@
 guix-build-coordinator-agent-dynamic-auth-agent-name
 guix-build-coordinator-agent-dynamic-auth-token
 
+guix-build-coordinator-agent-dynamic-auth-with-file
+guix-build-coordinator-agent-dynamic-auth-with-file?
+guix-build-coordinator-agent-dynamic-auth-with-file-agent-name
+guix-build-coordinator-agent-dynamic-auth-with-file-token-file
+
 guix-build-coordinator-agent-service-type
 
 guix-build-coordinator-queue-builds-configuration
@@ -180,6 +185,13 @@
   (agent-name  guix-build-coordinator-agent-dynamic-auth-agent-name)
   (token   guix-build-coordinator-agent-dynamic-auth-token))
 
+(define-record-type* 
+  guix-build-coordinator-agent-dynamic-auth-with-file
+  make-guix-build-coordinator-agent-dynamic-auth-with-file
+  guix-build-coordinator-agent-dynamic-auth-with-file?
+  (agent-name  
guix-build-coordinator-agent-dynamic-auth-with-file-agent-name)
+  (token-file  
guix-build-coordinator-agent-dynamic-auth-with-file-token-file))
+
 (define-record-type* 
   guix-build-coordinator-queue-builds-configuration
   make-guix-build-coordinator-queue-builds-configuration
@@ -381,7 +393,13 @@
(($ 
agent-name token)
 #~(#$(string-append "--name=" agent-name)
-   #$(string-append "--dynamic-auth-token=" 
token
+   #$(string-append "--dynamic-auth-token=" 
token)))
+   (($
+ 

+ agent-name token-file)
+#~(#$(string-append "--name=" agent-name)
+   #$(string-append "--dynamic-auth-token-file="
+token-file
   #$(simple-format #f "--max-parallel-builds=~A"
max-parallel-builds)
   #$@(if derivation-substitute-urls

[no subject]

[Mathieu Othacehe]

branch: master
commit 325edf2ffa3cfca35cbedbcabd88b778374808fb
Author: Mathieu Othacehe 
AuthorDate: Wed Mar 3 15:25:04 2021 +0100

Rewrite evaluation.
---
 Makefile.am   |   1 +
 bin/cuirass.in|  10 +-
 bin/evaluate.in   | 220 +---
 src/cuirass/base.scm  | 252 ++
 src/cuirass/database.scm  | 179 --
 src/cuirass/http.scm  |  67 ++-
 src/cuirass/metrics.scm   |   3 +-
 src/cuirass/notification.scm  | 118 +---
 src/cuirass/specification.scm | 153 +
 src/cuirass/templates.scm | 123 +
 src/schema.sql|  34 ++
 tests/database.scm| 113 ++-
 tests/http.scm|  77 +++--
 tests/metrics.scm |   7 +-
 14 files changed, 663 insertions(+), 694 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 06f0f5f..928d201 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -63,6 +63,7 @@ dist_pkgmodule_DATA = \
   src/cuirass/remote-worker.scm\
   src/cuirass/rss.scm  \
   src/cuirass/send-events.scm  \
+  src/cuirass/specification.scm\
   src/cuirass/ui.scm   \
   src/cuirass/utils.scm\
   src/cuirass/templates.scm \
diff --git a/bin/cuirass.in b/bin/cuirass.in
index 8dbb14f..e6f7564 100644
--- a/bin/cuirass.in
+++ b/bin/cuirass.in
@@ -33,6 +33,7 @@ exec ${GUILE:-@GUILE@} --no-auto-compile -e main -s "$0" "$@"
  (cuirass logging)
  (cuirass metrics)
  (cuirass notification)
+ (cuirass specification)
  (cuirass utils)
  (cuirass watchdog)
  (cuirass zabbix)
@@ -149,13 +150,8 @@ exec ${GUILE:-@GUILE@} --no-auto-compile -e main -s "$0" 
"$@"
  (with-database
  (with-notification
   (and specfile
-   (let ((new-specs (save-module-excursion
- (lambda ()
-   (set-current-module
-(make-user-module '()))
-   (primitive-load specfile)
-
- (for-each db-add-specification new-specs)))
+   (for-each db-add-specification
+ (read-specifications specfile)))
   (and paramfile (read-parameters paramfile))
 
   (if one-shot?
diff --git a/bin/evaluate.in b/bin/evaluate.in
index 19d0f12..aa87ddc 100644
--- a/bin/evaluate.in
+++ b/bin/evaluate.in
@@ -6,7 +6,7 @@ exec ${GUILE:-@GUILE@} --no-auto-compile -e main -s "$0" "$@"
  evaluate -- convert a specification to a job list
 ;;; Copyright © 2016, 2018 Ludovic Courtès 
 ;;; Copyright © 2016, 2017 Mathieu Lirzin 
-;;; Copyright © 2017, 2018 Mathieu Othacehe 
+;;; Copyright © 2017, 2018, 2021 Mathieu Othacehe 
 ;;; Copyright © 2018 Clément Lassieur 
 ;;;
 ;;; This file is part of Cuirass.
@@ -25,148 +25,86 @@ exec ${GUILE:-@GUILE@} --no-auto-compile -e main -s "$0" 
"$@"
 ;;; along with Cuirass.  If not, see .
 
 
-;; Note: Do not use any Guix modules (see below).
-(use-modules (ice-9 match)
+(use-modules (cuirass database)
+ (cuirass specification)
+ (guix channels)
+ (guix inferior)
+ (guix licenses)
+ (guix store)
+ (guix utils)
+ (ice-9 match)
  (ice-9 pretty-print)
- (srfi srfi-1)
- (srfi srfi-26))
-
-(define (ref module name)
-  "Dynamically link variable NAME under MODULE and return it."
-  (let ((m (resolve-interface module)))
-(module-ref m name)))
-
-(define (absolutize directory load-path)
-  (if (string-prefix? "/" load-path)
-  load-path
-  (string-append directory "/" load-path)))
-
-(define (input-checkout checkouts input-name)
-  "Find in CHECKOUTS the CHECKOUT corresponding to INPUT-NAME, and return it."
-  (find (lambda (checkout)
-  (string=? (assq-ref checkout #:input)
-input-name))
-checkouts))
-
-(define (spec-source spec checkouts)
-  "Find in CHECKOUTS the directory where the #:PROC-INPUT repository of SPEC
-has been checked out, and return it."
-  (let* ((input-name (assq-ref spec #:proc-input))
- (checkout (input-checkout checkouts input-name)))
-(assq-ref checkout #:directory)))
-
-(define (spec-load-path spec checkouts)
-  "Find in CHECKOUTS the load paths of each SPEC's #:LOAD-PATH-INPUTS and
-return them as a list."
-  (map (lambda (input-name)
- (let* ((checkout (input-checkout checkouts input-name))
-(directory (assq-r

[no subject]

[Mathieu Othacehe]

branch: master
commit b6067195106826dd327e51af6c6768a3f8669afb
Author: Mathieu Othacehe 
AuthorDate: Wed Mar 3 15:28:13 2021 +0100

Remove examples.

* Makefile.am (nobase_dist_pkgdata_DATA): Remove it.
* examples/gnu-system.scm: Remove it.
* examples/guix-jobs.scm: Remove it.
* examples/guix-track-git.scm: Remove it.
* examples/hello-git.scm: Remove it.
* examples/hello-singleton.scm: Remove it.
* examples/hello-subset.scm: Remove it.
* examples/random-jobs.scm: Remove it.
* examples/random.scm: Remove it.
---
 Makefile.am  |   9 --
 examples/gnu-system.scm  | 243 ---
 examples/guix-jobs.scm   |  47 -
 examples/guix-track-git.scm  | 225 ---
 examples/hello-git.scm   |  48 -
 examples/hello-singleton.scm |  41 
 examples/hello-subset.scm|  52 -
 examples/random-jobs.scm |  69 
 examples/random.scm  |  36 ---
 9 files changed, 770 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 8d071cb..06f0f5f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -248,15 +248,6 @@ MOSTLYCLEANFILES = $(bin_SCRIPTS) src/cuirass/config.scm
 info_TEXINFOS = doc/cuirass.texi
 doc_cuirass_TEXINFOS = doc/fdl-1.3.texi
 
-# Install the examples.
-nobase_dist_pkgdata_DATA = \
-  examples/random.scm  \
-  examples/random-jobs.scm \
-  examples/gnu-system.scm  \
-  examples/guix-jobs.scm   \
-  examples/hello-singleton.scm \
-  examples/hello-subset.scm
-
 ## -- ##
 ## Installation.  ##
 ## -- ##
diff --git a/examples/gnu-system.scm b/examples/gnu-system.scm
deleted file mode 100644
index ee2b571..000
--- a/examples/gnu-system.scm
+++ /dev/null
@@ -1,243 +0,0 @@
- gnu-system.scm - build jobs for Guix
-;;;
-;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès 
-;;; Copyright © 2016 Mathieu Lirzin 
-;;; Copyright © 2017 Jan Nieuwenhuizen 
-;;;
-;;; This file is part of Cuirass.
-;;;
-;;; Cuirass 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
-;;; your option) any later version.
-;;;
-;;; Cuirass is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with Cuirass.  If not, see .
-
-;; Attempt to use Guix modules from git repository.
-(eval-when (compile load eval)
-  ;; Ignore any available .go, and force recompilation.  This is because our
-  ;; checkout in the store has mtime set to the epoch, and thus .go files look
-  ;; newer, even though they may not correspond.
-  (set! %fresh-auto-compile #t))
-
-(use-modules (guix config)
- (guix store)
- (guix grafts)
- (guix packages)
- (guix derivations)
- (guix monads)
- ((guix licenses)
-  #:select (gpl3+ license-name license-uri license-comment))
- ((guix utils) #:select (%current-system))
- ((guix scripts system) #:select (read-operating-system))
- (gnu packages)
- (gnu packages commencement)
- (gnu packages guile)
- (gnu packages make-bootstrap)
- (gnu system)
- (gnu system vm)
- (gnu system install)
- (srfi srfi-1)
- (ice-9 match))
-
-(define (license->alist lcs)
-  "Return LCS  object as an alist."
-  ;; Sometimes 'license' field is a list of licenses.
-  (if (list? lcs)
-  (map license->alist lcs)
-  `((name . ,(license-name lcs))
-(uri . ,(license-uri lcs))
-(comment . ,(license-comment lcs)
-
-(define (package-metadata package)
-  "Convert PACKAGE to an alist suitable for Hydra."
-  `((#:description . ,(package-synopsis package))
-(#:long-description . ,(package-description package))
-(#:license . ,(license->alist (package-license package)))
-(#:home-page . ,(package-home-page package))
-(#:maintainers . ("bug-g...@gnu.org"))
-(#:max-silent-time . ,(or (assoc-ref (package-properties package)
- 'max-silent-time)
-  3600))  ;1 hour by default
-(#:timeout . ,(or (assoc-ref (package-properties package) 'timeout)
-  72000   ;20 hours by default
-
-(define (package-job store job-name package system)
-  "Return a job called JOB-NAME that builds PACKAGE on SYSTEM."
-  (lambda ()
-`((#:job-name . ,(string-ap

master updated (a5346d6 -> 325edf2)

[Mathieu Othacehe]

mothacehe pushed a change to branch master.

from a5346d6  remote: Enable core dump generation.
 new f5287dc  Add with-transaction.
 new b606719  Remove examples.
 new 325edf2  Rewrite evaluation.


Summary of changes:
 .dir-locals.el|   1 +
 Makefile.am   |  10 +-
 bin/cuirass.in|  10 +-
 bin/evaluate.in   | 220 +---
 examples/gnu-system.scm   | 243 
 examples/guix-jobs.scm|  47 
 examples/guix-track-git.scm   | 225 -
 examples/hello-git.scm|  48 
 examples/hello-singleton.scm  |  41 ---
 examples/hello-subset.scm |  52 -
 examples/random-jobs.scm  |  69 
 examples/random.scm   |  36 --
 src/cuirass/base.scm  | 252 ++
 src/cuirass/database.scm  | 189 +--
 src/cuirass/http.scm  |  67 ++-
 src/cuirass/metrics.scm   |   3 +-
 src/cuirass/notification.scm  | 118 +---
 src/cuirass/specification.scm | 153 +
 src/cuirass/templates.scm | 123 +
 src/schema.sql|  34 ++
 tests/database.scm| 113 ++-
 tests/http.scm|  77 +++--
 tests/metrics.scm |   7 +-
 23 files changed, 673 insertions(+), 1465 deletions(-)
 delete mode 100644 examples/gnu-system.scm
 delete mode 100644 examples/guix-jobs.scm
 delete mode 100644 examples/guix-track-git.scm
 delete mode 100644 examples/hello-git.scm
 delete mode 100644 examples/hello-singleton.scm
 delete mode 100644 examples/hello-subset.scm
 delete mode 100644 examples/random-jobs.scm
 delete mode 100644 examples/random.scm
 create mode 100644 src/cuirass/specification.scm

[no subject]

[Mathieu Othacehe]

branch: master
commit f5287dc11ed091bf4b9d1d34d9f5404704aa3b2d
Author: Mathieu Othacehe 
AuthorDate: Wed Mar 3 08:39:02 2021 +0100

Add with-transaction.

* src/cuirass/database.scm (with-transaction): New macro.
---
 .dir-locals.el   |  1 +
 src/cuirass/database.scm | 10 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/.dir-locals.el b/.dir-locals.el
index b0223cc..45731c6 100644
--- a/.dir-locals.el
+++ b/.dir-locals.el
@@ -13,6 +13,7 @@
   (eval put 'test-error 'scheme-indent-function 1)
   (eval put 'make-parameter 'scheme-indent-function 1)
   (eval put 'with-database 'scheme-indent-function 0)
+  (eval put 'with-transaction 'scheme-indent-function 0)
  (texinfo-mode
   (indent-tabs-mode)
   (fill-column . 72)
diff --git a/src/cuirass/database.scm b/src/cuirass/database.scm
index 1d309ce..cc4ff5a 100644
--- a/src/cuirass/database.scm
+++ b/src/cuirass/database.scm
@@ -107,7 +107,8 @@
 ;; Macros.
 exec-query/bind
 with-database
-with-db-worker-thread))
+with-db-worker-thread
+with-transaction))
 
 ;; Maximum priority for a Build or Specification.
 (define max-priority 9)
@@ -273,6 +274,13 @@ DB is bound to the argument of that critical section: the 
database connection."
 (number->string receive-timeout)
 caller-name))
 
+(define-syntax-rule (with-transaction exp ...)
+  "Evalute EXP within an SQL transaction."
+  (with-db-worker-thread db
+(exec-query db "BEGIN TRANSACTION;")
+exp ...
+(exec-query db "COMMIT;")))
+
 (define (read-sql-file file-name)
   "Return a list of string containing SQL instructions from FILE-NAME."
   (call-with-input-file file-name