Commit Graph

37402 Commits

Author SHA1 Message Date
Ricardo Wurmus 0dd84df121
gnu: r-ps: Update to 1.2.1.
* gnu/packages/cran.scm (r-ps): Update to 1.2.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 269182b0f1
gnu: r-rgraphviz: Update to 2.26.0.
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.26.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus bb47aca5e7
gnu: Add hdf5-1.10.
* gnu/packages/maths.scm (hdf5-1.10): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus d639d8884c
gnu: r-regioner: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.14.0.
[propagated-inputs]: Add r-biostrings.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus ed35d7ca1f
gnu: r-ruvseq: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 286157dc49
gnu: Add r-biocneighbors.
* gnu/packages/bioconductor.scm (r-biocneighbors): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 318bcbc451
gnu: r-dnabarcodes: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 6f1e1d0f88
gnu: r-inspect: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus c348cfed74
gnu: r-rots: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 016afac30f
gnu: r-glimma: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 6ea9ae9c39
gnu: r-goseq: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus b858338c76
gnu: r-ctc: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.56.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 5f2d0e635e
gnu: r-genomicinteractions: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus bbc4787cf2
gnu: r-interactionset: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus c4fed658a9
gnu: r-riboseqr: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus e22e462b33
gnu: r-riboprofiling: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus e9427b2c78
gnu: r-ripseeker: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus aa802eafb6
gnu: r-chipcomp: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 4728e27511
gnu: r-bayseq: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 57d2fcd9ee
gnu: r-chippeakanno: Update to 3.16.0.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 14520b640e
gnu: r-graph: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 95ee4a466b
gnu: r-multtest: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus a92f523026
gnu: r-qdnaseq: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 9add0933d0
gnu: r-cghcall: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 46cdceef4c
gnu: r-cghbase: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus f1c606ce8c
gnu: r-marray: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 98652568a4
gnu: r-diffbind: Update to 2.10.0.
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 6168692159
gnu: r-hpar: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 1e605c030f
gnu: Add r-biocmanager.
* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus b58940cb03
gnu: Add r-ncdf4.
* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus bfa5662e38
gnu: Add r-rcppannoy.
* gnu/packages/cran.scm (r-rcppannoy): New variable.
2018-11-07 12:26:31 +01:00
Mathieu Othacehe 8243f4e55a
gnu: slang: Use a correct location for terminfo dirs.
As termcap is disabled and no terminfo directory is given, slang is not able
to query terminal capabilities. Specifying a correct path for terminfo will
automatically disable termcap support in the configuration.

* gnu/packages/slang.scm (slang)[source]: Remove the snippet disabling
termcap.
[arguments]: Set MISC_TERMINFO_DIRS to a correct location.
2018-11-07 18:39:19 +09:00
Mathieu Othacehe a7903ca150
gnu: terminals: Change libtsm and kmscon repositories.
Those two packages (from the same author) are no longer maintained and do not
even compile. Switch to a fork that is maintained even if it does not have any
release yet.

* gnu/packages/terminals.scm (libtsm)[origin]: Use
"https://github.com/Aetf/libtsm" as new origin and switch to git-fetch method.
(kmscon)[origin]: Use "https://github.com/Aetf/kmscon" as new origin and
switch to git-fetch method.
2018-11-07 18:27:01 +09:00
Mathieu Othacehe 2d9dace8c2
services: kmscon: Add an auto-login option.
Add an auto-login option that behaves as the one of mingetty-service.

* gnu/services/base.scm (kmscon-configuration)[auto-login]: New field.
(kmscon-service-type): Pass it to kmscon command.
* doc/guix.texi (Base Services): Document it.
2018-11-07 18:21:42 +09:00
Mathieu Othacehe f4e8bc5f25
services: kmscon: Do not switch to vt at start.
* gnu/services/base.scm (kmscon-service-type): Add "--no-switchvt" to kmscon
command.
2018-11-07 18:15:00 +09:00
Mathieu Othacehe 581720bc74
gnu: Add guile-newt.
* gnu/packages/guile.scm (guile-newt): New variable.
2018-11-07 18:09:30 +09:00
Efraim Flashner cbb5d2e145
gnu: kodi: Fix typo.
This is a follow-up to 2c17bd7b29.

* gnu/packages/kodi.scm (kodi)[arguments]: Remove unwanted symbols.
2018-11-07 10:38:13 +02:00
Leo Famulari 02e2133bd2
gnu: LibreOffice: Update to 6.1.3.2.
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.3.2.
2018-11-06 23:13:50 -05:00
Leo Famulari b20aef98a0
gnu: GnuPG: Update to 2.2.11.
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.11.
2018-11-06 17:26:45 -05:00
Ludovic Courtès b07014f55a
pack: Add test for '--relocatable'.
* tests/guix-pack-relocatable.sh: New file.
* Makefile.am (SH_TESTS): Add it.
2018-11-06 23:21:24 +01:00
Ludovic Courtès 72dc64f8f7
store-copy: Canonicalize the mtime and permissions of the store copy.
Fixes a bug whereby directories in the output of 'guix pack -f tarball'
would not be read-only.

* guix/build/store-copy.scm (reset-permissions): New procedure.
(populate-store): Pass #:keep-mtime? #t to 'copy-recursively'.  Call
'reset-permissions'.
* tests/pack.scm ("self-contained-tarball"): In CHECK, define
'canonical?' and use it to check that every file has an mtime of 1 and
is read-only.
* tests/guix-pack.sh: Invoke "chmod -Rf +w" before "rm -rf" in trap.
2018-11-06 23:21:24 +01:00
Ludovic Courtès 1ff53787db
pack: Add test for 'self-contained-tarball' with localstatedir.
* tests/pack.scm ("self-contained-tarball + localstatedir"): New test.
2018-11-06 23:21:24 +01:00
Ludovic Courtès 598a6b87cc
pack: Squashfs backend now honors '--localstatedir'.
* guix/scripts/pack.scm (squashfs-image)[database]: New variable.
[build]: Add (gnu build install) to the closure.  Call
'install-database-and-gc-roots' when DATABASE is true, and invoke
mksquashfs once more.
* tests/pack.scm ("squashfs-image + localstatedir"): New test.
2018-11-06 23:21:24 +01:00
Ludovic Courtès f5a2fb1bfb
pack: Docker backend now honors '--localstatedir'.
* guix/docker.scm (build-docker-image): Add #:database parameter.
Create /var/guix/db, /var/guix/profiles, etc. when DATABASE is true.
* guix/scripts/pack.scm (docker-image): Export.  Remove #:deduplicate?
parameter.  Define 'database' and pass it to 'docker-image'.
* tests/pack.scm (test-assertm): Recompile the derivation of
%BOOTSTRAP-GUILE.
("docker-image + localstatedir"): New test.
2018-11-06 23:21:24 +01:00
Ludovic Courtès c5ce2db569
install: Add 'install-database-and-gc-roots'.
* gnu/build/install.scm (%root-profile): New variable.
(install-database-and-gc-roots): New procedure.
(populate-single-profile-directory): Replace inline code with a call to
'install-database-and-gc-roots'.
2018-11-06 23:21:24 +01:00
Ludovic Courtès b27ef1d46c
pack: Import (guix store database) only when '--localstatedir' is passed.
This is another way to address <https://bugs.gnu.org/32184>, which was
previously addressed in commit 19c924af4f.

* gnu/build/install.scm (register-closure): Move to...
* gnu/build/vm.scm (register-closure): ... here.  New procedure.
* guix/scripts/pack.scm (self-contained-tarball)[build]: Remove
now unneeded 'with-extensions' form and custom (guix config) module.
* tests/guix-pack.sh: Revert the strategy from
commit 19c924af4f.
* tests/pack.scm ("self-contained-tarball"): Likewise.
2018-11-06 23:21:23 +01:00
Ludovic Courtès ec4c81fe32
pack: Move store database creation to a separate derivation.
* guix/scripts/pack.scm (store-database): New procedure.
(self-contained-tarball): Use it when LOCALSTATEDIR? is true.
Remove 'schema' and add 'database'.
[build]: Pass DATABASE to 'populate-single-profile-directory'.
(squashfs-image): Remove #:deduplicate? parameter.
[build]: Remove (gnu build install) and (guix config) from the imported
modules.  Remove 'with-extensions'.
* gnu/build/install.scm (populate-single-profile-directory): Remove
 #:deduplicate?, #:register?, and #:schema; add #:database.  Remove call
to 'register-closure' and simply copy DATABASE instead.
2018-11-06 23:21:23 +01:00
Marius Bakke c6b05bacc0
gnu: nginx: Update to 1.14.1 [security fixes].
This fixes CVE-2018-16843, CVE-2018-16844, and CVE-2018-16845.

* gnu/packages/web.scm (nginx): Update to 1.14.1.
2018-11-06 21:34:30 +01:00
Ricardo Wurmus 9da4848632
guix: Update to Bioconductor 3.8.
* guix/import/cran.scm (%bioconductor-version): Update to 3.8.
* guix/build-system/r.scm (bioconductor-uri): Update archive URL.
2018-11-06 18:21:24 +01:00
Leo Famulari f25614229b
gnu: Syncthing: Update to 0.14.52.
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.52.
2018-11-06 11:16:22 -05:00