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guix-devel/guix
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Tobias Geerinckx-Rice 5713bbf157
Use HTTPS for bioconductor.org. 
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
 		2017-10-21 17:43:40 +02:00
..
build download: Download a nar when a VCS checkout fails. 2017-10-19 23:21:49 +02:00
build-system Use HTTPS for bioconductor.org. 2017-10-21 17:43:40 +02:00
import Use HTTPS for bioconductor.org. 2017-10-21 17:43:40 +02:00
scripts Add (guix progress). 2017-10-19 23:21:49 +02:00
store store: Support 'ssh://' URIs in 'GUIX_DAEMON_SOCKET'. 2017-04-21 19:17:36 +02:00
tests tests: Support multiple HTTP server instances. 2017-10-12 23:47:48 +02:00
base16.scm utils: Move base16 procedures to (guix base16). 2017-03-16 22:50:14 +01:00
base32.scm base32: Export the base32 charsets. 2017-07-21 17:03:24 +02:00
base64.scm base64: Turn into a regular Guile module. 2017-05-25 14:25:17 +02:00
build-system.scm
…
cache.scm cache: Work around 'time-monotonic' bug in Guile 2.2.2. 2017-04-22 14:42:15 +02:00
combinators.scm Add (guix memoization). 2017-01-28 18:55:20 +01:00
config.scm.in pull: Install (guix config) module to override the user's one. 2016-07-20 22:53:02 +02:00
cpio.scm linux-initrd: Produce cpio archives with zeroed timestamps, etc. 2015-06-24 18:05:03 +02:00
cve.scm cve: Disable position recording while reading the CVE list. 2017-09-19 23:58:25 +02:00
cvs-download.scm download: Download a nar when a VCS checkout fails. 2017-10-19 23:21:49 +02:00
derivations.scm derivations: Introduce 'read-derivation-from-file'. 2017-06-12 17:53:51 +02:00
discovery.scm discovery: Recurse into directories pointed to by a symlink. 2017-07-03 23:51:23 +02:00
docker.scm pack: Add '--target'. 2017-03-18 00:38:41 +01:00
download.scm guix: mirrors: Add kde archive mirror. 2017-10-10 17:01:32 +03:00
elf.scm elf: Add missing argument in 'elf-segment'. 2015-03-30 15:21:11 +02:00
ftp-client.scm ftp-client: Allow custom username and password for FTP servers. 2017-03-21 12:14:05 +01:00
gcrypt.scm
…
gexp.scm gexp: Slightly improve error reporting for 'local-file'. 2017-07-20 18:08:00 +02:00
git-download.scm download: Download a nar when a VCS checkout fails. 2017-10-19 23:21:49 +02:00
git.scm guix: git: Stop using libgit2-shutdown. 2017-07-01 16:32:42 +02:00
gnu-maintenance.scm upstream: Add new GNOME updater. 2017-09-26 00:35:06 +02:00
gnupg.scm ui: Rename '_' to 'G_'. 2017-05-03 16:16:17 +02:00
grafts.scm derivations: Introduce 'read-derivation-from-file'. 2017-06-12 17:53:51 +02:00
graph.scm Revert "graph: Provide access to the package record in the emit functions." 2017-08-24 23:55:51 +02:00
hash.scm Use (ice-9 binary-ports) instead of (rnrs io ports). 2016-10-19 15:54:10 +02:00
hg-download.scm download: Download a nar when a VCS checkout fails. 2017-10-19 23:21:49 +02:00
http-client.scm http-client: Reset cache TTL upon 304 "Not Modified" responses. 2017-09-26 00:35:06 +02:00
licenses.scm licenses: Add CC-Sampling+ 1.0. 2017-09-22 08:04:32 -04:00
memoization.scm memoization: (mlambda () ...) allows for inner 'define'. 2017-09-03 23:36:17 +02:00
modules.scm modules: Raise an error when a dependency could not be found. 2017-05-25 14:25:17 +02:00
monad-repl.scm monad-repl: Close connection when leaving the monad REPL. 2016-01-13 17:43:21 +01:00
monads.scm monads: Add a template and specialization mechanism for monadic procedures. 2017-05-02 23:41:13 +02:00
nar.scm ui: Rename '_' to 'G_'. 2017-05-03 16:16:17 +02:00
packages.scm packages: Use Guile 2.0 for grafting. 2017-08-24 00:41:44 +02:00
pk-crypto.scm publish: The public and private keys are now SRFI-39 parameters. 2017-03-22 14:05:59 +01:00
pki.scm Use (ice-9 binary-ports) instead of (rnrs io ports). 2016-10-19 15:54:10 +02:00
profiles.scm profiles: Only check file contents if the file exists. 2017-08-09 14:46:48 +02:00
progress.scm Add (guix progress). 2017-10-19 23:21:49 +02:00
records.scm records: Slight simplification. 2017-04-17 23:31:28 +02:00
scripts.scm scripts: Do not create the config directory. 2017-05-13 00:03:46 +02:00
search-paths.scm search-paths: Allow specs with #f as their separator. 2017-01-23 22:23:41 +01:00
serialization.scm serialization: Remove Guile < 2.0.9 workaround. 2017-04-17 23:31:28 +02:00
sets.scm
…
ssh.scm ssh: Improve error reporting when 'send-files' fails. 2017-06-04 23:00:32 +02:00
store.scm store: Add missing import. 2017-10-07 17:08:32 +02:00
svn-download.scm guix: Add download-svn-to-store. 2017-06-15 17:03:14 +02:00
tests.scm store: 'GUIX_DAEMON_SOCKET' can now be a URI. 2017-04-21 17:23:37 +02:00
ui.scm ui: Improve reporting of missing closing parentheses. 2017-10-10 23:12:03 +02:00
upstream.scm guix: lint: Add checker for new upstream versions. 2017-10-09 14:05:17 +03:00
utils.scm Add (guix progress). 2017-10-19 23:21:49 +02:00
workers.scm scripts: Set thread names. 2017-05-28 23:13:39 +02:00
zlib.scm zlib: Fix memory leak due to revealed ports not being GC'd. 2017-10-11 15:20:50 +02:00