--- Begin Message ---
Package: lintian
Version: 2.5.48
Severity: wishlist
Tags: patch
Hi,
Please find attached a patch which add the check of the canonical form
of the homepage field for Bioconductor R packages. It is similar to
the check for the CRAN packages already implemented in lintian.
Best,
Dylan
From f0d86d0cc54b1edde0b1ef643cc182969c7d6c46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dylan=20A=C3=AFssi?= <bob.dybian@gmail.com>
Date: Wed, 5 Oct 2016 22:55:29 +0200
Subject: [PATCH] c/fields: Tag non-canonical forms of Bioconductor homepage
---
checks/fields.desc | 15 +++++++++++++++
checks/fields.pm | 4 ++++
.../debian/debian/control.in | 16 ++++++++++++++++
t/tests/fields-bioconductor-homepage/desc | 4 ++++
t/tests/fields-bioconductor-homepage/tags | 2 ++
5 files changed, 41 insertions(+)
create mode 100644 t/tests/fields-bioconductor-homepage/debian/debian/control.in
create mode 100644 t/tests/fields-bioconductor-homepage/desc
create mode 100644 t/tests/fields-bioconductor-homepage/tags
diff --git a/checks/fields.desc b/checks/fields.desc
index a8143f6..7df3dee 100644
--- a/checks/fields.desc
+++ b/checks/fields.desc
@@ -1318,3 +1318,18 @@ Info: The Homepage field for this package points to an uncanonical CRAN URL.
not:
.
https://cran.r-project.org/web/packages/foo/index.html
+
+Tag: homepage-for-bioconductor-package-not-canonical
+Severity: wishlist
+Certainty: certain
+Info: The Homepage field for this package points to an uncanonical Bioconductor URL.
+ Please update to use the current canonical URL instead. The canonical URL is
+ recommended for use in publications, etc., will always redirect to current
+ release version (or devel if package is not in release yet). For example, the
+ link for the package "foo" should be:
+ .
+ https://bioconductor.org/packages/foo/
+ .
+ not:
+ .
+ https://www.bioconductor.org/packages/(release|devel|*)/bioc/html/foo.html
diff --git a/checks/fields.pm b/checks/fields.pm
index 66b8d77..4d7343c 100644
--- a/checks/fields.pm
+++ b/checks/fields.pm
@@ -619,6 +619,10 @@ sub run {
if ($homepage=~ m,/cran\.r-project\.org/web/packages/.+,){
tag 'homepage-for-cran-package-not-canonical', $orig;
}
+ if ($homepage=~ m,bioconductor\.org/packages/.*/bioc/html/.*\.html*$,)
+ {
+ tag 'homepage-for-bioconductor-package-not-canonical', $orig;
+ }
} elsif (not $info->native) {
if ($type eq 'source') {
my $binary_has_homepage_field = 0;
diff --git a/t/tests/fields-bioconductor-homepage/debian/debian/control.in b/t/tests/fields-bioconductor-homepage/debian/debian/control.in
new file mode 100644
index 0000000..385c886
--- /dev/null
+++ b/t/tests/fields-bioconductor-homepage/debian/debian/control.in
@@ -0,0 +1,16 @@
+Source: {$source}
+Priority: extra
+Section: {$section}
+Maintainer: {$author}
+Standards-Version: {$standards_version}
+Build-Depends: {$build_depends}
+Homepage: https://www.bioconductor.org/packages/release/bioc/html/foo.html
+
+Package: {$source}
+Architecture: {$architecture}
+Depends: $\{shlibs:Depends\}, $\{misc:Depends\}
+Description: {$description}
+ This is a test package designed to exercise some feature or tag of
+ Lintian. It is part of the Lintian test suite and may do very odd
+ things. It should not be installed like a regular package. It may
+ be an empty package.
\ No newline at end of file
diff --git a/t/tests/fields-bioconductor-homepage/desc b/t/tests/fields-bioconductor-homepage/desc
new file mode 100644
index 0000000..aeea583
--- /dev/null
+++ b/t/tests/fields-bioconductor-homepage/desc
@@ -0,0 +1,4 @@
+Testname: fields-bioconductor-homepage
+Version: 1.0
+Description: Bioconductor Homepage URLs should be canonical
+Test-For: homepage-for-bioconductor-package-not-canonical
\ No newline at end of file
diff --git a/t/tests/fields-bioconductor-homepage/tags b/t/tests/fields-bioconductor-homepage/tags
new file mode 100644
index 0000000..b539a90
--- /dev/null
+++ b/t/tests/fields-bioconductor-homepage/tags
@@ -0,0 +1,2 @@
+I: fields-bioconductor-homepage source: homepage-for-bioconductor-package-not-canonical https://www.bioconductor.org/packages/release/bioc/html/foo.html
+I: fields-bioconductor-homepage: homepage-for-bioconductor-package-not-canonical https://www.bioconductor.org/packages/release/bioc/html/foo.html
--
2.1.4
--- End Message ---
--- Begin Message ---
Source: lintian
Source-Version: 2.5.49
We believe that the bug you reported is fixed in the latest version of
lintian, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 839874@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Niels Thykier <niels@thykier.net> (supplier of updated lintian package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sat, 22 Oct 2016 13:42:28 +0000
Source: lintian
Binary: lintian
Architecture: source
Version: 2.5.49
Distribution: unstable
Urgency: medium
Maintainer: Debian Lintian Maintainers <lintian-maint@debian.org>
Changed-By: Niels Thykier <niels@thykier.net>
Description:
lintian - Debian package checker
Closes: 731987 839874 840009 841000 841356 841442 841455
Changes:
lintian (2.5.49) unstable; urgency=medium
.
* Summary of tag changes:
+ Added:
- homepage-for-bioconductor-package-not-canonical
.
* checks/debhelper.desc:
+ [CL] Drop double leading spaces in includes-maint-script-parameters
paragraph that was causing indentation when rendered on lintian.d.o.
* checks/fields.{pm,desc}:
+ [NT] Apply patch from Dylan Aïssi to tag non-canonical uses of
the bioconductor homepage in the Homepage field. (Closes: #839874)
+ [JW] Apply patch from Dylan Aïssi to tag r-other packages not in
section "gnu-r". (Closes: #841455)
* checks/init.d.pm:
+ [JW] Don't require version constraint for lsb-base dependencies.
The needed version has been available for many stable releases.
* checks/shared-libs.pm:
+ [JW] Don't complain about executable bit for ld.so shipped in
multi-arch directories.
+ [JW] Don't complain about missing SONAME for position-independent
executables. Thanks to Reuben Thomas for the bug report.
(Closes: #731987)
+ [JW] Check for PT_GNU_STACK existence on all architectures.
* checks/source-copyright.pm:
+ [RA, JW] Fix handling punctuation characters in license expressions
in machine-readable copyright files. (Closes: #841356)
* checks/watch-file.pm:
+ [JW] Assume that watch files containing the pgpmode option (different
than "none") verify upstream signature. Thanks to Robert Luberda for
the bug report. (Closes: #841000)
.
* data/cruft/non-distributable-files:
+ [BR] Add some rapidjson files.
* data/debhelper/compat-level:
+ [NT] Bump the deprecated debhelper compat level to match the one
in debhelper.
* data/files/privacy-breaker-tag-attr:
+ [BR] Apply patch from Frederic Bonnard detecting audio tags.
(Closes: #840009)
* data/spelling/corrections*:
+ [JW, PW] Add more corrections.
.
* lib/Lintian/Unpacker.pm:
+ [NT] Use the new "do_fork()" sub to ensure works do not inherit
the default signal handler, which could allow any number of workers
to promote themselves to independent "masters" - effectively
creating a fork-bomb with an ill-timed signal.
* lib/Lintian/Util.pm:
+ [NT] Add a "do_fork()" sub to ensure signal handling is
reset for child processes.
.
* t/tests/shared-libs-non-pic-i386/debian/Makefile:
+ [JW] Pass -fno-PIE and -fno-pie to GCC, so that the test works even
when the compiler enables PIE by default. (Closes: #841442)
Checksums-Sha1:
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43a7b19cbc81c1b5003c8312862f547af2f8cf33 1234964 lintian_2.5.49.tar.xz
Checksums-Sha256:
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29118b03d38db0ba7342399c83322f26a794fc7b206628823ff6f523ed990289 1234964 lintian_2.5.49.tar.xz
Files:
929ceae1648664bef60ac0f85f30f2e9 2781 devel optional lintian_2.5.49.dsc
8cbe59f1d430f1f0008262ceaf46d4a4 1234964 devel optional lintian_2.5.49.tar.xz
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