Your message dated Wed, 22 May 2013 13:02:47 +0000 with message-id <[email protected]> and subject line Bug#687968: fixed in cufflinks 2.1.1-1 has caused the Debian Bug report #687968, regarding New upstream version to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 687968: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=687968 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: cufflinks Version: 1.3.0-2 Severity: wishlist Tags: patch Hi team, here at European Institute of Oncology we managed to upgrade cufflinks packaging to 2.0.2 version (current stable), starting from your good work. Here is the changelog: * New upstream release * Adding libeigen3-dev to Build-Depends * Hardened build * Fixed autoconf stuff (eigen-related) * Parallel compile We attach the relevant patch, we would be glad if you could consider to adopt and release new version in debian. Bests, ale -- System Information: Debian Release: wheezy/sid APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 3.2.0-3-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages cufflinks depends on: ii dpkg 1.16.8 ii libboost-thread1.49.0 1.49.0-3.1 ii libc6 2.13-35 ii libgcc1 1:4.7.1-8 ii libstdc++6 4.7.1-8 ii python 2.7.3-2 ii zlib1g 1:1.2.7.dfsg-13 cufflinks recommends no packages. cufflinks suggests no packages. -- no debconf informationIndex: packages/cufflinks/trunk/debian/control =================================================================== --- packages/cufflinks/trunk/debian/control (revision 38) +++ packages/cufflinks/trunk/debian/control (revision 43) @@ -8,5 +8,6 @@ Charles Plessy <[email protected]> Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>=1.38.0), - libboost-thread-dev, libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~) + libboost-thread-dev, libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~), + hardening-wrapper, libeigen3-dev Standards-Version: 3.9.3 Homepage: http://cufflinks.cbcb.umd.edu/ Index: packages/cufflinks/trunk/debian/changelog =================================================================== --- packages/cufflinks/trunk/debian/changelog (revision 38) +++ packages/cufflinks/trunk/debian/changelog (revision 43) @@ -1,2 +1,13 @@ +cufflinks (2.0.2-0ieo1) unstable; urgency=low + + [ Alessandro -oggei- Ogier ] + * New upstream release + * Adding libeigen3-dev to Build-Depends + * Hardened build + * Fixed autoconf stuff (eigen-related) + * Parallel compile + + -- oggei <[email protected]> Mon, 17 Sep 2012 13:31:47 +0200 + cufflinks (1.3.0-2) unstable; urgency=low Index: packages/cufflinks/trunk/debian/patches/series =================================================================== --- packages/cufflinks/trunk/debian/patches/series (revision 38) +++ packages/cufflinks/trunk/debian/patches/series (revision 43) @@ -3,2 +3,3 @@ 0003-fix_includes_path.patch gcc-4.7.patch +wrong-assumptions Index: packages/cufflinks/trunk/debian/patches/wrong-assumptions =================================================================== --- packages/cufflinks/trunk/debian/patches/wrong-assumptions (revision 43) +++ packages/cufflinks/trunk/debian/patches/wrong-assumptions (revision 43) @@ -0,0 +1,32 @@ +Description: wrong assumptions on user intelligence + If I describe my eigen path to $dir, i don't really mean $dir/include + . + cufflinks (2.0.2-1) UNRELEASED; urgency=low + . + * New upstream release +Author: oggei <[email protected]> + +--- +The information above should follow the Patch Tagging Guidelines, please +checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here +are templates for supplementary fields that you might want to add: + +Origin: <vendor|upstream|other>, <url of original patch> +Bug: <url in upstream bugtracker> +Bug-Debian: http://bugs.debian.org/<bugnumber> +Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber> +Forwarded: <no|not-needed|url proving that it has been forwarded> +Reviewed-By: <name and email of someone who approved the patch> +Last-Update: <YYYY-MM-DD> + +--- cufflinks-2.0.2.orig/ax_check_eigen.m4 ++++ cufflinks-2.0.2/ax_check_eigen.m4 +@@ -50,7 +50,7 @@ succeeded=no + + dnl first we check the system location for eigen libraries + if test "$ac_eigen_path" != ""; then +-EIGEN_CPPFLAGS="-I$ac_eigen_path/include" ++EIGEN_CPPFLAGS="-I$ac_eigen_path" + else + for ac_eigen_path_tmp in /usr /usr/local /opt /opt/local ; do + if test -d "$ac_eigen_path_tmp/include/eigen" && test -r "$ac_eigen_path_tmp/include/eigen"; then Index: packages/cufflinks/trunk/debian/rules =================================================================== --- packages/cufflinks/trunk/debian/rules (revision 38) +++ packages/cufflinks/trunk/debian/rules (revision 43) @@ -4,6 +4,16 @@ #export DH_VERBOSE=1 +export DEB_BUILD_HARDENING=1 +export DEB_BUILD_HARDENING_FORMAT=0 +export DEB_BUILD_OPTIONS="parallel=$(shell getconf _NPROCESSORS_ONLN)" + %: dh $@ --with autoreconf + +override_dh_auto_configure: + dh_auto_configure -- --with-eigen=/usr/include/eigen3/ + +override_dh_auto_build: + dh_auto_build -- -j$(shell getconf _NPROCESSORS_ONLN) override_dh_auto_clean:
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--- Begin Message ---Source: cufflinks Source-Version: 2.1.1-1 We believe that the bug you reported is fixed in the latest version of cufflinks, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated cufflinks 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Wed, 22 May 2013 13:27:40 +0200 Source: cufflinks Binary: cufflinks Architecture: source amd64 Version: 2.1.1-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: cufflinks - Transcript assembly, differential expression and regulation for R Closes: 675985 687968 Changes: cufflinks (2.1.1-1) unstable; urgency=low . [Carlos Borroto] * New upstream release. * Added libeigen3-dev to build-deps. * Modified fix_includes_path to properly include Eigen library. * Bumped libboost-dev requirement to >= 1.47.0 . [ Alexandre Mestiashvili ] * Imported debian/patches/0004-fix-m64-usage-and-lfs.patch, Closes: #675985 . [ Andreas Tille ] * Upstream release 2.1.1 (+ adapted patches) Closes: #687968 * debian/control: - Removed: DM-Upload-Allowed - Standards-Version: 3.9.4 - Debhelper 9 (also d/compat) requires d/p/format-security.patch for hardening via --format-security - normalised format Checksums-Sha1: 086c53f21493475b09e0aab87ffe31b23e6ff3c3 1545 cufflinks_2.1.1-1.dsc 9c5bf3d3872e8dd358ba7d7407644ab2cbbfdcb6 705930 cufflinks_2.1.1.orig.tar.gz f44e124768943921d5810bebed80ce16c23c9d39 14050 cufflinks_2.1.1-1.debian.tar.gz 5c66d7766a871e6b9c55ca666437e1d590424113 983906 cufflinks_2.1.1-1_amd64.deb Checksums-Sha256: 33329b6d906f0d6cbb82b4291ba7d91e02d72562a5aa712477c6c10d38255c60 1545 cufflinks_2.1.1-1.dsc 9cbaf1d8f53aa53e6d6beec12420125ee487f9de520417a6b1add3306d01a81e 705930 cufflinks_2.1.1.orig.tar.gz 0c5f6bd027cf75c9ef9b88309caeff3bff97b34544825a8beb9f9947dea4b49e 14050 cufflinks_2.1.1-1.debian.tar.gz 9506792c9f8a680b852690c6be1ad976a0fa15ffc1c94b13e3f7e75e350e3590 983906 cufflinks_2.1.1-1_amd64.deb Files: 6ca329a736b03e74e2f2fb641d907d4f 1545 non-free/science optional cufflinks_2.1.1-1.dsc 3c1f34264122565b1697706a5f0fd242 705930 non-free/science optional cufflinks_2.1.1.orig.tar.gz dcbc95a1aea7377937b834733587f8c6 14050 non-free/science optional cufflinks_2.1.1-1.debian.tar.gz d5661f1d69fd6996a9a58306390bc81c 983906 non-free/science optional cufflinks_2.1.1-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iEYEARECAAYFAlGcv5cACgkQYDBbMcCf01prFgCfQu9fzkUgfeIJUo5fyGadc8cH 1rwAn1kxZkPlzP3pPTYGIWb5QOznBw4X =kykg -----END PGP SIGNATURE-----
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