cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/x86_64-pc-linux-gnu-g++ -D_FILE_OFFSET_BITS=64 -DNDEBUG -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools.cpp Linking CXX executable /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools-2.3.0 -rdynamic /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools-utils.a -ljsoncpp /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so.2.3.0 -lz -Wl,-rpath,/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib: CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o: In function `BamTools::FilterTool::FilterToolPrivate::ParseFilterObject(std::string const&, Json::Value const&)': bamtools_filter.cpp:(.text+0x5466): undefined reference to `Json::Value::operator=(Json::Value const&)' collect2: error: ld returned 1 exit status src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:412: recipe for target '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools-2.3.0' failed make[2]: *** [/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools-2.3.0] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build' CMakeFiles/Makefile2:399: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/all' failed make[1]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build' Makefile:116: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-biology/bamtools-2.3.0::gentoo failed (compile phase): * emake failed *
Created attachment 403750 [details] build.log
Replicated this build failure with the dev-libs/jsoncpp-1.6.2 It built fine with 0.10.1 & 0.10.2 Plan: file upstream to inform build fails with proof of replication using dep dev-libs/jsoncpp-1.6.2. You can add to URL: if you have permissions otherwise add it in a Comment and I can add it there. For now prepare a unified diff setting >=dev-libs/jsoncpp-0.5.0-r1 <~dev-libs/jsoncpp-1.0 *bamtools-2.3.0 (17 Sep 2013) it needs a new release to keep up with the advance in dev-libs/jsoncpp-1.6.2
Hi Ian, I do not understand whether you are going to do the work or not. ;-) Please note there is also bamtools-9999.ebuild in science overlay. Would be great if you could adjust the ebuild DEPs. Martin
(In reply to Martin Mokrejš from comment #3) > Hi Ian, > I do not understand whether you are going to do the work or not. ;-) I can only conclude I didn't make myself clear. I am always prepared to do the 'work' to make a commit on behalf of a user. I asked you to follow / execute the steps of Plan: It appears upstream have used <=dev-libs/jsoncpp-1.0 and either have not indicated that jsoncpp-1.6.2 breaks the build, or it is mentioned in notes and you haven't noticed or found it. It is not normal or acceptable for the most recent version of a dep present in portage to be incompatible with build system of the package. The fix for now is to simply make a unified diff with the lines I have listed in Plan: Although it's a formality I'm simply adhering to the style roughly set by proxy-maint. Put it this way. If I fix it with that version bordering, my commit msg has to say something like; "fix to broken build by setting version bordering to jsoncpp, ascertained by me wrt bug #550144, upstream not notified re version incompatibility" It SHOULD read something like "fix to broken build by setting version bordering, patch provided by proxy maintainer in bug #550144, issue filed upstream, fixes said bug" Currently I have no such patch. Attaching the patch is a 2 minute job but yes I can simply commit what I have already determined. Filing upstream is a task commonly done by most keen informed users however I have no prior dealings with you and don't know what you do and don't know. Feel free to inform me. A a user it's 'reasonable' that you've not covered these things yet. I simply don't know. > Please note there is also bamtools-9999.ebuild in science overlay. Would be > great if you could adjust the ebuild DEPs. > Martin I have no dealings with the science overlay therefore cannot commit to it. That is the realm of the science or sci-biology herd. As luck would have it none of them have taken the slightest notice but I have.
added a minimal bug report upstream: https://github.com/pezmaster31/bamtools/issues/108 (btw, 2.4.0 is out - should I file the patch here or on ::science?)
* commit a1fa6d43da19c366f38412fc7760186e3b68e708 * Author: Justin Lecher <jlec@gentoo.org> * Date: Sun Aug 16 13:18:23 2015 +0200 * * sci-biology/bamtools: Restrict Version of dev-libs/jsoncpp in deps, bug #550144 https://github.com/pezmaster31/bamtools/issues/108 * * Package-Manager: portage-2.2.20.1 * Signed-off-by: Justin Lecher <jlec@gentoo.org>
REOPENing, I get this still with jsoncpp-0.10.1: # emerge -pv jsoncpp These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] dev-libs/jsoncpp-0.10.2-r1::gentoo [0.10.1::gentoo] USE="-doc {-test}" 193 KiB # [100%] Linking CXX executable /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools-2.3.0 -rdynamic /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools-utils.a -ljsoncpp /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so.2.3.0 -lz -Wl,-rpath,/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib: CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o: In function `BamTools::FilterTool::FilterToolPrivate::ParseFilterObject(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Json::Value const&)': bamtools_filter.cpp:(.text+0x6ed6): undefined reference to `Json::Value::get(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Json::Value const&) const' bamtools_filter.cpp:(.text+0x6f14): undefined reference to `Json::Value::asString[abi:cxx11]() const' CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o: In function `BamTools::FilterTool::FilterToolPrivate::ParseScript()': bamtools_filter.cpp:(.text+0x808d): undefined reference to `Json::Reader::parse(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Json::Value&, bool)' bamtools_filter.cpp:(.text+0x80ae): undefined reference to `Json::Reader::getFormatedErrorMessages[abi:cxx11]() const' bamtools_filter.cpp:(.text+0x837c): undefined reference to `Json::Value::asString[abi:cxx11]() const' bamtools_filter.cpp:(.text+0x8905): undefined reference to `Json::Value::asString[abi:cxx11]() const' collect2: error: ld returned 1 exit status src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:434: recipe for target '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/bin/bamtools-2.3.0' failed Seems there is a typo, Justin, in the upstream https://github.com/pezmaster31/bamtools/issues/108 bug. Seems you wanted the following? -0.5.0 < jsoncpp < 1.0 is required -0.5.0 >= jsoncpp < 1.0 is required Or version number sorting issue in Gentoo ebuilds? 0.10 not being higher than 0.5?
(In reply to Michael Schubert from comment #5) > added a minimal bug report upstream: > https://github.com/pezmaster31/bamtools/issues/108 > > (btw, 2.4.0 is out - should I file the patch here or on ::science?) commit 778b9cad7be047675ab8b1c8b0d54e5f4f2c7f4c Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> Date: Fri Apr 1 01:10:46 2016 +0200 sci-biology/bamtools: version bump; still suffers gentoo bug #550144
commit 72bcf8aa8b3c95da31c4ae6bf4ccec376a7ec3ea Author: David Seifert <soap@gentoo.org> Date: Wed Dec 14 23:42:36 2016 +0100 sci-biology/bamtools: Version bump to 2.4.1 Gentoo-bug: 550144, 596208 * Make C++ mode agnostic * Unbundle jsoncpp and use more modern versions
