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Bug 1606895
Summary: | ncbi-blast+: FTBFS in Fedora 29: c++/src/corelib/test_boost.cpp:73:10: fatal error: boost/test/test_observer.hpp: No such file or directory | ||||||||||
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Product: | [Fedora] Fedora | Reporter: | Mohan Boddu <mboddu> | ||||||||
Component: | ncbi-blast+ | Assignee: | Jan Kaluža <jkaluza> | ||||||||
Status: | CLOSED EOL | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||
Severity: | unspecified | Docs Contact: | |||||||||
Priority: | unspecified | ||||||||||
Version: | 29 | CC: | jkaluza, ppisar, releng | ||||||||
Target Milestone: | --- | ||||||||||
Target Release: | --- | ||||||||||
Hardware: | Unspecified | ||||||||||
OS: | Unspecified | ||||||||||
Whiteboard: | |||||||||||
Fixed In Version: | Doc Type: | If docs needed, set a value | |||||||||
Doc Text: | Story Points: | --- | |||||||||
Clone Of: | Environment: | ||||||||||
Last Closed: | 2019-08-08 13:21:55 UTC | Type: | --- | ||||||||
Regression: | --- | Mount Type: | --- | ||||||||
Documentation: | --- | CRM: | |||||||||
Verified Versions: | Category: | --- | |||||||||
oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||||||
Cloudforms Team: | --- | Target Upstream Version: | |||||||||
Embargoed: | |||||||||||
Bug Depends On: | |||||||||||
Bug Blocks: | 1602938, 1674516 | ||||||||||
Attachments: |
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Description
Mohan Boddu
2018-07-20 22:09:32 UTC
Created attachment 1469549 [details]
build.log
Created attachment 1469550 [details]
root.log
file root.log too big, will only attach last 32768 bytes
Created attachment 1469551 [details]
state.log
This bug appears to have been reported against 'rawhide' during the Fedora 29 development cycle. Changing version to '29'. + ./configure --build=ppc64-redhat-linux-gnu --host=ppc64-redhat-linux-gnu --program-prefi x= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbin dir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/u sr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir =/usr/share/man --infodir=/usr/share/info --with-dll --with-mt --without-autodep --without -makefile-auto-update --with-flat-makefile --without-caution --without-dbapi --without-lzo --with-runpath=/usr/lib64/ncbi-blast+ --with-build-root=BUILD --without-strip --with-symb ols configure: error: --program-prefix=: unknown option; use --help to show usage configure: error: --disable-dependency-tracking: unknown option; use --help to show usage configure: error: --sbindir=/usr/sbin: unknown option; use --help to show usage configure: error: --sysconfdir=/etc: unknown option; use --help to show usage configure: error: --datadir=/usr/share: unknown option; use --help to show usage configure: error: --libexecdir=/usr/libexec: unknown option; use --help to show usage configure: error: --localstatedir=/var: unknown option; use --help to show usage configure: error: --sharedstatedir=/var/lib: unknown option; use --help to show usage configure: error: --mandir=/usr/share/man: unknown option; use --help to show usage configure: error: --infodir=/usr/share/info: unknown option; use --help to show usage configure: creating cache config.cache [...] configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++ 8 error: Bad exit status from /var/tmp/rpm-tmp.16zHQU (%build) *** Bug 1675442 has been marked as a duplicate of this bug. *** > configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++ 8
I fixed this error by porting an upstream fix for checking GCC version. I pushed to fix into master branch as 6b39dc33867a0e81cea50bed29f80c02c1c12bad commit.
But there is another error: There seems to be change between Boost 1.58 and 1.59 causing failure of building the tests:
make[1]: Entering directory '/home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/BUILD/build/corelib'
/usr/bin/g++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-narrowing -D_MT -D_REENTRANT -D_THREAD_SAFE -I/home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/BUILD/inc -I/home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/include /home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/src/corelib/test_boost.cpp -o test_boost.o
/home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/src/corelib/test_boost.cpp:73:10: fatal error: boost/test/test_observer.hpp: No such file or directory
73 | #include <boost/test/test_observer.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I tried to port the code from 2.9.0, but I ended up with: In file included from /home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/src/corelib /test_boost.cpp:50: /home/test/fedora/ncbi-blast+/ncbi-blast-2.2.31+-src/c++/include/corelib/test_boost.hpp:78 8:53: error: 'boost::unit_test::decorator::collector' has not been declared 788 | boost::unit_test::decorator::collector& decorator) | ^~~~~~~~~ I really recommend rebasing to 2.9.0 (if it helps). I will left it to the maintainer as I'm not going to spent my time with reviewing 286 MB of source code. Dear Maintainer, your package has not been built successfully in 30. Action is required from you. If you can fix your package to build, perform a build in koji, and either create an update in bodhi, or close this bug without creating an update, if updating is not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to acknowledge this. Following the latest policy for such packages [2], your package can be orphaned if this bug remains in NEW state more than 8 weeks. A week before the mass branching of Fedora 31 according to the schedule [3], any packages which still have open FTBFS bugs from Fedora 30 will be retired. [1] https://fedoraproject.org/wiki/Updates_Policy [2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [3] https://fedoraproject.org/wiki/Releases/31/Schedule Dear Maintainer, your package has not been built successfully in 30. Action is required from you. If you can fix your package to build, perform a build in koji, and either create an update in bodhi, or close this bug without creating an update, if updating is not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to acknowledge this. Following the latest policy for such packages [2], your package can be orphaned if this bug remains in NEW state more than 8 weeks. A week before the mass branching of Fedora 31 according to the schedule [3], any packages which still have open FTBFS bugs from Fedora 30 will be retired. [1] https://fedoraproject.org/wiki/Updates_Policy [2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [3] https://fedoraproject.org/wiki/Releases/31/Schedule Dear Maintainer, your package has not been built successfully in 30. Action is required from you. If you can fix your package to build, perform a build in koji, and either create an update in bodhi, or close this bug without creating an update, if updating is not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to acknowledge this. Following the latest policy for such packages [2], your package can be orphaned if this bug remains in NEW state more than 8 weeks. A week before the mass branching of Fedora 31 according to the schedule [3], any packages which still have open FTBFS bugs from Fedora 30 will be retired. [1] https://fedoraproject.org/wiki/Updates_Policy [2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [3] https://fedoraproject.org/wiki/Releases/31/Schedule Dear Maintainer, your package has not been built successfully in 30. Action is required from you. If you can fix your package to build, perform a build in koji, and either create an update in bodhi, or close this bug without creating an update, if updating is not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to acknowledge this. Following the latest policy for such packages [2], your package can be orphaned if this bug remains in NEW state more than 8 weeks. A week before the mass branching of Fedora 31 according to the schedule [3], any packages which still have open FTBFS bugs from Fedora 30 will be retired. [1] https://fedoraproject.org/wiki/Updates_Policy [2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [3] https://fedoraproject.org/wiki/Releases/31/Schedule The package was retired. |