Your message dated Tue, 09 Mar 2021 19:33:25 +0000
with message-id <[email protected]>
and subject line Bug#984889: fixed in assembly-stats 1.0.1+ds-3
has caused the Debian Bug report #984889,
regarding assembly-stats natively FTBFS: error: gtest/gtest.h: No such file or
directory
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
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
984889: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984889
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: assembly-stats
Version: 1.0.1+ds-2
Severity: important
X-Debbugs-Cc: [email protected]
Control: tags -1 patch
Dear Maintainer,
assembly-stats natively FTBFS reason being it forcefully compiles test
files, while the test dependency libgtest-dev is annotated with <!nocheck>
It should respect the nocheck option, and not compile the test files in
such a case.
In order to reproduce this, pass DEB_BUILD_OPTIONS=nocheck and set build
profile to nocheck as well. With sbuild:
$ DEB_BUILD_OPTIONS=nocheck sbuild -j5 -d unstable --source-only-changes
--run-lintian --lintian-opts='--color always --display-info
--display-experimental --pedantic' --profiles=nocheck
and it results in error:
/usr/bin/c++ -I/usr/include/gtest -Wall -O3 -pthread -o
CMakeFiles/runUnitTests.dir/stats_unittest.cpp.o -c
/<<PKGBUILDDIR>>/stats_unittest.cpp
/<<PKGBUILDDIR>>/filetype_unittest.cpp:2:10: fatal error: gtest/gtest.h: No
such file or directory
2 | #include "gtest/gtest.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [CMakeFiles/runUnitTests.dir/build.make:111:
CMakeFiles/runUnitTests.dir/filetype_unittest.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/<<PKGBUILDDIR>>/stats_unittest.cpp:2:10: fatal error: gtest/gtest.h: No such
file or directory
2 | #include "gtest/gtest.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
/<<PKGBUILDDIR>>/fastq_unittest.cpp:5:10: fatal error: gtest/gtest.h: No such
file or directory
5 | #include "gtest/gtest.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [CMakeFiles/runUnitTests.dir/build.make:124:
CMakeFiles/runUnitTests.dir/stats_unittest.cpp.o] Error 1
make[3]: *** [CMakeFiles/runUnitTests.dir/build.make:98:
CMakeFiles/runUnitTests.dir/fastq_unittest.cpp.o] Error 1
/<<PKGBUILDDIR>>/fasta_unittest.cpp:3:10: fatal error: gtest/gtest.h: No such
file or directory
3 | #include "gtest/gtest.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [CMakeFiles/runUnitTests.dir/build.make:85:
CMakeFiles/runUnitTests.dir/fasta_unittest.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:251: CMakeFiles/runUnitTests.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
The patch for the same is given below:
diff --git a/debian/patches/do-not-test-forcefully.patch
b/debian/patches/do-not-test-forcefully.patch
new file mode 100644
index 0000000..1fc749f
--- /dev/null
+++ b/debian/patches/do-not-test-forcefully.patch
@@ -0,0 +1,23 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -5,11 +5,15 @@
+
+ file(COPY test_files DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+ #add_subdirectory(gtest-1.7.0)
+-enable_testing()
+-include_directories(/usr/include/gtest)
+-add_executable(runUnitTests fasta_unittest.cpp fastq_unittest.cpp
filetype_unittest.cpp stats_unittest.cpp)
+-target_link_libraries(runUnitTests gtest gtest_main fasta fastq filetype
stats)
+-add_test(runUnitTests runUnitTests)
++option(BUILD_TESTS "Parameter to enable/disable build time tests" ON)
++
++if(BUILD_TESTS)
++ enable_testing()
++ include_directories(/usr/include/gtest)
++ add_executable(runUnitTests fasta_unittest.cpp fastq_unittest.cpp
filetype_unittest.cpp stats_unittest.cpp)
++ target_link_libraries(runUnitTests gtest gtest_main fasta fastq
filetype stats)
++ add_test(runUnitTests runUnitTests)
++endif()
+
+ add_library(fasta fasta.cpp)
+ add_library(fastq fastq.cpp)
diff --git a/debian/patches/series b/debian/patches/series
index 9fc23ad..49aafd6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
use_debian_packages_gtest.patch
+do-not-test-forcefully.patch
diff --git a/debian/rules b/debian/rules
index aae41d2..9f13e4b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,5 +11,8 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
+override_dh_auto_configure:
+ dh_auto_configure -- -DBUILD_TESTS=$(if $(filter
nocheck,$(DEB_BUILD_OPTIONS)),OFF,ON)
+
override_dh_auto_install:
dh_install obj-$(DEB_BUILD_GNU_TYPE)/assembly-stats usr/bin
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 5.7.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: unable to detect
Versions of packages assembly-stats depends on:
ii libc6 2.31-3
ii libgcc-s1 11-20210220-1
ii libstdc++6 11-20210220-1
assembly-stats recommends no packages.
assembly-stats suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: assembly-stats
Source-Version: 1.0.1+ds-3
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
assembly-stats, 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.
Nilesh Patra <[email protected]> (supplier of updated assembly-stats 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: SHA512
Format: 1.8
Date: Wed, 10 Mar 2021 00:39:38 +0530
Source: assembly-stats
Architecture: source
Version: 1.0.1+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 984889 984890
Changes:
assembly-stats (1.0.1+ds-3) unstable; urgency=medium
.
* Team Upload.
[ Andreas Tille ]
* No publication found, Add conda-id
.
[ Nilesh Patra ]
* Do not forcefully compile tests (Closes: #984889)
* Use DEB_HOST_GNU_TYPE instead of DEB_BUILD_GNU_TYPE
(Closes: #984890)
* Add debug flag
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