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bcgsc / orca

:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
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Address failed tests #94

Closed sjackman closed 5 years ago

sjackman commented 5 years ago

See https://cloud.docker.com/u/bcgsc/repository/registry-1.docker.io/bcgsc/orca/builds/1800f55e-41da-4adb-930a-aaedbc6d6322

sjackman commented 5 years ago 
+ brew linkage --test emboss
Unwanted system libraries:
/lib/x86_64-linux-gnu/libsystemd.so.0
sjackman commented 5 years ago 
+ brew linkage --test mothur
Missing libraries:
libboost_iostreams.so.1.67.0
libreadline.so.7
sjackman commented 5 years ago 
+ brew linkage --test openjdk
Missing libraries:
libasound.so.2
libawt.so
libawt_xawt.so
libjava.so
libjvm.so
Unwanted system libraries:
/lib/x86_64-linux-gnu/libthread_db.so.1
sjackman commented 5 years ago 
+ brew linkage --test protobuf
Conflicting libraries:
python
python@2
sjackman commented 5 years ago 
+ brew linkage --test squeakr
Missing libraries:
libboost_system-mt.so.1.67.0
libboost_thread-mt.so.1.67.0
sjackman commented 5 years ago 
+ brew linkage --test xssp
Missing libraries:
libboost_filesystem.so.1.67.0
libboost_iostreams-mt.so.1.67.0
libboost_program_options-mt.so.1.67.0
libboost_regex-mt.so.1.67.0
libboost_system.so.1.67.0
libboost_thread-mt.so.1.67.0
libboost_timer.so.1.67.0
libboost_unit_test_framework-mt.so.1.67.0
sjackman commented 5 years ago 
+ brew test abyss-explorer
Testing brewsci/bio/abyss-explorer
==> /home/linuxbrew/.linuxbrew/Cellar/abyss-explorer/1.3.4/bin/abyss-explorer --help
Picked up _JAVA_OPTIONS: -Duser.home=/root/.cache/Homebrew/java_cache
Error: brewsci/bio/abyss-explorer: failed
An exception occurred within a child process:
Test::Unit::AssertionFailedError: </Usage/> expected to be =~
<"">.
sjackman commented 5 years ago 
+ brew test bioperl
Testing brewsci/bio/bioperl
==> bp_biogetseq.pl -h </dev/null 2>&1
Error: brewsci/bio/bioperl: failed
An exception occurred within a child process:
Test::Unit::AssertionFailedError: <0> expected but was
<126>.
sjackman commented 5 years ago 
+ brew test boost
Testing boost
==> /home/linuxbrew/.linuxbrew/bin/g++ test.cpp -std=c++14 -stdlib=libc++ -o test
Last 15 lines from /root/.cache/Homebrew/Logs/boost/test.01.g++:
2019-05-10 19:07:46 +0000
/home/linuxbrew/.linuxbrew/bin/g++
test.cpp
-std=c++14
-stdlib=libc++
-o
test
g++: error: unrecognized command line option '-stdlib=libc++'
Error: boost: failed
sjackman commented 5 years ago 
+ brew test igvtools
Testing brewsci/science/igvtools
==> /home/linuxbrew/.linuxbrew/Cellar/igvtools/2.3.98/bin/igvtools
Last 15 lines from /root/.cache/Homebrew/Logs/igvtools/test.01.igvtools:
2019-05-10 19:23:39 +0000
/home/linuxbrew/.linuxbrew/Cellar/igvtools/2.3.98/bin/igvtools
Error: Unable to access jarfile /home/linuxbrew/.linuxbrew/Homebrew/Cellar/igvtools/2.3.98/libexec/igvtools.jar
Error: brewsci/science/igvtools: failed
sjackman commented 5 years ago 
+ brew test maker
Testing brewsci/bio/maker
==> /home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/bin/maker --version
Last 15 lines from /root/.cache/Homebrew/Logs/maker/test.01.maker:
2019-05-10 19:31:04 +0000
/home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/bin/maker
--version
/home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/bin/maker: /home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/libexec/bin/maker: /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/bin/perl: bad interpreter: No such file or directory
/home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/bin/maker: line 2: /home/linuxbrew/.linuxbrew/Cellar/maker/2.31.10/libexec/bin/maker: Success
Error: brewsci/bio/maker: failed
sjackman commented 5 years ago 
+ brew test mothur
Testing brewsci/bio/mothur
==> /home/linuxbrew/.linuxbrew/Cellar/mothur/1.40.3/bin/mothur -h
Last 15 lines from /root/.cache/Homebrew/Logs/mothur/test.01.mothur:
2019-05-10 19:33:47 +0000
/home/linuxbrew/.linuxbrew/Cellar/mothur/1.40.3/bin/mothur
-h
/home/linuxbrew/.linuxbrew/Cellar/mothur/1.40.3/bin/mothur: error while loading shared libraries: libreadline.so.7: cannot open shared object file: No such file or directory
Error: brewsci/bio/mothur: failed
sjackman commented 5 years ago 
+ brew test mrbayes
Testing brewsci/bio/mrbayes
==> /home/linuxbrew/.linuxbrew/Cellar/mrbayes/3.2.7/bin/mb primates.nex
Last 15 lines from /root/.cache/Homebrew/Logs/mrbayes/test.01.mb:
2019-05-10 19:34:09 +0000
/home/linuxbrew/.linuxbrew/Cellar/mrbayes/3.2.7/bin/mb
primates.nex
Error: brewsci/bio/mrbayes: failed
sjackman commented 5 years ago 
+ brew test nanopolish
Testing brewsci/bio/nanopolish
==> /home/linuxbrew/.linuxbrew/Cellar/nanopolish/0.10.2/bin/nanopolish --help
==> /home/linuxbrew/.linuxbrew/Cellar/nanopolish/0.10.2/bin/nanopolish extract -o out.fasta /home/linuxbrew/.linuxbrew/Cellar/nanopolish/0.10.2/share/nanopolish/test/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5 2>&1
Error: brewsci/bio/nanopolish: failed
An exception occurred within a child process:
Test::Unit::AssertionFailedError: <0> expected but was
<134>.
sjackman commented 5 years ago 
+ brew test nlopt
Testing nlopt
==> /home/linuxbrew/.linuxbrew/bin/gcc test.c -o test -L/home/linuxbrew/.linuxbrew/opt/nlopt/lib -lnlopt -lm
Last 15 lines from /root/.cache/Homebrew/Logs/nlopt/test.01.gcc:
/home/linuxbrew/.linuxbrew/opt/nlopt/lib/libnlopt.a(local.o): In function `local(Trial&, TBox&, TBox&, double, double*, Global&, int, RVector const&, nlopt_stopping*)':
local.cc:(.text+0xcfa): undefined reference to `std::cout'
local.cc:(.text+0xd06): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
local.cc:(.text+0xe4f): undefined reference to `std::cout'
local.cc:(.text+0xe5b): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
local.cc:(.text+0xe75): undefined reference to `operator delete[](void*)'
local.cc:(.text+0xe87): undefined reference to `operator delete[](void*)'
local.cc:(.text+0xea9): undefined reference to `operator delete[](void*)'
local.cc:(.text+0xebb): undefined reference to `operator delete[](void*)'
local.cc:(.text+0xecd): undefined reference to `operator delete[](void*)'
/home/linuxbrew/.linuxbrew/opt/nlopt/lib/libnlopt.a(local.o):local.cc:(.text+0xedf): more undefined references to `operator delete[](void*)' follow
/home/linuxbrew/.linuxbrew/opt/nlopt/lib/libnlopt.a(local.o): In function `_GLOBAL__sub_I_local.cc':
local.cc:(.text.startup+0xc): undefined reference to `std::ios_base::Init::Init()'
local.cc:(.text.startup+0x13): undefined reference to `std::ios_base::Init::~Init()'
collect2: error: ld returned 1 exit status
Error: nlopt: failed
sjackman commented 5 years ago 
+ brew test open-mpi
Testing open-mpi
==> /home/linuxbrew/.linuxbrew/Cellar/open-mpi/4.0.1_1/bin/mpicc hello.c -o hello
==> ./hello
==> /home/linuxbrew/.linuxbrew/Cellar/open-mpi/4.0.1_1/bin/mpirun ./hello
Last 15 lines from /root/.cache/Homebrew/Logs/open-mpi/test.03.mpirun:
mpirun has detected an attempt to run as root.
Running as root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.
We strongly suggest that you run mpirun as a non-root user.
You can override this protection by adding the --allow-run-as-root option
to the cmd line or by setting two environment variables in the following way:
the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this
protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and
add one more layer of certainty that you want to do so.
We reiterate our advice against doing so - please proceed at your own risk.
--------------------------------------------------------------------------
Error: open-mpi: failed
sjackman commented 5 years ago 
+ brew test squeakr
Testing brewsci/bio/squeakr
==> /home/linuxbrew/.linuxbrew/Cellar/squeakr/0.5_1/bin/squeakr-count -h 2>&1
Error: brewsci/bio/squeakr: failed
An exception occurred within a child process:
Test::Unit::AssertionFailedError: <0> expected but was
<127>.
sjackman commented 5 years ago 
+ brew test wiggletools
Testing brewsci/bio/wiggletools
==> python2 test.py
pgrep: write error: Bad file descriptor
Error: brewsci/bio/wiggletools: failed
An exception occurred within a child process:
Timeout::Error: execution expired
sjackman commented 5 years ago 
+ brew test xssp
Testing brewsci/bio/xssp
==> Downloading https://files.rcsb.org/download/3ZZZ.pdb.gz
==> /home/linuxbrew/.linuxbrew/Cellar/xssp/3.0.5/bin/mkdssp -i 3zzz.pdb -o /tmp/xssp-test-20190510-25137-2mss8/test.dssp
Last 15 lines from /root/.cache/Homebrew/Logs/xssp/test.01.mkdssp:
2019-05-10 20:02:47 +0000
/home/linuxbrew/.linuxbrew/Cellar/xssp/3.0.5/bin/mkdssp
-i
3zzz.pdb
-o
/tmp/xssp-test-20190510-25137-2mss8/test.dssp
/home/linuxbrew/.linuxbrew/Cellar/xssp/3.0.5/bin/mkdssp: error while loading shared libraries: libboost_iostreams-mt.so.1.67.0: cannot open shared object file: No such file or directory
Error: brewsci/bio/xssp: failed
sjackman commented 5 years ago

Skip the brew linkage --test failures for

Bump the revision and rebuild the bottle because of boost:

Skip the brew test failures for

lcoombe commented 5 years ago

For the bumping revisions -- just to ensure I understand properly -- This is just changing the revision in the formula, and doing the pull-request/publish bottle process again to rebuild the bottle with a newer boost version??

sjackman commented 5 years ago

Yes, that's right.

sjackman commented 5 years ago

In the latest bcgsc/orca-6 Docker image, for each of the brew test … failures, run the brew test yourself interactively, and if it passes (fails to replicate the test failure), add it to the list of ignored test failures.

lcoombe commented 5 years ago

All brew test.. failures but wiggletools also failed the interactive brew test

sjackman commented 5 years ago

mrbayes

$ /home/linuxbrew/.linuxbrew/Cellar/mrbayes/3.2.7/bin/mb
Illegal instruction (core dumped)
$ gdb /home/linuxbrew/.linuxbrew/Cellar/mrbayes/3.2.7/bin/mb core.*
(gdb) x/i $pc
=> 0x49a50b <SetUpMoveTypes+235>:   
    vmovsd 0x751d3(%rip),%xmm18        # 0x50f6e8

So this bottle is using the AVX instruction vmovsd. It's not supposed, but it can be hard to prevent. I suggest ignoring this test failure.

lcoombe commented 5 years ago

Nanopolish Looks like the second test fails:

root@34b05582f87b:/home/linuxbrew# nanopolish extract -o out.fasta /home/linuxbrew/.linuxbrew/Cellar/nanopolish/0.10.2/share/nanopolish/test/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5 2>&1
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
...
root@34b05582f87b:/home/linuxbrew# echo $?
134

EDIT: Saw your update on the summary comment.

sjackman commented 5 years ago

@lcoombe Please update abricate to version 0.8.13. That should hopefully resolve the brew postinstall abricate issue.

lcoombe commented 5 years ago

@lcoombe Please update abricate to version 0.8.13. That should hopefully resolve the brew postinstall abricate issue.

For sure! I'll get on that update now.

sjackman commented 5 years ago

These sixteen issues have been addressed! Thank you, Lauren!