Closed tmozgach closed 7 years ago
@sjackman could you please look at? 1 month ago it worked. May be it is really better to use structure of the following image? https://hub.docker.com/r/bioperl/bioperl-deps/~/dockerfile/
Failed 10/325 test programs. 0/17866 subtests failed.
Looks like the first failed test is t/LocalDB/Fasta.t:27
------------- EXCEPTION -------------
MSG: Could not open index file /tmp/NsAzDID6hk/dbfa/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Fasta.t:27
-------------------------------------
# Looks like your test exited with 2 before it could output anything.
t/LocalDB/Fasta.t ......................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 109/109 subtests
BDB1557 library build did not include support for cryptography
: No such file or directory
Start an interactive container from the Docker image right before this failure, and confirm that you can reproduce the failure interactively.
Google the above error message, and see what you can find.
@sjackman That error was produced interactively. I didn't find anything in Google except that
Sometimes you may see a failed test. Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a failed test may not affect your usage of BioPerl.
If there’s a failed test and you think that the failed test will not affect how you intend to use BioPerl then do
`cpan>force install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz`
I wouldn't be very comfortable with force installing, since we don't yet know whether it affects the functionality of BioPerl. There should hopefully be a more detailed log giving a more informative error message. Perhaps the failure is related to this message:
BDB1557 library build did not include support for cryptography
Googling "library build did not include support for cryptography"
(with quotes)
suggests that it may be a problem with berkeley-db
, which I'm guessing is a dependency of t/LocalDB/Fasta.t
.
That's a berkeley-db
error message:
https://github.com/berkeleydb/libdb/blob/master/src/env/env_method.c#L816
The berkeley-db
bottle does not appear to have cryptography support.
I tried brew install -s berkeley-db
The problem is…
checking if --with-cryptography option specified... no
https://gist.github.com/anonymous/db85021ee01c0daff2849620709b3a8c#file-01-configure-L66
@tmozgach Can you see if adding configure --with-cryptography
to the berkeley-db
formula helps?
If it does, please open a PR against berkeley-db
adding --with-cryptography
and bump the revision
.
Install perl
from the source, install Bio::Perl
=> succeed
Install perl
from the bottle, install Bio::Perl
=> failed
Install previous version berkley-db
, Install perl
from the bottle, install Bio::Perl
=> succeed
Rebuild bottle of perl
fixes the problem.
One month ago it worked.
on docker2, run
docker run -ti 24b21f10017c
thencpanm -i Bio::Root::Version
The following log: