Bio-RetrieveAssemblies-1.0.1 fails to install

[tseemann]

I note in the manual you use "cpan -f" to force install.
I didn't use it - and this happened:
Do I need to force?

AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
  /bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/*.t t/Bio/RetrieveAssemblies/*.t
t/Bio/RetrieveAssemblies.t ................ 1/? Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 2/?
#   Failed test 'Expected file for command -q Mycobacterium -a -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'
#   at t/lib/TestHelper.pm line 31.
Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 3/?
#   Failed test 'Expected file for command -q Mycobacterium -f fasta PRJEB8877 exists: downloaded_files/CVMX01.1.fsa_nt.gz'
#   at t/lib/TestHelper.pm line 31.
Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 4/?
#   Failed test 'Expected file for command -q Mycobacterium -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'
#   at t/lib/TestHelper.pm line 31.
Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 5/?
#   Failed test 'Expected file for command -q Mycobacterium -o my_dir PRJEB8877 exists: my_dir/CVMX01.1.gbff.gz'
#   at t/lib/TestHelper.pm line 31.
Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 6/?
#   Failed test 'Expected file for command -q Mycobacterium PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz'
#   at t/lib/TestHelper.pm line 31.
# Looks like you failed 5 tests of 6.
t/Bio/RetrieveAssemblies.t ................ Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/6 subtests
t/Bio/RetrieveAssemblies/AccessionFile.t .. ok
t/Bio/RetrieveAssemblies/RefWeak.t ........ ok
t/Bio/RetrieveAssemblies/WGS.t ............ ok
t/requires_external.t ..................... ok

Test Summary Report
-------------------
t/Bio/RetrieveAssemblies.t              (Wstat: 1280 Tests: 6 Failed: 5)
  Failed tests:  2-6
  Non-zero exit status: 5
Files=5, Tests=33, 95 wallclock secs ( 0.02 usr  0.01 sys +  1.40 cusr  0.20 csys =  1.63 CPU)
Result: FAIL
Failed 1/5 test programs. 5/33 subtests failed.
make: *** [test_dynamic] Error 255
  AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
  /bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
Stopping: 'install' failed for 'A/AJ/AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz'.

[andrewjpage]

Hi Torsten,
The tests try to connect to NCBI's live site so failures can be one of two
things:
1.) NCBI is down or your institution has been blocked,
2.) the software doesn't work through proxies (yet).

Its supposed to pick up proxy settings using HTTP_PROXY, but I've found it
doesnt, and havent had time to make it work. Sorry,
Andrew

On 14 June 2015 at 00:52, Torsten Seemann notifications@github.com wrote:

I note in the manual you use "cpan -f" to force install.
I didn't use it - and this happened:
Do I need to force?

AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
/bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t t/Bio/.t t/Bio/RetrieveAssemblies/.t
t/Bio/RetrieveAssemblies.t ................ 1/? Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 2/?

Failed test 'Expected file for command -q Mycobacterium -a -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'

at t/lib/TestHelper.pm line 31.

Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 3/?

Failed test 'Expected file for command -q Mycobacterium -f fasta PRJEB8877 exists: downloaded_files/CVMX01.1.fsa_nt.gz'

at t/lib/TestHelper.pm line 31.

Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 4/?

Failed test 'Expected file for command -q Mycobacterium -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'

at t/lib/TestHelper.pm line 31.

Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 5/?

Failed test 'Expected file for command -q Mycobacterium -o my_dir PRJEB8877 exists: my_dir/CVMX01.1.gbff.gz'

at t/lib/TestHelper.pm line 31.

Unable to get remote page at t/lib/TestHelper.pm line 28.
t/Bio/RetrieveAssemblies.t ................ 6/?

Failed test 'Expected file for command -q Mycobacterium PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz'

at t/lib/TestHelper.pm line 31.

Looks like you failed 5 tests of 6.

t/Bio/RetrieveAssemblies.t ................ Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/6 subtests
t/Bio/RetrieveAssemblies/AccessionFile.t .. ok
t/Bio/RetrieveAssemblies/RefWeak.t ........ ok
t/Bio/RetrieveAssemblies/WGS.t ............ ok
t/requires_external.t ..................... ok

Test Summary Report

t/Bio/RetrieveAssemblies.t (Wstat: 1280 Tests: 6 Failed: 5)
Failed tests: 2-6
Non-zero exit status: 5
Files=5, Tests=33, 95 wallclock secs ( 0.02 usr 0.01 sys + 1.40 cusr 0.20 csys = 1.63 CPU)
Result: FAIL
Failed 1/5 test programs. 5/33 subtests failed.
make: *** [test_dynamic] Error 255
AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz
Stopping: 'install' failed for 'A/AJ/AJPAGE/Bio-RetrieveAssemblies-1.0.1.tar.gz'.

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#151.

[tseemann]

I don't think 1. or 2. apply in my case.... that's odd.

I've tried using the retrieve_assemblies command and it just sits there doing nothing forever.

So there probably is something wrong at my end.

[andrewjpage]

I've released a new version which uses wget to retrieve data instead of the proper perl way of doing it, but it seems a lot more robust, so it does the trick. Let me know how you get on.

[tseemann]

CPAN doesn't think there is a new version yet.

[andrewjpage]

I've just pushed up a change so that cpan will pick up the module version
properly (1.1.2). It'll take an hour or two before indexed and available
on cpan.

On 23 June 2015 at 10:02, Torsten Seemann notifications@github.com wrote:

CPAN doesn't think there is a new version yet.

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