Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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tests failing on OSX #21

Closed mkohram closed 7 years ago

mkohram commented 7 years ago

Hi,

When trying to install on OSX I get this. Can't figure out what to do next.

10:54 $ perl INSTALL.pl --NO_HTSLIB

Hello! This installer is configured to install v87 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done
It looks like you have an older version (80) of the API installed.
This installer will install a limited set of the API v87 for use by the VEP only

Skip to the next step (n) to install cache files

Do you want to continue installing the API (y/n)? y

Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
./t/AnnotationSource.t ............................... ok    
./t/AnnotationSource_BaseVariation.t ................. ok    
./t/AnnotationSource_Cache.t ......................... ok   
./t/AnnotationSource_Cache_RegFeat.t ................. 1/? Can't locate object method "_finish_annotation" via package "Bio::EnsEMBL::Variation::VariationFeature" at ./t/AnnotationSource_Cache_RegFeat.t line 165, <__ANONIO__> line 139.
# Tests were run but no plan was declared and done_testing() was not seen.
./t/AnnotationSource_Cache_RegFeat.t ................. Dubious, test returned 25 (wstat 6400, 0x1900)
All 44 subtests passed 
./t/AnnotationSource_Cache_Transcript.t .............. 62/? Can't locate object method "_finish_annotation" via package "Bio::EnsEMBL::Variation::VariationFeature" at ./t/AnnotationSource_Cache_Transcript.t line 250, <__ANONIO__> line 139.
# Tests were run but no plan was declared and done_testing() was not seen.
./t/AnnotationSource_Cache_Transcript.t .............. Dubious, test returned 25 (wstat 6400, 0x1900)
All 62 subtests passed 
./t/AnnotationSource_Cache_Variation.t ............... ok    
./t/AnnotationSource_Cache_VariationTabix.t .......... 16/? Can't locate object method "alt_alleles" via package "Bio::EnsEMBL::Variation::VariationFeature" at /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/BaseVariation.pm line 231.
# Tests were run but no plan was declared and done_testing() was not seen.
./t/AnnotationSource_Cache_VariationTabix.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)
All 20 subtests passed 
./t/AnnotationSource_Database_RegFeat.t .............. ok    
./t/AnnotationSource_Database_StructuralVariation.t .. ok    
./t/AnnotationSource_Database_Transcript.t ........... ok    
./t/AnnotationSource_Database_Variation.t ............ ok    
./t/AnnotationSource_File.t .......................... ok    
./t/AnnotationSource_File_BED.t ...................... ok    
./t/AnnotationSource_File_BigWig.t ................... ok    
./t/AnnotationSource_File_GFF.t ...................... ok    
./t/AnnotationSource_File_GTF.t ...................... ok    
./t/AnnotationSource_File_VCF.t ...................... ok    
./t/AnnotationSourceAdaptor.t ........................ ok    
./t/BaseVEP.t ........................................ 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: ./t/BaseVEP.t:118
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/BaseVEP.t ........................................ Dubious, test returned 2 (wstat 512, 0x200)
All 24 subtests passed 
./t/CacheDir.t ....................................... ok    
./t/Config.t ......................................... ok    
./t/FilterSet.t ...................................... ok     
./t/InputBuffer.t .................................... 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::BaseVEP::get_slice /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:232
STACK: Bio::EnsEMBL::VEP::InputBuffer::finish_annotation /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/InputBuffer.pm:244
STACK: ./t/InputBuffer.t:280
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/InputBuffer.t .................................... Dubious, test returned 2 (wstat 512, 0x200)
All 44 subtests passed 
    (less 10 skipped subtests: 34 okay)
./t/OutputFactory.t .................................. 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: ./t/OutputFactory.t:51
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/OutputFactory.t .................................. Dubious, test returned 2 (wstat 512, 0x200)
All 4 subtests passed 
./t/OutputFactory_JSON.t ............................. ok    
./t/OutputFactory_Tab.t .............................. 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: main::get_annotated_buffer_runner ./t/OutputFactory_Tab.t:284
STACK: ./t/OutputFactory_Tab.t:102
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/OutputFactory_Tab.t .............................. Dubious, test returned 2 (wstat 512, 0x200)
All 6 subtests passed 
./t/OutputFactory_VCF.t .............................. 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: main::get_runner ./t/OutputFactory_VCF.t:556
STACK: ./t/OutputFactory_VCF.t:62
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/OutputFactory_VCF.t .............................. Dubious, test returned 2 (wstat 512, 0x200)
All 5 subtests passed 
./t/OutputFactory_VEP_output.t ....................... 3/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: main::get_annotated_buffer_runner ./t/OutputFactory_VEP_output.t:278
STACK: ./t/OutputFactory_VEP_output.t:101
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/OutputFactory_VEP_output.t ....................... Dubious, test returned 2 (wstat 512, 0x200)
All 8 subtests passed 
./t/Parser.t ......................................... 1/? # Tests were run but no plan was declared and done_testing() was not seen.
./t/Parser.t ......................................... Dubious, test returned 2 (wstat 512, 0x200)
All 50 subtests passed 
./t/Parser_HGVS.t .................................... ok    
./t/Parser_ID.t ...................................... ok   
./t/Parser_VCF.t ..................................... ok    
./t/Parser_VEP_input.t ............................... ok    
./t/Runner.t ......................................... 1/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: ./t/Runner.t:190
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/Runner.t ......................................... Dubious, test returned 2 (wstat 512, 0x200)
All 14 subtests passed 
./t/Stats.t .......................................... 8/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Object did not provide a get_all_ids method
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/Root/Root.pm:368
STACK: Bio::DB::SeqI::get_all_primary_ids /Users/kohb9m/opt/ensembl-api/src/bioperl-1.6.1/Bio/DB/SeqI.pm:153
STACK: Bio::EnsEMBL::VEP::Stats::log_fasta_chromosomes /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm:104
STACK: Bio::EnsEMBL::VEP::BaseVEP::fasta_db /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:291
STACK: Bio::EnsEMBL::VEP::Runner::init /Users/kohb9m/tmp/new_vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:83
STACK: main::get_annotated_buffer_runner ./t/Stats.t:459
STACK: ./t/Stats.t:78
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/Stats.t .......................................... Dubious, test returned 2 (wstat 512, 0x200)
All 11 subtests passed 
./t/Utils.t .......................................... ok    
./t/version.t ........................................ ok   

Test Summary Report
-------------------
./t/AnnotationSource_Cache_RegFeat.t               (Wstat: 6400 Tests: 44 Failed: 0)
  Non-zero exit status: 25
  Parse errors: No plan found in TAP output
./t/AnnotationSource_Cache_Transcript.t            (Wstat: 6400 Tests: 62 Failed: 0)
  Non-zero exit status: 25
  Parse errors: No plan found in TAP output
./t/AnnotationSource_Cache_VariationTabix.t        (Wstat: 65280 Tests: 20 Failed: 0)
  Non-zero exit status: 255
  Parse errors: No plan found in TAP output
./t/BaseVEP.t                                      (Wstat: 512 Tests: 24 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/InputBuffer.t                                  (Wstat: 512 Tests: 44 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/OutputFactory.t                                (Wstat: 512 Tests: 4 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/OutputFactory_Tab.t                            (Wstat: 512 Tests: 6 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/OutputFactory_VCF.t                            (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/OutputFactory_VEP_output.t                     (Wstat: 512 Tests: 8 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/Parser.t                                       (Wstat: 512 Tests: 50 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/Runner.t                                       (Wstat: 512 Tests: 14 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
./t/Stats.t                                        (Wstat: 512 Tests: 11 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=37, Tests=1054, 22 wallclock secs ( 0.19 usr  0.13 sys + 19.28 cusr  1.54 csys = 21.14 CPU)
Result: FAIL
Failed 12/37 test programs. 0/1054 subtests failed.
willmclaren commented 7 years ago

It looks like the test run within the installer is not picking up the versions of the modules (Ensembl and BioPerl) installed, but rather some existing elsewhere on your system.

You may find that actually the install has been successful; you can confirm with:

prove t/*.t

In the meantime I'll have a look why the new modules are not being picked up.

mkohram commented 7 years ago

That makes sense, I did have another version installed which I was adding to PERL5LIB. Didn't know they were gonna collide. Does this look good:

15:03 $ perl INSTALL.pl --NO_HTSLIB

Hello! This installer is configured to install v87 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done
It looks like you already have v87 of the API installed.
You shouldn't need to install the API

Skip to the next step (n) to install cache files

Do you want to continue installing the API (y/n)? y

Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
./t/AnnotationSource.t ............................... ok    
./t/AnnotationSource_BaseVariation.t ................. ok    
./t/AnnotationSource_Cache.t ......................... ok   
./t/AnnotationSource_Cache_RegFeat.t ................. ok    
./t/AnnotationSource_Cache_Transcript.t .............. ok    
./t/AnnotationSource_Cache_Variation.t ............... ok    
./t/AnnotationSource_Cache_VariationTabix.t .......... ok    
./t/AnnotationSource_Database_RegFeat.t .............. ok    
./t/AnnotationSource_Database_StructuralVariation.t .. ok    
./t/AnnotationSource_Database_Transcript.t ........... ok    
./t/AnnotationSource_Database_Variation.t ............ ok    
./t/AnnotationSource_File.t .......................... ok    
./t/AnnotationSource_File_BED.t ...................... ok    
./t/AnnotationSource_File_BigWig.t ................... ok    
./t/AnnotationSource_File_GFF.t ...................... ok    
./t/AnnotationSource_File_GTF.t ...................... ok    
./t/AnnotationSource_File_VCF.t ...................... ok    
./t/AnnotationSourceAdaptor.t ........................ ok    
./t/BaseVEP.t ........................................ 1/? 
#   Failed test 'fasta_db - stored chr lengths'
#   at ./t/BaseVEP.t line 124.
#     Structures begin differing at:
#          $got->{97} = '21'
#     $expected->{97} = Does not exist
# Looks like you failed 1 test of 44.
./t/BaseVEP.t ........................................ Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/44 subtests 
    (less 8 skipped subtests: 35 okay)
./t/CacheDir.t ....................................... ok    
./t/Config.t ......................................... ok    
./t/FilterSet.t ...................................... ok     
./t/InputBuffer.t .................................... ok    
./t/OutputFactory.t .................................. 54/? 
--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------
./t/OutputFactory.t .................................. 77/? 
#   Failed test 'TranscriptVariationAllele_to_output_hash - HGVSc'
#   at ./t/OutputFactory.t line 953.
#          got: 'ENST00000352957.8:c.991N>A'
#     expected: 'ENST00000352957.8:c.991G>A'
# Looks like you failed 1 test of 129.
./t/OutputFactory.t .................................. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/129 subtests 
    (less 1 skipped subtest: 127 okay)
./t/OutputFactory_JSON.t ............................. ok    
./t/OutputFactory_Tab.t .............................. 10/? 
--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------
./t/OutputFactory_Tab.t .............................. 15/? 
#   Failed test 'get_all_lines_by_InputBuffer - everything'
#   at ./t/OutputFactory_Tab.t line 228.
#          got: 'rs142513484    21:25585733 T   ENSG00000154719 ENST00000307301 Transcript  3_prime_UTR_variant 1122    rs142513484 MODIFIER    -   -1  -   SNV MRPL39  HGNC    HGNC:14027  protein_coding  YES 5   A2  CCDS33522.1 ENSP00000305682 Q9NYK5  -   UPI00001AEAC0   -   -   -   11/11   -   -   ENST00000307301.11:c.*18N>A -   -   0.0010  0.0030  0.0014  0.0000  0.0000  0.0000  0.005   0   4.119e-04   0.0004133   0.004681    0.000173    0   0   0   0   0   -   -   -   -   -   -   -   -'
#     expected: 'rs142513484    21:25585733 T   ENSG00000154719 ENST00000307301 Transcript  3_prime_UTR_variant 1122    rs142513484 MODIFIER    -   -1  -   SNV MRPL39  HGNC    HGNC:14027  protein_coding  YES 5   A2  CCDS33522.1 ENSP00000305682 Q9NYK5  -   UPI00001AEAC0   -   -   -   11/11   -   -   ENST00000307301.11:c.*18G>A -   -   0.0010  0.0030  0.0014  0.0000  0.0000  0.0000  0.005   0   4.119e-04   0.0004133   0.004681    0.000173    0   0   0   0   0   -   -   -   -   -   -   -   -'
./t/OutputFactory_Tab.t .............................. 16/? 
#   Failed test 'get_all_lines_by_InputBuffer - configure fields'
#   at ./t/OutputFactory_Tab.t line 248.
#          got: '21:25585733    ENST00000307301.11:c.*18N>A'
#     expected: '21:25585733    ENST00000307301.11:c.*18G>A'
# Looks like you failed 2 tests of 16.
./t/OutputFactory_Tab.t .............................. Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/16 subtests 
    (less 1 skipped subtest: 13 okay)
./t/OutputFactory_VCF.t .............................. 24/? 
#   Failed test 'VariationFeature_to_VCF_record - deletion - seq lookup'
#   at ./t/OutputFactory_VCF.t line 248.
#     Structures begin differing at:
#          $got->[3] = 'NA'
#     $expected->[3] = 'GA'

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------
./t/OutputFactory_VCF.t .............................. 29/? 
#   Failed test 'get_all_lines_by_InputBuffer - everything'
#   at ./t/OutputFactory_VCF.t line 330.
#          got: '21 25585733    rs142513484 C   T   .   .   CSQ=T|3_prime_UTR_variant|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|11/11||ENST00000307301.11:c.*18N>A||1122|||||rs142513484||-1||SNV|HGNC|HGNC:14027|YES|5|A2|CCDS33522.1|ENSP00000305682|Q9NYK5||UPI00001AEAC0||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|10/10||ENST00000352957.8:c.991N>A|ENSP00000284967.6:p.Ala331Thr|1033|991|331|A/T|Gca/Aca|rs142513484||-1||SNV|HGNC|HGNC:14027||1|P3|CCDS13573.1|ENSP00000284967|Q9NYK5||UPI00001AEE66||tolerated_low_confidence(0.17)|benign(0.021)|||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|upstream_gene_variant|MODIFIER|AP000223.42|ENSG00000260583|Transcript|ENST00000567517|antisense||||||||||rs142513484|2407|-1||SNV|Clone_based_vega_gene||YES|||||||||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001963192|TF_binding_site||||||||||rs142513484||||SNV||||||||||||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0|||||||| GT  0|0'
#     expected: '21 25585733    rs142513484 C   T   .   .   CSQ=T|3_prime_UTR_variant|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|11/11||ENST00000307301.11:c.*18G>A||1122|||||rs142513484||-1||SNV|HGNC|HGNC:14027|YES|5|A2|CCDS33522.1|ENSP00000305682|Q9NYK5||UPI00001AEAC0||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|10/10||ENST00000352957.8:c.991G>A|ENSP00000284967.6:p.Ala331Thr|1033|991|331|A/T|Gca/Aca|rs142513484||-1||SNV|HGNC|HGNC:14027||1|P3|CCDS13573.1|ENSP00000284967|Q9NYK5||UPI00001AEE66||tolerated_low_confidence(0.17)|benign(0.021)|||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|upstream_gene_variant|MODIFIER|AP000223.42|ENSG00000260583|Transcript|ENST00000567517|antisense||||||||||rs142513484|2407|-1||SNV|Clone_based_vega_gene||YES|||||||||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001963192|TF_binding_site||||||||||rs142513484||||SNV||||||||||||||||0.0010|0.0030|0.0014|0.0000|0.0000|0.0000|0.005|0|4.119e-04|0.0004133|0.004681|0.000173|0|0|0|0|0|||||||| GT  0|0'
./t/OutputFactory_VCF.t .............................. 41/? # Looks like you failed 2 tests of 43.
./t/OutputFactory_VCF.t .............................. Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/43 subtests 
    (less 1 skipped subtest: 40 okay)
./t/OutputFactory_VEP_output.t ....................... 1/? 
--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right.
---------------------------------------------------
./t/OutputFactory_VEP_output.t ....................... 17/? 
#   Failed test 'get_all_lines_by_InputBuffer - everything'
#   at ./t/OutputFactory_VEP_output.t line 196.
#          got: 'IMPACT=MODIFIER;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=MRPL39;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:14027;BIOTYPE=protein_coding;CANONICAL=YES;TSL=5;APPRIS=A2;CCDS=CCDS33522.1;ENSP=ENSP00000305682;SWISSPROT=Q9NYK5;UNIPARC=UPI00001AEAC0;EXON=11/11;HGVSc=ENST00000307301.11:c.*18N>A;AF=0.0010;AFR_AF=0.0030;AMR_AF=0.0014;EAS_AF=0.0000;EUR_AF=0.0000;SAS_AF=0.0000;AA_AF=0.005;EA_AF=0;ExAC_AF=4.119e-04;ExAC_Adj_AF=0.0004133;ExAC_AFR_AF=0.004681;ExAC_AMR_AF=0.000173;ExAC_EAS_AF=0;ExAC_FIN_AF=0;ExAC_NFE_AF=0;ExAC_OTH_AF=0;ExAC_SAS_AF=0'
#     expected: 'IMPACT=MODIFIER;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=MRPL39;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:14027;BIOTYPE=protein_coding;CANONICAL=YES;TSL=5;APPRIS=A2;CCDS=CCDS33522.1;ENSP=ENSP00000305682;SWISSPROT=Q9NYK5;UNIPARC=UPI00001AEAC0;EXON=11/11;HGVSc=ENST00000307301.11:c.*18G>A;AF=0.0010;AFR_AF=0.0030;AMR_AF=0.0014;EAS_AF=0.0000;EUR_AF=0.0000;SAS_AF=0.0000;AA_AF=0.005;EA_AF=0;ExAC_AF=4.119e-04;ExAC_Adj_AF=0.0004133;ExAC_AFR_AF=0.004681;ExAC_AMR_AF=0.000173;ExAC_EAS_AF=0;ExAC_FIN_AF=0;ExAC_NFE_AF=0;ExAC_OTH_AF=0;ExAC_SAS_AF=0'
# Looks like you failed 1 test of 19.
./t/OutputFactory_VEP_output.t ....................... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/19 subtests 
    (less 1 skipped subtest: 17 okay)
./t/Parser.t ......................................... 1/? 
#   Failed test 'validate_vf - check_ref ok'
#   at ./t/Parser.t line 184.
#          got: '0'
#     expected: '1'

#   Failed test 'validate_vf - check_ref long ok'
#   at ./t/Parser.t line 191.
#          got: '0'
#     expected: '1'
# Looks like you failed 2 tests of 87.
./t/Parser.t ......................................... Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/87 subtests 
    (less 11 skipped subtests: 74 okay)
./t/Parser_HGVS.t .................................... ok    
./t/Parser_ID.t ...................................... ok   
./t/Parser_VCF.t ..................................... ok    
./t/Parser_VEP_input.t ............................... ok    
./t/Runner.t ......................................... ok    
./t/Stats.t .......................................... 8/? 
#   Failed test 'finished_stats - charts data'
#   at ./t/Stats.t line 320.
#     Structures begin differing at:
#          $got->[5]{1} = Does not exist
#     $expected->[5]{1} = '0'
# Looks like you failed 1 test of 28.
./t/Stats.t .......................................... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/28 subtests 
./t/Utils.t .......................................... ok    
./t/version.t ........................................ ok   

Test Summary Report
-------------------
./t/BaseVEP.t                                      (Wstat: 256 Tests: 44 Failed: 1)
  Failed test:  26
  Non-zero exit status: 1
./t/OutputFactory.t                                (Wstat: 256 Tests: 129 Failed: 1)
  Failed test:  77
  Non-zero exit status: 1
./t/OutputFactory_Tab.t                            (Wstat: 512 Tests: 16 Failed: 2)
  Failed tests:  15-16
  Non-zero exit status: 2
./t/OutputFactory_VCF.t                            (Wstat: 512 Tests: 43 Failed: 2)
  Failed tests:  24, 29
  Non-zero exit status: 2
./t/OutputFactory_VEP_output.t                     (Wstat: 256 Tests: 19 Failed: 1)
  Failed test:  17
  Non-zero exit status: 1
./t/Parser.t                                       (Wstat: 512 Tests: 87 Failed: 2)
  Failed tests:  51, 54
  Non-zero exit status: 2
./t/Stats.t                                        (Wstat: 256 Tests: 28 Failed: 1)
  Failed test:  22
  Non-zero exit status: 1
Files=37, Tests=1432, 90 wallclock secs ( 0.24 usr  0.15 sys + 78.35 cusr 10.32 csys = 89.06 CPU)
Result: FAIL
Failed 7/37 test programs. 10/1432 subtests failed.
willmclaren commented 7 years ago

Seems there's still an issue with sequence lookup, almost certainly because you're using added --NO_HTSLIB. I'll have a look into this in due course.

The rest of the code seems to be functioning OK.

VivekTodur commented 7 years ago

Similar issues with Ubuntu 14.04 version as well, Refer the below error log,

Downloading required Ensembl API files

Testing VEP script scripts/variant_effect_predictor/t/convert_cache.t ............. ERROR: Could not find test data path /t/testdata/ scripts/variant_effect_predictor/t/convert_cache.t ............. Dubious, test returned 2 (wstat 512, 0x200) No subtests run scripts/variant_effect_predictor/t/variant_effect_predictor.t .. ERROR: Could not find test data path /t/testdata/ scripts/variant_effect_predictor/t/variant_effect_predictor.t .. Dubious, test returned 2 (wstat 512, 0x200) No subtests run scripts/variant_effect_predictor/t/filter_vep.t ................ ok

Test Summary Report

scripts/variant_effect_predictor/t/convert_cache.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: No plan found in TAP output scripts/variant_effect_predictor/t/variant_effect_predictor.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: No plan found in TAP output Files=3, Tests=29, 3 wallclock secs ( 0.04 usr 0.00 sys + 3.04 cusr 0.22 csys = 3.30 CPU) Result: FAIL Failed 2/3 test programs. 0/29 subtests failed.

willmclaren commented 7 years ago

@VivekTodur your error report refers to the older version of VEP (https://github.com/Ensembl/ensembl-tools) which will soon be phased out.

VivekTodur commented 7 years ago

Thank you so much @willmclaren .

But I tried with the latest build from here(https://github.com/Ensembl/ensembl-vep/archive/release/87.25.tar.gz), but still getting error, Below are the brief,

Testing VEP installation ./t/FilterSet.t ...................................... ok
./t/AnnotationSource_Database_Variation.t ............ ok
./t/AnnotationSource_Cache_Variation.t ............... ok
./t/AnnotationSource_File_VCF.t ...................... ok
./t/AnnotationSource_BaseVariation.t ................. ok
./t/Parser.t ......................................... ok
./t/CacheDir.t ....................................... ok
./t/Parser_HGVS.t .................................... ok
./t/AnnotationSourceAdaptor.t ........................ ok
./t/AnnotationSource_Cache_Transcript.t .............. ok
./t/Runner.t ......................................... 1/?

Failed test 'get_stats_file_handle - extension handling 2'

at ./t/Runner.t line 293.

Failed test 'get_stats_file_handle - extension handling 3'

at ./t/Runner.t line 296.

-------------------- EXCEPTION -------------------- MSG: ERROR: Stats file /home/Vt/Programs/ensembl-vep-release-87.25/t/testdata/user_file24900.txt.txt already exists. Specify a different output file with --stats_file or overwrite existing file with --force_overwrite

STACK Bio::EnsEMBL::VEP::BaseRunner::get_stats_file_handle /home/Vt/Programs/ensembl-vep-release-87.25/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:177 STACK Bio::EnsEMBL::VEP::BaseRunner::dump_stats /home/Vt/Programs/ensembl-vep-release-87.25/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:193 STACK Bio::EnsEMBL::VEP::Runner::finish /home/Vt/Programs/ensembl-vep-release-87.25/modules/Bio/EnsEMBL/VEP/Runner.pm:102 STACK Bio::EnsEMBL::VEP::Runner::run /home/Vt/Programs/ensembl-vep-release-87.25/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK toplevel ./t/Runner.t:316 Date (localtime) = Tue Feb 28 18:07:33 2017 Ensembl API version = 87

Tests were run but no plan was declared and done_testing() was not seen.

Looks like your test exited with 25 just after 29.

./t/Runner.t ......................................... Dubious, test returned 25 (wstat 6400, 0x1900) Failed 2/29 subtests ./t/Config.t ......................................... ok
./t/AnnotationSource_Database_StructuralVariation.t .. ok
./t/OutputFactory_JSON.t ............................. ok
./t/AnnotationSource_File.t .......................... ok
./t/Parser_VCF.t ..................................... ok
./t/AnnotationSource_File_GTF.t ...................... ok
./t/Stats.t .......................................... ok
./t/Parser_VEP_input.t ............................... ok
./t/BaseVEP.t ........................................ ok
./t/Utils.t .......................................... ok
./t/AnnotationSource_Cache_VariationTabix.t .......... ok
./t/OutputFactory_Tab.t .............................. ok
./t/AnnotationSource_File_BED.t ...................... ok
./t/OutputFactory_VEP_output.t ....................... ok
./t/AnnotationSource_File_GFF.t ...................... ok
./t/OutputFactory_VCF.t .............................. ok
./t/AnnotationSource_Database_RegFeat.t .............. ok
./t/AnnotationSource_Database_Transcript.t ........... ok
./t/InputBuffer.t .................................... ok
./t/AnnotationSource_Cache_RegFeat.t ................. ok
./t/AnnotationSource.t ............................... ok
./t/version.t ........................................ fatal: Not a git repository (or any of the parent directories): .git ./t/version.t ........................................ 1/?

Failed test 'get current git branch'

at ./t/version.t line 31.

Looks like you failed 1 test of 1.

./t/version.t ........................................ Dubious, test returned 1 (wstat 256, 0x100) Failed 1/1 subtests ./t/AnnotationSource_Cache.t ......................... ok
./t/Parser_ID.t ...................................... ok
./t/AnnotationSource_File_BigWig.t ................... ok
./t/OutputFactory.t .................................. ok

Test Summary Report

./t/Runner.t (Wstat: 6400 Tests: 29 Failed: 2) Failed tests: 27-28 Non-zero exit status: 25 Parse errors: No plan found in TAP output ./t/version.t (Wstat: 256 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 1 Files=37, Tests=1391, 54 wallclock secs ( 0.26 usr 0.05 sys + 50.29 cusr 0.98 csys = 51.58 CPU) Result: FAIL Failed 2/37 test programs. 3/1391 subtests failed.

christianbioinf commented 7 years ago

I also get a test failed error for OSX with perl INSTALL.pl.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done

Setting up directories
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files
Attempting to install Bio::DB::HTS and htslib.

>>> If this fails, try re-running with --NO_HTSLIB

 - checking out HTSLib
Cloning into 'htslib'...
Note: checking out '6bed35a3eaefa3baa2c7e0166ceba442212f166b'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

 - building HTSLIB in ./htslib
In /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib
echo '/* Empty config.h generated by Makefile */' > config.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3.2-dirty"' > version.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:3100:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:311: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                 ~~~~~^~~~~~~~~~~~~~~~~
cram/cram_io.c:3100:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:345: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                              ~~~~~~~~~~^~~~~
cram/cram_io.c:3100:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:367: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                                                    ~~~~~~~~~~^~~~~
cram/cram_io.c:3100:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:388: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                                                                          ~~~~~~~~~^~~~~
cram/cram_io.c:3158:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:311: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                 ~~~~~^~~~~~~~~~~~~~~~~
cram/cram_io.c:3158:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:345: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                              ~~~~~~~~~~^~~~~
cram/cram_io.c:3158:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:367: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                                                    ~~~~~~~~~~^~~~~
cram/cram_io.c:3158:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:388: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
                                                                                                                                                                                                                                                                                                                                                                                          ~~~~~~~~~^~~~~
8 warnings generated.
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/vlen.o cram/vlen.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gcc -dynamiclib -install_name /usr/local/lib/libhts.1.dylib -current_version 1.3.255 -compatibility_version 1  -o libhts.dylib kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o -lz 
ln -sf libhts.dylib libhts.1.dylib
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzip.o bgzip.c
gcc -pthread  -o bgzip bgzip.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o htsfile.o htsfile.c
gcc -pthread  -o htsfile htsfile.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tabix.o tabix.c
gcc -pthread  -o tabix tabix.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc -pthread  -o test/fieldarith test/fieldarith.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/hfile.o test/hfile.c
gcc -pthread  -o test/hfile test/hfile.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/sam.o test/sam.c
gcc -pthread  -o test/sam test/sam.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -pthread  -o test/test-regidx test/test-regidx.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test_view.o test/test_view.c
gcc -pthread  -o test/test_view test/test_view.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -pthread  -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -pthread  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz 
clang: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
 - unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/
./Bio/tmp/Bio-DB-HTS-master - moving files to ./biodbhts
 - making Bio::DB:HTS
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.7'
Building Bio-DB-HTS
cc -I/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/htslib -I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE -DXS_VERSION="2.7" -DVERSION="2.7" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -Os -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs')
env LD_RUN_PATH=/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE cc -mmacosx-version-min=10.12.5 -arch x86_64 -arch i386 -bundle -undefined dynamic_lookup -fstack-protector -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bundle lib/Bio/DB/HTS/Faidx.o -L/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib -Wl,-rpath,/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib -lhts -lpthread -lz
ld: warning: ignoring file /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib, file was built for x86_64 which is not the architecture being linked (i386): /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib
cc -I/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/htslib -I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE -DVERSION="2.7" -DXS_VERSION="2.7" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -Os -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
lib/Bio/DB/HTS.xs:189:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
lib/Bio/DB/HTS.xs:645:11: warning: multiple unsequenced modifications to 'seq' [-Wunsequenced]
    seq = Newxz(seq,b->core.l_qseq+1,char);
        ~ ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/handy.h:1581:25: note: expanded from macro 'Newxz'
#define Newxz(v,n,t)    (v = (MEM_WRAP_CHECK_(n,t) (t*)MEM_LOG_ALLOC(n,t,safecalloc((n),sizeof(t)))))
                           ^
lib/Bio/DB/HTS.xs:659:22: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
    RETVAL = newSVpv(bam_get_qual(b),b->core.l_qseq);
             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/htslib/sam.h:227:26: note: expanded from macro 'bam_get_qual'
#define bam_get_qual(b)  ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
                         ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
lib/Bio/DB/HTS.xs:740:51: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
                                               strncat(d,s,left);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/secure/_string.h:132:34: note: expanded from macro 'strncat'
  __builtin___strncat_chk (dest, src, len, __darwin_obsz (dest))
                                 ^~~
lib/Bio/DB/HTS.xs:812:34: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
       XPUSHs(sv_2mortal(newSVpv(s,2)));
                                 ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:554:46: note: expanded from macro 'sv_2mortal'
#define sv_2mortal(a)           Perl_sv_2mortal(aTHX_ a)
                                                      ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/pp.h:298:43: note: expanded from macro 'XPUSHs'
#define XPUSHs(s)       (EXTEND(sp,1), *++sp = (s))
                                                ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
lib/Bio/DB/HTS.xs:835:19: warning: assigning to 'uint8_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
      b->data     = SvPV(ST(1),len);
                  ^ ~~~~~~~~~~~~~~~
lib/Bio/DB/HTS.xs:838:20: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
    RETVAL=newSVpv(b->data,b->l_data);
                   ^~~~~~~
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
7 warnings generated.
lib/Bio/DB/HTS.xs:189:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
lib/Bio/DB/HTS.xs:645:11: warning: multiple unsequenced modifications to 'seq' [-Wunsequenced]
    seq = Newxz(seq,b->core.l_qseq+1,char);
        ~ ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/handy.h:1581:25: note: expanded from macro 'Newxz'
#define Newxz(v,n,t)    (v = (MEM_WRAP_CHECK_(n,t) (t*)MEM_LOG_ALLOC(n,t,safecalloc((n),sizeof(t)))))
                           ^
lib/Bio/DB/HTS.xs:659:22: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
    RETVAL = newSVpv(bam_get_qual(b),b->core.l_qseq);
             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/htslib/sam.h:227:26: note: expanded from macro 'bam_get_qual'
#define bam_get_qual(b)  ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
                         ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
lib/Bio/DB/HTS.xs:740:51: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
                                               strncat(d,s,left);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/secure/_string.h:132:34: note: expanded from macro 'strncat'
  __builtin___strncat_chk (dest, src, len, __darwin_obsz (dest))
                                 ^~~
lib/Bio/DB/HTS.xs:812:34: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
       XPUSHs(sv_2mortal(newSVpv(s,2)));
                                 ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:554:46: note: expanded from macro 'sv_2mortal'
#define sv_2mortal(a)           Perl_sv_2mortal(aTHX_ a)
                                                      ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/pp.h:298:43: note: expanded from macro 'XPUSHs'
#define XPUSHs(s)       (EXTEND(sp,1), *++sp = (s))
                                                ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
lib/Bio/DB/HTS.xs:835:19: warning: assigning to 'uint8_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
      b->data     = SvPV(ST(1),len);
                  ^ ~~~~~~~~~~~~~~~
lib/Bio/DB/HTS.xs:838:20: warning: passing 'uint8_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
    RETVAL=newSVpv(b->data,b->l_data);
                   ^~~~~~~
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/embed.h:379:42: note: expanded from macro 'newSVpv'
#define newSVpv(a,b)            Perl_newSVpv(aTHX_ a,b)
                                                   ^
/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/proto.h:2865:56: note: passing argument to parameter 's' here
PERL_CALLCONV SV*       Perl_newSVpv(pTHX_ const char *const s, const STRLEN len)
                                                             ^
7 warnings generated.
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
env LD_RUN_PATH=/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE cc -mmacosx-version-min=10.12.5 -arch x86_64 -arch i386 -bundle -undefined dynamic_lookup -fstack-protector -o blib/arch/auto/Bio/DB/HTS/HTS.bundle lib/Bio/DB/HTS.o -L/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib -Wl,-rpath,/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib -lhts -lpthread -lz
ld: warning: ignoring file /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib, file was built for x86_64 which is not the architecture being linked (i386): /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
./t/AnnotationSource.t ............................... ok
./t/AnnotationSource_Cache.t ......................... ok
./t/AnnotationSource_Cache_RegFeat.t ................. ok
./t/AnnotationSource_Cache_Transcript.t .............. ok
./t/AnnotationSource_Cache_Variation.t ............... ok
./t/AnnotationSource_Cache_VariationTabix.t .......... ok
./t/AnnotationSource_Database_RegFeat.t .............. ok
./t/AnnotationSource_Database_StructuralVariation.t .. ok
./t/AnnotationSource_Database_Transcript.t ........... ok
./t/AnnotationSource_Database_Variation.t ............ ok
./t/AnnotationSource_File.t .......................... ok
./t/AnnotationSource_File_BED.t ...................... ok
./t/AnnotationSource_File_BigWig.t ................... ok
./t/AnnotationSource_File_GFF.t ...................... ok
./t/AnnotationSource_File_GTF.t ...................... ok
./t/AnnotationSource_File_VCF.t ...................... ok
./t/AnnotationSourceAdaptor.t ........................ ok
./t/bam_edit.t ....................................... ok
./t/BaseVEP.t ........................................ ok
./t/CacheDir.t ....................................... ok
./t/Config.t ......................................... ok
./t/FilterSet.t ...................................... ok
./t/InputBuffer.t .................................... ok
./t/OutputFactory.t .................................. ok
./t/OutputFactory_JSON.t ............................. ok
./t/OutputFactory_Tab.t .............................. ok
./t/OutputFactory_VCF.t .............................. ok
./t/OutputFactory_VEP_output.t ....................... ok
./t/Parser.t ......................................... ok
./t/Parser_HGVS.t .................................... ok
./t/Parser_ID.t ...................................... ok
./t/Parser_VCF.t ..................................... ok
./t/Parser_VEP_input.t ............................... ok

#   Failed test 'get_stats_file_handle - extension handling 2'
#   at ./t/Runner.t line 371.

#   Failed test 'get_stats_file_handle - extension handling 3'
#   at ./t/Runner.t line 374.

-------------------- EXCEPTION --------------------
MSG: ERROR: Stats file /Users/christian/Documents/tools/vep/89.3/binary/mac/t/testdata/user_file23407.txt.txt already exists. Specify a different output file with --stats_file or overwrite existing file with --force_overwrite

STACK Bio::EnsEMBL::VEP::BaseRunner::get_stats_file_handle /Users/christian/Documents/tools/vep/89.3/binary/mac/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:273
STACK Bio::EnsEMBL::VEP::BaseRunner::dump_stats /Users/christian/Documents/tools/vep/89.3/binary/mac/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:301
STACK Bio::EnsEMBL::VEP::Runner::finish /Users/christian/Documents/tools/vep/89.3/binary/mac/modules/Bio/EnsEMBL/VEP/Runner.pm:161
STACK Bio::EnsEMBL::VEP::Runner::run /Users/christian/Documents/tools/vep/89.3/binary/mac/modules/Bio/EnsEMBL/VEP/Runner.pm:193
STACK toplevel ./t/Runner.t:394
Date (localtime)    = Thu Jun 15 15:03:16 2017
Ensembl API version = 89
---------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
./t/Runner.t ......................................... 
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 2/37 subtests 
./t/Stats.t .......................................... ok
./t/TranscriptTree.t ................................. ok
./t/Utils.t .......................................... ok
./t/version.t ........................................ ok

Test Summary Report
-------------------
./t/Runner.t                                       (Wstat: 6400 Tests: 37 Failed: 2)
  Failed tests:  35-36
  Non-zero exit status: 25
  Parse errors: No plan found in TAP output
Files=38, Tests=1503, 216 wallclock secs ( 0.39 usr  0.22 sys + 116.29 cusr  4.94 csys = 121.84 CPU)
Result: FAIL
Failed 1/38 test programs. 2/1503 subtests failed.

Note that the HTSLIB install also seems not right since I get these warnings

ld: warning: ignoring file /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib, file was built for x86_64 which is not the architecture being linked (i386): /Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/libhts.dylib

which might be caused by

cc -I/Users/christian/Documents/tools/vep/89.3/binary/mac/htslib/htslib -I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE -DXS_VERSION="2.7" -DVERSION="2.7" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -Os -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c

where -arch x86_64 -arch i386 are specified.

willmclaren commented 7 years ago

@christianbioinf looks like there's an issue with the specific version of htslib we're using and OSX.

It's resolved by using a newer version; the fix for getting this working is a bit hacky, so apologies. We're looking into ways of making this neater for future versions, but htslib seems to be making it deliberately difficult for us!

cd [path/to]/ensembl-vep/htslib
git pull
git checkout master

At this stage you can try to run make. This may fail if you don't have the lzma and/or bz2 libraries installed (this is the reason why VEP installs 1.3.2 by default, the dependencies were introduced in 1.4 and VEP doesn't use CRAM for which they are required...).

make clean
make

If it fails, you will need the autoreconf binary installed in your system to create a configure file that you can use to bypass the above dependency. If you don't have it, you can get it with brew:

brew install automake

Then:

autoreconf
./configure --disable-bz2 --disable-lzma
make

Then go back to the VEP directory and try INSTALL.pl again:

cd ../
perl INSTALL.pl

Bio::DB::HTS should now install OK.

The two test failures in Runner.t I have been unable to recreate, but the chances of whatever is causing those failures causing you any problems is very slim. I've put in a change for the next release which might fix it, but I'm not 100% sure.

christianbioinf commented 7 years ago

@willmclaren Thanks a lot for your effort.

Actually, I now realized that the issue only occurs with the newest release 89.3 and not with a github-cloned version. Still, your fix resolves the compiling warnings with 89.3 and Bio::DB::HTS.

The two test failures remain but are not present with the github-cloned version and hence they should not be present in the new release. If it is available, I would be happy to test it again since I would like to work on a released version rather than on an arbitrary commit.

willmclaren commented 7 years ago

Thanks, that's helped me track it down - the issue was that there was a "." character in the directory name that a regular expression was scanning; this will crop up if you download the release zip as it will have, for example, "89.3" in the path.

It's definitely safe to ignore those errors. I'll put in a fix that will appear in the next release.

On a further note, you do not need to download the releases as zips. If you git clone the repo, you can check out specific release tags with e.g.

git checkout release/89.3

and this will give you the exact same content as downloading that zip.