[Bioc-devel] Problem with ensemble-VEP install on merida1

[Shepherd, Lori]

I think we have fixed the issue and it should clear up on tonights build report.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, October 7, 2019 1:04 PM
To: Jonathon Hill <jhill using byu.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Problem with ensemble-VEP install on merida1

This needs to be fixed on the server.  Thank you for making me aware. I will look into it.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jonathon Hill <jhill using byu.edu>
Sent: Monday, October 7, 2019 11:23 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Problem with ensemble-VEP install on merida1

Hi all,

My package passes all tests on linux, but fails on the OS X check (exact error is below). It appears to be a problem with the VEP perl modules on the server. Specifically, it is complaining that Bio::DB::HTS::Tabix is not installed. Is there something I can do or does it need to be fixed on the server?

Thanks,

Jonathon Hill


##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2
###
##############################################################################
##############################################################################


* checking for file �MMAPPR2/DESCRIPTION� ... OK
* preparing �MMAPPR2�:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR


-------------------- EXCEPTION --------------------
MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed

STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:162
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:228
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/ensembl-vep/vep:224
Date (localtime)    = Sat Oct  5 23:32:12 2019
Ensembl API version = 98
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed

STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:162
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:228
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/ensembl-vep/vep:224
Date (localtime)    = Sat Oct  5 23:32:27 2019
Ensembl API version = 98
---------------------------------------------------
Quitting from lines 128-135 (MMAPPR2.Rmd)
Error: processing vignette 'MMAPPR2.Rmd' failed with diagnostics:
file(s) do not exist:
  '/tmp/Rtmpv2ka4U/file11068648095bc'
--- failed re-building �MMAPPR2.Rmd�

SUMMARY: processing the following file failed:
  �MMAPPR2.Rmd�

Error: Vignette re-building failed.
Execution halted


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