##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2
###
##############################################################################
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* checking for file ‘MMAPPR2/DESCRIPTION’ ... OK
* preparing ‘MMAPPR2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MMAPPR2.Rmd’ using rmarkdown
running: bash  -c "# Cooking show code to account for cases when samtools is not installed
echo '#!/bin/bash' > /tmp/samtools
chmod 755 /tmp/samtools"

-------------------- 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:170
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /usr/local/ensembl-vep/vep:232
Date (localtime)    = Fri Mar  1 20:39:07 2024
Ensembl API version = 109
---------------------------------------------------

-------------------- 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:170
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /usr/local/ensembl-vep/vep:232
Date (localtime)    = Fri Mar  1 20:39:47 2024
Ensembl API version = 109
---------------------------------------------------

Quitting from lines 128-135 [mmappr-steps] (MMAPPR2.Rmd)
Error: processing vignette 'MMAPPR2.Rmd' failed with diagnostics:
file(s) do not exist:
  '/tmp/Rtmp1HjxQB/filec7c414209bfb'
--- failed re-building ‘MMAPPR2.Rmd’

SUMMARY: processing the following file failed:
  ‘MMAPPR2.Rmd’

Error: Vignette re-building failed.
Execution halted