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### Running command:
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###   /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"
Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module) (@INC contains: /usr/local/ensembl-vep/modules /usr/local/ensembl-vep /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3/darwin-thread-multi-2level /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /usr/local/ensembl-vep/vep line 20.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/vep line 20.
Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module) (@INC contains: /usr/local/ensembl-vep/modules /usr/local/ensembl-vep /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3/darwin-thread-multi-2level /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /usr/local/ensembl-vep/vep line 20.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/vep line 20.

Quitting from lines 128-135 [mmappr-steps] (MMAPPR2.Rmd)
Error: processing vignette 'MMAPPR2.Rmd' failed with diagnostics:
file(s) do not exist:
  '/tmp/Rtmp5a6Ws1/file160003133da4a'
--- failed re-building ‘MMAPPR2.Rmd’

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

Error: Vignette re-building failed.
Execution halted