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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpressHTS_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.44.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ArrayExpressHTS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rsamtools’
A package should be listed in only one of these fields.
Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘sampling’ ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘assignPipelineOptions’ ‘createServerLog’ ‘getPipelineOption’
  ‘processOneProjectAlignment’ ‘processOneProjectAlnReport’
  ‘processOneProjectEstimation’ ‘processOneProjectRawReport’
  ‘setProjectData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 1
Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 2
Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 3
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     fasta_formatter not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     cufflinks not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     samtools not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     bwa not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     mmseq not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     bam2hits not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     bowtie not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING ***
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS]     tophat not found
Tue Apr 12 10:25:25 2022 [AEHTS] 
Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Apr 12 10:25:25 2022 [AEHTS] 
calculate_dustyScore: no visible global function definition for
  ‘srswor’
cleanupCluster: no visible global function definition for ‘stopCluster’
cleanupCluster: no visible global function definition for
  ‘cleanupClusters’
createServerLog: no visible global function definition for
  ‘sinkWorkerOutput’
cufflinks_to_granges: no visible global function definition for ‘Rle’
fastq_to_shortreadq: no visible global function definition for ‘subseq’
getEnsemblAnnotation: no visible global function definition for
  ‘.path.package’
make_indexes_old: no visible global function definition for ‘subseq’
plot_readoccurence_cdf: no visible global function definition for
  ‘srswor’
prepareCluster: no visible global function definition for ‘makeCluster’
prepareCluster: no visible global function definition for
  ‘mergeClusters’
prepareCluster: no visible global function definition for
  ‘clusterApply’
prepareCluster: no visible global function definition for
  ‘clusterEvalQ’
readSDRF: no visible global function definition for
  ‘read.AnnotatedDataFrame’
runProjects: no visible global function definition for ‘clusterApply’
runProjects: no visible global function definition for ‘clusterEvalQ’
runProjects: no visible global function definition for ‘clusterApplyLB’
Undefined global functions or variables:
  .path.package Rle cleanupClusters clusterApply clusterApplyLB
  clusterEvalQ makeCluster mergeClusters read.AnnotatedDataFrame
  sinkWorkerOutput srswor stopCluster subseq
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.