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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ArrayExpressHTS_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.46.0’
* 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 ... WARNING
Found the following significant warnings:
  addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  fltbam.c:40:21: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness [-Wpointer-sign]
  fltbam.c:40:30: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness [-Wpointer-sign]
  fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
  fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’; did you mean ‘ferror’? [-Wimplicit-function-declaration]
  fltbam.c:125:25: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
  fltbam.c:126:37: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
  functions.c:29:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:30:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:68:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:69:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:70:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:71:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/ArrayExpressHTS.Rcheck/00install.out’ for details.
* 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 Oct 18 18:36:39 2022 [AEHTS] Setting Options Step 1
Tue Oct 18 18:36:39 2022 [AEHTS] Setting Options Step 2
Tue Oct 18 18:36:39 2022 [AEHTS] Setting Options Step 3
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     fasta_formatter not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     cufflinks not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     samtools not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     bwa not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     mmseq not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     bam2hits not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     bowtie not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] *** WARNING ***
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS]     tophat not found
Tue Oct 18 18:36:39 2022 [AEHTS] 
Tue Oct 18 18:36:39 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 18 18:36:39 2022 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 18 18:36:39 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 ‘/home/biocbuild/bbs-3.15-bioc/R/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 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: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.