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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings girafe_1.46.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/girafe.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'girafe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'girafe' version '1.46.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead',
  'genomeIntervals', 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'girafe' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'genomeIntervals'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' call to 'MASS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'genomeIntervals:::intervalsForOverlap'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
agiFromBam: no visible binding for global variable 'mclapply'
agiFromBam: no visible global function definition for 'scanBamHeader'
agiFromBam: no visible global function definition for 'ScanBamParam'
agiFromBam : <anonymous>: no visible global function definition for
  'IRangesList'
agiFromBam : <anonymous>: no visible global function definition for
  'scanBamFlag'
agiFromBam : <anonymous>: no visible global function definition for
  'scanBam'
countReadsAnnotated: no visible binding for global variable 'mclapply'
countReadsAnnotated: no visible binding for global variable 'fraction1'
fracOverlap: no visible binding for global variable 'fraction1'
fracOverlap: no visible binding for global variable 'fraction2'
getFeatureCounts: no visible binding for global variable 'fraction1'
getFeatureCounts: no visible binding for global variable 'Index1'
intPhred: no visible binding for global variable 'mclapply'
oldAGIoverlap: no visible binding for global variable 'mclapply'
plotReads: no visible binding for global variable 'x.start'
plotReads: no visible binding for global variable 'x.end'
plotReads: no visible binding for global variable 'y'
reduceOne: no visible binding for global variable 'fraction1'
reduceOne: no visible binding for global variable 'fraction2'
trimAdapter: no visible global function definition for 'DNAString'
trimAdapter: no visible global function definition for 'narrow'
windowCountAndGC: no visible binding for global variable 'n.reads'
windowCountAndGC: no visible global function definition for 'Views'
windowCountAndGC: no visible global function definition for 'unmasked'
windowCountAndGC: no visible global function definition for
  'alphabetFrequency'
clusters,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
clusters,Genome_intervals: no visible binding for global variable
  'mclapply'
coverage,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
coverage,AlignedGenomeIntervals : <anonymous>: no visible binding for
  global variable 'on.minus'
interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no
  visible binding for global variable 'mclapply'
reduce,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
reduce,Genome_intervals: no visible binding for global variable
  'mclapply'
reduce,Genome_intervals: no visible binding for global variable
  'fraction1'
reduce,Genome_intervals: no visible binding for global variable
  'fraction2'
Undefined global functions or variables:
  DNAString IRangesList Index1 ScanBamParam Views alphabetFrequency
  fraction1 fraction2 mclapply n.reads narrow on.minus scanBam
  scanBamFlag scanBamHeader unmasked x.end x.start y
* 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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/girafe/libs/i386/girafe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/girafe/libs/x64/girafe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
AlignedGenomeIntervals-class 11.34   1.03   14.42
negbinomsig                   7.27   0.60    7.86
perWindow                     7.20   0.33    7.53
trimAdapter                   0.15   0.23    5.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
AlignedGenomeIntervals-class 9.33   0.80   10.65
negbinomsig                  7.81   0.34    8.16
perWindow                    7.87   0.22    8.09
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/girafe.Rcheck/00check.log'
for details.