BioC 3.2: CHECK report for R453Plus1Toolbox on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.19.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.19.1’
* 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 ‘R453Plus1Toolbox’ can be installed ... [21s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.annotateVariants_MapperSet: no visible binding for global variable
  ‘Hsapiens’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.getEnsemblInfo: no visible binding for global variable ‘cds_length’
.getEnsemblInfo: no visible binding for global variable
  ‘ensembl_transcript_id’
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
.plotVariants: no visible binding for global variable ‘mutation’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
annotateVariants,MapperSet-BSgenome: no visible binding for global
  variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
  variable ‘Hsapiens’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
detectBreakpoints,list: no visible binding for global variable
  ‘Hsapiens’
subset,AVASet : .local: no visible binding for global variable
  ‘referenceSeqID’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:46:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(buffer, fileLen, 1, file);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.245	0.000	0.244
AVASet	0.125	0.000	0.126
AnnotatedVariants-class	0.003	0.000	0.002
MapperSet-class	0.029	0.004	0.034
MapperSet	0.006	0.000	0.006
SFFContainer-class	0.002	0.000	0.002
SFFRead-class	0.002	0.000	0.002
alignShortReads	1.881	0.004	1.889
annotateVariants	0.001	0.000	0.002
assayDataAmp	0.005	0.000	0.004
ava2vcf	0.208	0.004	0.212
avaSetExample	0.014	0.000	0.013
avaSetFiltered	0.022	0.000	0.022
avaSetFiltered_annot	0.002	0.000	0.002
breakpoints	0.003	0.000	0.003
calculateTiTv	0.008	0.004	0.010
captureArray	0.002	0.000	0.002
coverageOnTarget	0.112	0.008	0.121
demultiplexReads	0.082	0.000	0.082
detectBreakpoints	0.507	0.000	0.512
fDataAmp	0.015	0.000	0.015
featureDataAmp	0.014	0.000	0.015
filterChimericReads	1.713	0.000	1.735
genomeSequencerMIDs	0.027	0.000	0.027
getAlignedReads	0.072	0.000	0.072
getVariantPercentages	0.036	0.000	0.037
htmlReport	3.236	0.055	3.342
mapperSetExample	0.006	0.000	0.006
mergeBreakpoints	4.847	0.044	4.908
mutationInfo	0.002	0.000	0.002
plotAmpliconCoverage	0.001	0.000	0.001
plotChimericReads	2.966	0.004	2.971
plotVariants	0.005	0.000	0.004
plotVariationFrequency	0.000	0.000	0.001
qualityReportSFF	0	0	0
readSFF	0.061	0.000	0.060
readsOnTarget	0.248	0.000	0.249
referenceSequences	0.005	0.004	0.008
regions	0.003	0.000	0.004
removeLinker	0.022	0.000	0.022
sequenceCaptureLinkers	0.004	0.000	0.005
setVariantFilter	0.055	0.004	0.059
variants	0.003	0.000	0.003
writeSFF	0.032	0.000	0.032

BioC 3.2: CHECK report for R453Plus1Toolbox on zin1

Summary

Command output