BioC 3.4: CHECK report for R453Plus1Toolbox on malbec1

Package: R453Plus1Toolbox

Version: 1.24.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.24.0.tar.gz

StartedAt: 2017-04-15 00:41:35 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:45:54 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 259.8 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.24.0’
* 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 ‘R453Plus1Toolbox’ can be installed ... 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: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
  Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse
  cds_length ensembl_transcript_id mutation 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 installed files from ‘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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-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:46:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(buffer, fileLen, 1, file);
   ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	0.228	0.008	0.237
AVASet	0.116	0.000	0.115
AnnotatedVariants-class	0.000	0.000	0.001
MapperSet-class	0.024	0.000	0.024
MapperSet	0.004	0.000	0.005
SFFContainer-class	0.004	0.000	0.002
SFFRead-class	0.000	0.000	0.001
alignShortReads	2.148	0.000	2.150
annotateVariants	0.004	0.000	0.002
assayDataAmp	0.004	0.000	0.005
ava2vcf	0.164	0.000	0.162
avaSetExample	0.008	0.004	0.013
avaSetFiltered	0.016	0.004	0.018
avaSetFiltered_annot	0.004	0.000	0.002
breakpoints	0.000	0.004	0.003
calculateTiTv	0.012	0.000	0.009
captureArray	0.000	0.000	0.001
coverageOnTarget	0.096	0.004	0.097
demultiplexReads	0.096	0.004	0.100
detectBreakpoints	0.424	0.024	0.447
fDataAmp	0.012	0.000	0.013
featureDataAmp	0.012	0.000	0.014
filterChimericReads	1.696	0.004	1.699
genomeSequencerMIDs	0.016	0.000	0.016
getAlignedReads	0.064	0.000	0.066
getVariantPercentages	0.028	0.000	0.028
htmlReport	2.460	0.048	2.534
mapperSetExample	0.004	0.000	0.005
mergeBreakpoints	3.388	0.028	3.422
mutationInfo	0.000	0.000	0.003
plotAmpliconCoverage	0	0	0
plotChimericReads	2.132	0.000	2.135
plotVariants	0.004	0.000	0.004
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.056	0.000	0.054
readsOnTarget	0.224	0.000	0.224
referenceSequences	0.008	0.000	0.007
regions	0.004	0.000	0.003
removeLinker	0.016	0.000	0.017
sequenceCaptureLinkers	0.000	0.000	0.003
setVariantFilter	0.048	0.000	0.048
variants	0.000	0.000	0.002
writeSFF	0.024	0.000	0.025