Package: R453Plus1Toolbox

Version: 1.33.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings R453Plus1Toolbox_1.33.0.tar.gz

StartedAt: 2019-04-09 02:58:17 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:04:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 379.8 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings R453Plus1Toolbox_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.33.0’
* 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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   2.8Mb
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints 7.35  0.083   7.759
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL R453Plus1Toolbox
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.262	0.004	0.326
AVASet	0.211	0.004	0.214
AnnotatedVariants-class	0.002	0.000	0.002
MapperSet-class	0.035	0.000	0.035
MapperSet	0.007	0.000	0.008
SFFContainer-class	0.002	0.000	0.002
SFFRead-class	0.001	0.000	0.001
alignShortReads	1.991	0.017	2.137
annotateVariants	0.001	0.000	0.001
assayDataAmp	0.003	0.004	0.007
ava2vcf	0.264	0.000	0.276
avaSetExample	0.02	0.00	0.02
avaSetFiltered	0.026	0.000	0.027
avaSetFiltered_annot	0.003	0.000	0.002
breakpoints	0.007	0.000	0.007
calculateTiTv	0.013	0.000	0.012
captureArray	0.002	0.000	0.002
coverageOnTarget	0.201	0.000	0.211
demultiplexReads	0.091	0.000	0.091
detectBreakpoints	0.744	0.068	0.846
fDataAmp	0.018	0.000	0.018
featureDataAmp	0.013	0.004	0.017
filterChimericReads	4.396	0.004	4.486
genomeSequencerMIDs	0.026	0.000	0.027
getAlignedReads	0.091	0.003	0.106
getVariantPercentages	0.038	0.000	0.039
htmlReport	3.237	0.040	3.504
mapperSetExample	0.007	0.000	0.008
mergeBreakpoints	7.350	0.083	7.759
mutationInfo	0.003	0.000	0.003
plotAmpliconCoverage	0.000	0.000	0.001
plotChimericReads	2.576	0.004	2.786
plotVariants	0.001	0.002	0.004
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.126	0.004	0.147
readsOnTarget	0.065	0.000	0.068
referenceSequences	0.011	0.000	0.010
regions	0.004	0.000	0.004
removeLinker	0.022	0.003	0.026
sequenceCaptureLinkers	0.006	0.000	0.008
setVariantFilter	0.060	0.004	0.084
variants	0.004	0.000	0.004
writeSFF	0.048	0.000	0.047