Package: R453Plus1Toolbox

Version: 1.34.0

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_1.34.0.tar.gz

StartedAt: 2019-10-16 04:16:02 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:22:28 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 386.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.34.0’
* 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 ... WARNING
Found the following significant warnings:
  readSFF.c:46:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck/00install.out’ for details.
* 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 7.11  0.092   7.333
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL R453Plus1Toolbox
###
##############################################################################
##############################################################################


* 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	0.287	0.004	0.311
AVASet	0.237	0.000	0.248
AnnotatedVariants-class	0.002	0.000	0.002
MapperSet-class	0.036	0.004	0.039
MapperSet	0.008	0.000	0.008
SFFContainer-class	0.001	0.000	0.001
SFFRead-class	0.001	0.000	0.001
alignShortReads	2.706	0.008	2.816
annotateVariants	0.002	0.000	0.002
assayDataAmp	0.006	0.000	0.006
ava2vcf	0.305	0.003	0.382
avaSetExample	0.017	0.000	0.017
avaSetFiltered	0.021	0.004	0.025
avaSetFiltered_annot	0.002	0.000	0.003
breakpoints	0.004	0.003	0.006
calculateTiTv	0.012	0.000	0.012
captureArray	0.002	0.000	0.002
coverageOnTarget	0.232	0.000	0.245
demultiplexReads	0.099	0.000	0.099
detectBreakpoints	0.846	0.068	0.936
fDataAmp	0.022	0.000	0.021
featureDataAmp	0.016	0.004	0.021
filterChimericReads	4.365	0.000	4.427
genomeSequencerMIDs	0.022	0.000	0.023
getAlignedReads	0.083	0.004	0.119
getVariantPercentages	0.030	0.004	0.035
htmlReport	3.256	0.036	3.319
mapperSetExample	0.007	0.000	0.007
mergeBreakpoints	7.110	0.092	7.333
mutationInfo	0.003	0.000	0.003
plotAmpliconCoverage	0.001	0.000	0.000
plotChimericReads	2.585	0.008	2.594
plotVariants	0.004	0.000	0.005
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.118	0.000	0.133
readsOnTarget	0.056	0.000	0.056
referenceSequences	0.010	0.000	0.011
regions	0.004	0.000	0.004
removeLinker	0.025	0.000	0.027
sequenceCaptureLinkers	0.006	0.000	0.005
setVariantFilter	0.058	0.004	0.063
variants	0.004	0.000	0.004
writeSFF	0.047	0.000	0.047