Package: R453Plus1Toolbox

Version: 1.37.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.37.0.tar.gz

StartedAt: 2020-01-16 07:55:26 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:05:01 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 575.2 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.37.0’
* 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  5.0Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   2.6Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
mergeBreakpoints    10.989  0.371  11.358
htmlReport           6.364  0.756   7.173
filterChimericReads  5.449  0.276   5.725
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL R453Plus1Toolbox
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c readSFF.c -o readSFF.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c writeSFF.c -o writeSFF.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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	0.356	0.024	0.386
AVASet	0.356	0.017	0.374
AnnotatedVariants-class	0.003	0.000	0.003
MapperSet-class	0.068	0.040	0.108
MapperSet	0.011	0.006	0.017
SFFContainer-class	0.003	0.001	0.004
SFFRead-class	0.001	0.000	0.002
alignShortReads	2.504	0.016	2.533
annotateVariants	0.003	0.000	0.003
assayDataAmp	0.008	0.004	0.013
ava2vcf	0.421	0.015	0.436
avaSetExample	0.027	0.006	0.033
avaSetFiltered	0.031	0.006	0.037
avaSetFiltered_annot	0.002	0.002	0.005
breakpoints	0.005	0.004	0.010
calculateTiTv	0.012	0.005	0.017
captureArray	0.002	0.003	0.005
coverageOnTarget	0.410	0.041	0.453
demultiplexReads	0.199	0.037	0.235
detectBreakpoints	1.707	0.271	1.989
fDataAmp	0.034	0.009	0.044
featureDataAmp	0.027	0.008	0.035
filterChimericReads	5.449	0.276	5.725
genomeSequencerMIDs	0.057	0.010	0.067
getAlignedReads	0.138	0.018	0.156
getVariantPercentages	0.062	0.012	0.074
htmlReport	6.364	0.756	7.173
mapperSetExample	0.008	0.003	0.011
mergeBreakpoints	10.989	0.371	11.358
mutationInfo	0.005	0.005	0.009
plotAmpliconCoverage	0	0	0
plotChimericReads	4.337	0.046	4.384
plotVariants	0.008	0.002	0.010
plotVariationFrequency	0	0	0
qualityReportSFF	0.000	0.001	0.001
readSFF	0.179	0.004	0.184
readsOnTarget	0.109	0.003	0.112
referenceSequences	0.014	0.006	0.020
regions	0.005	0.005	0.010
removeLinker	0.035	0.001	0.037
sequenceCaptureLinkers	0.011	0.000	0.012
setVariantFilter	0.089	0.008	0.098
variants	0.003	0.003	0.006
writeSFF	0.074	0.001	0.075