BioC 3.1: CHECK report for R453Plus1Toolbox on zin2

Package: R453Plus1Toolbox

Version: 1.18.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.18.0.tar.gz

StartedAt: 2015-10-09 04:39:54 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:44:00 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 245.5 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.18.0’
* 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 ... [19s/19s] 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
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 5.005  0.036   5.193
* 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-3.1-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.243	0.008	0.251
AVASet	0.116	0.016	0.132
AnnotatedVariants-class	0.001	0.000	0.002
MapperSet-class	0.019	0.012	0.031
MapperSet	0.006	0.000	0.006
SFFContainer-class	0.002	0.000	0.002
SFFRead-class	0.002	0.000	0.002
alignShortReads	1.532	0.000	1.547
annotateVariants	0.001	0.000	0.002
assayDataAmp	0.003	0.000	0.005
ava2vcf	0.205	0.000	0.215
avaSetExample	0.017	0.000	0.017
avaSetFiltered	0.022	0.004	0.026
avaSetFiltered_annot	0.002	0.000	0.003
breakpoints	0.004	0.000	0.003
calculateTiTv	0.012	0.000	0.012
captureArray	0.002	0.000	0.002
coverageOnTarget	0.148	0.016	0.172
demultiplexReads	0.101	0.000	0.109
detectBreakpoints	0.543	0.000	0.569
fDataAmp	0.017	0.000	0.017
featureDataAmp	0.017	0.000	0.016
filterChimericReads	1.901	0.004	1.943
genomeSequencerMIDs	0.025	0.000	0.025
getAlignedReads	0.081	0.000	0.081
getVariantPercentages	0.034	0.000	0.034
htmlReport	3.231	0.055	3.376
mapperSetExample	0.002	0.004	0.006
mergeBreakpoints	5.005	0.036	5.193
mutationInfo	0.003	0.000	0.002
plotAmpliconCoverage	0	0	0
plotChimericReads	2.919	0.000	2.924
plotVariants	0.005	0.000	0.005
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.061	0.000	0.060
readsOnTarget	0.264	0.004	0.269
referenceSequences	0.008	0.000	0.007
regions	0.002	0.000	0.003
removeLinker	0.02	0.00	0.02
sequenceCaptureLinkers	0.005	0.000	0.004
setVariantFilter	0.052	0.000	0.057
variants	0.003	0.000	0.003
writeSFF	0.027	0.000	0.027