BioC 3.2: CHECK report for hiReadsProcessor on windows1.bioconductor.org

Package: hiReadsProcessor

Version: 1.6.0

Command: rm -rf hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && mkdir hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiReadsProcessor.buildbin-libdir hiReadsProcessor_1.6.0.tar.gz >hiReadsProcessor.Rcheck\00install.out 2>&1 && cp hiReadsProcessor.Rcheck\00install.out hiReadsProcessor-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiReadsProcessor.buildbin-libdir --install="check:hiReadsProcessor-install.out" --force-multiarch --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz

StartedAt: 2015-10-27 02:44:08 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:49:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 319.4 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && mkdir hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiReadsProcessor.buildbin-libdir hiReadsProcessor_1.6.0.tar.gz >hiReadsProcessor.Rcheck\00install.out 2>&1 && cp hiReadsProcessor.Rcheck\00install.out hiReadsProcessor-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiReadsProcessor.buildbin-libdir --install="check:hiReadsProcessor-install.out" --force-multiarch --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/hiReadsProcessor.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hiReadsProcessor/DESCRIPTION' ... OK
* this is package 'hiReadsProcessor' version '1.6.0'
* 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 whether package 'hiReadsProcessor' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chunkize: no visible global function definition for 'breakInChunks'
chunkize: no visible global function definition for 'detectCores'
clusterSites: no visible binding for global variable 'n'
clusterSites: no visible global function definition for 'desc'
clusterSites: no visible global function definition for 'contains'
clusterSites: no visible binding for global variable 'clusteredValue'
clusterSites: no visible binding for global variable
  'clusteredValue.freq'
crossOverCheck: no visible binding for global variable 'n'
decodeByBarcode: no visible global function definition for 'metadata<-'
decodeByBarcode: no visible global function definition for 'metadata'
extractSeqs : <anonymous>: no visible global function definition for
  'metadata'
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'IRanges'
extractSeqs : <anonymous> : <anonymous>: no visible global function
  definition for 'IRanges'
findBarcodes: no visible global function definition for 'metadata<-'
findBarcodes: no visible global function definition for 'metadata'
findIntegrations : <anonymous>: no visible global function definition
  for 'IRanges'
findVector : <anonymous>: no visible global function definition for
  'IRanges'
getSonicAbund: no visible binding for global variable 'n'
pairwiseAlignSeqs: no visible global function definition for
  'IRangesList'
pairwiseAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for
  'IRangesList'
pslToRangedObject: no visible global function definition for 'IRanges'
read.BAMasPSL: no visible global function definition for 'ScanBamParam'
read.BAMasPSL: no visible global function definition for 'scanBamFlag'
read.BAMasPSL: no visible global function definition for 'DataFrame'
read.SeqFolder: no visible global function definition for 'SimpleList'
read.psl: no visible global function definition for 'mclapply'
read.psl : <anonymous>: no visible binding for global variable
  'matches'
read.psl : <anonymous>: no visible binding for global variable
  'misMatches'
read.psl : <anonymous>: no visible binding for global variable
  'qBaseInsert'
read.psl : <anonymous>: no visible binding for global variable
  'tBaseInsert'
read.psl: no visible binding for global variable 'matches'
read.psl: no visible binding for global variable 'misMatches'
read.psl: no visible binding for global variable 'qBaseInsert'
read.psl: no visible binding for global variable 'tBaseInsert'
read.sampleInfo: no visible global function definition for 'SimpleList'
troubleshootLinkers : <anonymous>: no visible global function
  definition for 'try_default'
vpairwiseAlignSeqs: no visible global function definition for 'Rle'
vpairwiseAlignSeqs: no visible global function definition for
  'runLength'
vpairwiseAlignSeqs: no visible global function definition for 'IRanges'
vpairwiseAlignSeqs: no visible global function definition for
  'runValue'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
** running examples for arch 'x64' ... [27s] 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: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/hiReadsProcessor.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'hiReadsProcessor' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'hiReadsProcessor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiReadsProcessor' as hiReadsProcessor_1.6.0.zip
* DONE (hiReadsProcessor)

name	user	system	elapsed
addFeature	0.11	0.00	0.11
addListNameToReads	0.3	0.0	0.3
annotateSites	0	0	0
blatSeqs	0	0	0
chunkize	0.03	0.00	0.03
clusterSites	0	0	0
crossOverCheck	0.09	0.00	0.09
dereplicateReads	0.03	0.00	0.03
doRCtest	0.03	0.00	0.03
extractFeature	0.11	0.00	0.11
extractSeqs	0.53	0.01	0.55
findAndTrimSeq	0.83	0.05	0.88
findBarcodes	0.35	0.00	0.34
findIntegrations	0	0	0
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0	0	0
findVector	0	0	0
getIntegrationSites	0.72	0.00	0.72
getSectorsForSamples	0.17	0.00	0.18
getSonicAbund	1.16	0.04	1.20
isuSites	1.17	0.02	1.19
otuSites	1.27	0.00	1.26
pairUpAlignments	0	0	0
pairwiseAlignSeqs	1.60	0.03	1.64
primerIDAlignSeqs	1.61	0.06	1.67
pslCols	0	0	0
pslToRangedObject	0.07	0.00	0.07
read.BAMasPSL	0	0	0
read.SeqFolder	1.97	0.02	2.22
read.blast8	0	0	0
read.psl	0	0	0
read.sampleInfo	2.06	0.00	2.06
read.seqsFromSector	0	0	0
removeReadsWithNs	0.03	0.00	0.03
replicateReads	0.05	0.00	0.05
sampleSummary	0.70	0.03	0.73
splitByBarcode	0.03	0.00	0.03
splitSeqsToFiles	0	0	0
startgfServer	0	0	0
trimSeqs	0.03	0.00	0.03
vpairwiseAlignSeqs	0.61	0.00	0.61
write.listedDNAStringSet	0	0	0
write.psl	0.03	0.02	0.05

name	user	system	elapsed
addFeature	0.09	0.00	0.10
addListNameToReads	0.36	0.00	0.36
annotateSites	0	0	0
blatSeqs	0	0	0
chunkize	0.05	0.00	0.04
clusterSites	0	0	0
crossOverCheck	0.10	0.00	0.11
dereplicateReads	0.36	0.00	0.36
doRCtest	0.04	0.00	0.03
extractFeature	0.09	0.01	0.11
extractSeqs	0.61	0.00	0.61
findAndTrimSeq	1.25	0.00	1.25
findBarcodes	0.37	0.00	0.38
findIntegrations	0	0	0
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0	0	0
findVector	0	0	0
getIntegrationSites	0.75	0.00	0.75
getSectorsForSamples	0.10	0.00	0.09
getSonicAbund	0.76	0.05	0.81
isuSites	1.67	0.00	1.68
otuSites	1.80	0.00	1.79
pairUpAlignments	0	0	0
pairwiseAlignSeqs	1.44	0.05	1.49
primerIDAlignSeqs	1.64	0.01	1.65
pslCols	0	0	0
pslToRangedObject	0.07	0.00	0.08
read.BAMasPSL	0	0	0
read.SeqFolder	2.00	0.02	1.90
read.blast8	0	0	0
read.psl	0	0	0
read.sampleInfo	2.55	0.00	2.53
read.seqsFromSector	0	0	0
removeReadsWithNs	0.03	0.00	0.04
replicateReads	0.06	0.00	0.06
sampleSummary	0.63	0.00	0.62
splitByBarcode	0.03	0.00	0.03
splitSeqsToFiles	0	0	0
startgfServer	0	0	0
trimSeqs	0.03	0.00	0.04
vpairwiseAlignSeqs	0.74	0.00	0.73
write.listedDNAStringSet	0	0	0
write.psl	0.03	0.00	0.03