BioC 3.0: CHECK report for hiReadsProcessor on zin1

Package: hiReadsProcessor

Version: 1.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.0.0.tar.gz

StartedAt: 2015-04-10 01:01:47 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:06:32 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 285.3 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.0.0’
* 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 ‘hiReadsProcessor’ can be installed ... [25s/28s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
blatListedSet : <anonymous>: no visible binding for global variable
  ‘GRangesList’
chunkize: no visible global function definition for ‘breakInChunks’
chunkize: no visible global function definition for ‘detectCores’
clusterSites: no visible global function definition for ‘mcols’
clusterSites: no visible global function definition for ‘strand’
clusterSites: no visible global function definition for ‘mcols<-’
clusterSites : <anonymous>: no visible binding for global variable
  ‘queryHits’
crossOverCheck: no visible global function definition for ‘strand’
crossOverCheck: no visible global function definition for ‘mcols’
crossOverCheck: no visible global function definition for ‘mcols<-’
crossOverCheck: no visible binding for global variable ‘queryHits’
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> : <anonymous>: no visible
  global function definition for ‘end<-’
extractSeqs : <anonymous> : <anonymous>: no visible global function
  definition for ‘IRanges’
extractSeqs : <anonymous> : <anonymous>: no visible global function
  definition for ‘end<-’
findAndRemoveVector: no visible global function definition for ‘reduce’
findAndRemoveVector : <anonymous>: no visible global function
  definition for ‘ranges’
findAndRemoveVector: no visible global function definition for
  ‘GRangesList’
findAndRemoveVector: no visible global function definition for ‘mcols’
findBarcodes: no visible global function definition for ‘metadata<-’
findBarcodes: no visible global function definition for ‘metadata’
findIntegrations: no visible global function definition for ‘mcols’
findIntegrations: no visible global function definition for ‘mcols<-’
findIntegrations : <anonymous>: no visible global function definition
  for ‘mcols’
findIntegrations : <anonymous>: no visible global function definition
  for ‘ranges<-’
findIntegrations : <anonymous>: no visible global function definition
  for ‘IRanges’
findLTRs: no visible global function definition for ‘end<-’
findLTRs: no visible global function definition for ‘start<-’
findVector : <anonymous>: no visible global function definition for
  ‘IRanges’
findVector : <anonymous>: no visible global function definition for
  ‘ranges’
findVector: no visible global function definition for ‘end<-’
findVector: no visible global function definition for ‘start<-’
getIntegrationSites: no visible global function definition for ‘mcols’
getIntegrationSites: no visible global function definition for
  ‘mcols<-’
getIntegrationSites: no visible global function definition for ‘strand’
getIntegrationSites: no visible global function definition for ‘flank’
getSonicAbund: no visible global function definition for ‘mcols’
getSonicAbund: no visible global function definition for ‘strand’
getSonicAbund: no visible global function definition for ‘mcols<-’
isuSites: no visible global function definition for ‘mcols’
isuSites: no visible global function definition for ‘mcols<-’
otuSites: no visible global function definition for ‘mcols’
otuSites: no visible global function definition for ‘strand’
otuSites: no visible global function definition for ‘mcols<-’
otuSites : <anonymous>: no visible global function definition for
  ‘mcols’
otuSites : <anonymous>: no visible global function definition for
  ‘mcols<-’
otuSites: no visible global function definition for ‘GRangesList’
pairUpAlignments: no visible global function definition for ‘mcols’
pairUpAlignments: no visible global function definition for ‘mcols<-’
pairUpAlignments: no visible global function definition for ‘GRanges’
pairUpAlignments: no visible global function definition for ‘ranges’
pairUpAlignments: no visible global function definition for ‘strand’
pairUpAlignments: no visible global function definition for ‘reduce’
pairUpAlignments : <anonymous>: no visible global function definition
  for ‘mcols’
pairUpAlignments : <anonymous>: no visible binding for global variable
  ‘queryHits’
pairUpAlignments : <anonymous>: no visible global function definition
  for ‘mcols<-’
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 ‘resize’
primerIDAlignSeqs: no visible global function definition for
  ‘IRangesList’
pslToRangedObject: no visible global function definition for ‘GRanges’
pslToRangedObject: no visible global function definition for ‘IRanges’
pslToRangedObject: no visible global function definition for ‘mcols’
pslToRangedObject: no visible global function definition for ‘mcols<-’
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 ‘mcols’
read.BAMasPSL: no visible global function definition for ‘mcols<-’
read.BAMasPSL: no visible global function definition for ‘DataFrame’
read.SeqFolder: no visible global function definition for ‘SimpleList’
read.sampleInfo: no visible global function definition for ‘SimpleList’
vpairwiseAlignSeqs: no visible global function definition for ‘Rle’
vpairwiseAlignSeqs: no visible global function definition for
  ‘runLength’
vpairwiseAlignSeqs: no visible global function definition for ‘reduce’
vpairwiseAlignSeqs: no visible global function definition for ‘GRanges’
vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’
vpairwiseAlignSeqs: no visible global function definition for ‘ranges’
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 ... [32s/32s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.

* 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
* DONE (hiReadsProcessor)

name	user	system	elapsed
addFeature	0.108	0.000	0.110
addListNameToReads	0.656	0.024	0.685
annotateSites	0	0	0
blatSeqs	0	0	0
chunkize	0.056	0.000	0.059
clusterSites	0.000	0.000	0.001
crossOverCheck	0.288	0.000	0.294
dereplicateReads	0.044	0.000	0.043
doRCtest	0.040	0.016	0.072
extractFeature	0.124	0.004	0.132
extractSeqs	0.956	0.040	0.997
findAndTrimSeq	1.592	0.016	1.649
findBarcodes	0.304	0.000	0.303
findIntegrations	0.000	0.000	0.001
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0.000	0.000	0.001
findVector	0	0	0
getIntegrationSites	0.661	0.000	0.658
getSectorsForSamples	0.104	0.004	0.110
getSonicAbund	0.700	0.004	0.710
isuSites	1.640	0.356	2.028
otuSites	1.928	0.476	1.937
pairUpAlignments	0	0	0
pairwiseAlignSeqs	1.356	0.184	1.420
primerIDAlignSeqs	1.460	0.104	1.564
pslCols	0.000	0.000	0.001
pslToRangedObject	0.064	0.008	0.072
read.BAMasPSL	0	0	0
read.SeqFolder	2.576	0.020	2.658
read.blast8	0.004	0.000	0.000
read.psl	0.092	0.004	0.095
read.sampleInfo	2.404	0.008	2.451
read.seqsFromSector	0	0	0
removeReadsWithNs	0.036	0.000	0.035
replicateReads	0.068	0.000	0.068
sampleSummary	0.776	0.000	0.813
splitByBarcode	0.044	0.000	0.050
splitSeqsToFiles	0.000	0.000	0.001
startgfServer	0	0	0
trimSeqs	0.060	0.000	0.062
vpairwiseAlignSeqs	0.676	0.144	0.866
write.listedDNAStringSet	0	0	0
write.psl	0.028	0.000	0.030