BioC 3.3: CHECK report for hiReadsProcessor on linux2.bioconductor.org

Package: hiReadsProcessor

Version: 1.7.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.7.0.tar.gz

StartedAt: 2015-10-27 04:50:16 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:54:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 223.9 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/hiReadsProcessor.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.7.0’
* 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 ... [21s/21s] 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
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’
Undefined global functions or variables:
  DataFrame IRanges IRangesList Rle ScanBamParam SimpleList
  breakInChunks clusteredValue clusteredValue.freq contains desc
  detectCores matches mclapply metadata metadata<- misMatches n
  qBaseInsert runLength runValue scanBamFlag tBaseInsert try_default
* 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 ... [37s/31s] 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
  ‘/home/biocbuild/bbs-3.3-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	0.09	0.00	0.09
addListNameToReads	0.288	0.008	0.296
annotateSites	0	0	0
blatSeqs	0	0	0
chunkize	0.036	0.000	0.037
clusterSites	0	0	0
crossOverCheck	0.098	0.000	0.098
dereplicateReads	0.039	0.000	0.039
doRCtest	0.038	0.012	0.935
extractFeature	1.561	0.363	0.111
extractSeqs	0.494	0.012	0.505
findAndTrimSeq	1.142	0.016	1.157
findBarcodes	0.342	0.000	0.342
findIntegrations	0	0	0
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0.001	0.000	0.000
findVector	0.001	0.000	0.000
getIntegrationSites	0.706	0.000	0.705
getSectorsForSamples	0.085	0.000	0.085
getSonicAbund	0.311	0.016	0.329
isuSites	1.436	0.000	1.435
otuSites	1.650	0.000	1.651
pairUpAlignments	0.000	0.000	0.001
pairwiseAlignSeqs	3.781	0.931	2.871
primerIDAlignSeqs	2.885	0.406	2.478
pslCols	0	0	0
pslToRangedObject	0.048	0.000	0.048
read.BAMasPSL	0	0	0
read.SeqFolder	2.553	0.024	2.457
read.blast8	0.001	0.000	0.000
read.psl	0.001	0.000	0.001
read.sampleInfo	2.714	0.004	2.688
read.seqsFromSector	0.001	0.000	0.000
removeReadsWithNs	0.020	0.004	0.027
replicateReads	0.05	0.00	0.05
sampleSummary	0.662	0.000	0.663
splitByBarcode	0.030	0.000	0.031
splitSeqsToFiles	0.001	0.000	0.000
startgfServer	0	0	0
trimSeqs	0.025	0.000	0.026
vpairwiseAlignSeqs	3.496	0.924	2.615
write.listedDNAStringSet	0.001	0.000	0.001
write.psl	0.041	0.004	0.045