BioC 3.0: CHECK report for hiReadsProcessor on oaxaca

Package: hiReadsProcessor

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hiReadsProcessor_1.0.0.tar.gz

StartedAt: 2015-04-10 00:28:49 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:34:32 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 343.0 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hiReadsProcessor_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [30s/37s] 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 ... [40s/39s] 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
  ‘/Users/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	0.143	0.009	0.151
addListNameToReads	0.560	0.010	0.579
annotateSites	0	0	0
blatSeqs	0.001	0.000	0.001
chunkize	0.067	0.001	0.068
clusterSites	0	0	0
crossOverCheck	0.365	0.007	0.379
dereplicateReads	0.060	0.001	0.061
doRCtest	0.051	0.035	0.089
extractFeature	0.161	0.017	0.179
extractSeqs	0.964	0.033	1.001
findAndTrimSeq	1.697	0.079	1.803
findBarcodes	0.315	0.002	0.317
findIntegrations	0	0	0
findLTRs	0.000	0.000	0.001
findLinkers	0.000	0.000	0.001
findPrimers	0	0	0
findVector	0	0	0
getIntegrationSites	0.750	0.007	0.773
getSectorsForSamples	0.130	0.006	0.137
getSonicAbund	0.485	0.050	0.560
isuSites	2.098	0.735	2.145
otuSites	2.556	1.082	2.583
pairUpAlignments	0	0	0
pairwiseAlignSeqs	1.391	0.333	1.472
primerIDAlignSeqs	1.819	0.162	2.061
pslCols	0.001	0.001	0.001
pslToRangedObject	0.091	0.006	0.098
read.BAMasPSL	0.001	0.000	0.000
read.SeqFolder	3.384	0.055	3.661
read.blast8	0.001	0.000	0.001
read.psl	0.149	0.009	0.602
read.sampleInfo	3.276	0.008	3.273
read.seqsFromSector	0	0	0
removeReadsWithNs	0.054	0.001	0.055
replicateReads	0.105	0.001	0.106
sampleSummary	0.977	0.014	1.020
splitByBarcode	0.066	0.000	0.066
splitSeqsToFiles	0.000	0.000	0.001
startgfServer	0.001	0.000	0.001
trimSeqs	0.080	0.001	0.080
vpairwiseAlignSeqs	0.827	0.236	1.033
write.listedDNAStringSet	0.000	0.000	0.001
write.psl	0.036	0.006	0.042