BioC 3.2: CHECK report for hiReadsProcessor on oaxaca

Package: hiReadsProcessor

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz

StartedAt: 2015-10-27 04:39:09 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:44:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 305.3 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘hiReadsProcessor’ can be installed ... [27s/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
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 ... [48s/40s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
pairwiseAlignSeqs 4.369  2.121   3.991
* 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
  ‘/Users/biocbuild/bbs-3.2-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	0.136	0.008	0.144
addListNameToReads	0.454	0.008	0.462
annotateSites	0.000	0.000	0.001
blatSeqs	0.001	0.000	0.000
chunkize	0.070	0.001	0.071
clusterSites	0.001	0.000	0.001
crossOverCheck	0.175	0.003	0.177
dereplicateReads	0.054	0.000	0.055
doRCtest	0.052	0.016	1.222
extractFeature	1.697	0.876	0.208
extractSeqs	0.903	0.045	0.949
findAndTrimSeq	1.264	0.082	1.345
findBarcodes	0.389	0.001	0.390
findIntegrations	0.000	0.000	0.001
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0.000	0.000	0.001
findVector	0.000	0.000	0.001
getIntegrationSites	0.791	0.008	0.799
getSectorsForSamples	0.114	0.007	0.120
getSonicAbund	0.680	0.068	0.763
isuSites	1.659	0.023	1.681
otuSites	1.881	0.006	1.889
pairUpAlignments	0	0	0
pairwiseAlignSeqs	4.369	2.121	3.991
primerIDAlignSeqs	2.400	0.637	3.008
pslCols	0.001	0.000	0.001
pslToRangedObject	0.080	0.004	0.083
read.BAMasPSL	0.001	0.000	0.001
read.SeqFolder	2.590	0.044	2.760
read.blast8	0	0	0
read.psl	0.001	0.000	0.001
read.sampleInfo	2.465	0.008	2.446
read.seqsFromSector	0.000	0.000	0.001
removeReadsWithNs	0.054	0.000	0.055
replicateReads	0.086	0.001	0.087
sampleSummary	0.809	0.009	0.818
splitByBarcode	0.059	0.000	0.059
splitSeqsToFiles	0.001	0.000	0.001
startgfServer	0.001	0.000	0.001
trimSeqs	0.050	0.001	0.050
vpairwiseAlignSeqs	3.244	1.698	3.589
write.listedDNAStringSet	0.000	0.000	0.001
write.psl	0.030	0.005	0.035