BioC 3.2: CHECK report for hiReadsProcessor on zin1

Package: hiReadsProcessor

Version: 1.6.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz

StartedAt: 2016-04-23 01:51:33 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:55:25 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 231.6 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hiReadsProcessor’ can be installed ... [21s/20s] 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 ... [37s/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

Status: 2 NOTEs
See
  ‘/home/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	0.1	0.0	0.1
addListNameToReads	0.339	0.016	0.354
annotateSites	0.000	0.000	0.001
blatSeqs	0.001	0.000	0.000
chunkize	0.054	0.000	0.054
clusterSites	0.000	0.000	0.001
crossOverCheck	0.128	0.000	0.127
dereplicateReads	0.041	0.000	0.041
doRCtest	0.038	0.012	0.841
extractFeature	1.442	0.312	0.142
extractSeqs	0.631	0.004	0.634
findAndTrimSeq	1.255	0.024	1.277
findBarcodes	0.353	0.004	0.357
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	0.701	0.000	0.702
getSectorsForSamples	0.089	0.000	0.089
getSonicAbund	0.649	0.024	0.699
isuSites	1.420	0.000	1.418
otuSites	1.725	0.000	1.722
pairUpAlignments	0.000	0.000	0.001
pairwiseAlignSeqs	3.783	0.802	2.950
primerIDAlignSeqs	2.938	0.373	2.477
pslCols	0.000	0.000	0.001
pslToRangedObject	0.060	0.001	0.061
read.BAMasPSL	0.000	0.000	0.001
read.SeqFolder	2.152	0.020	2.126
read.blast8	0.001	0.000	0.001
read.psl	0.001	0.000	0.001
read.sampleInfo	2.237	0.000	2.227
read.seqsFromSector	0	0	0
removeReadsWithNs	0.032	0.000	0.032
replicateReads	0.059	0.000	0.059
sampleSummary	0.674	0.003	0.677
splitByBarcode	0.044	0.000	0.045
splitSeqsToFiles	0	0	0
startgfServer	0.001	0.000	0.001
trimSeqs	0.033	0.000	0.033
vpairwiseAlignSeqs	3.458	0.889	2.626
write.listedDNAStringSet	0	0	0
write.psl	0.031	0.004	0.034