BioC 3.2: CHECK report for hiReadsProcessor on oaxaca

Package: hiReadsProcessor

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.3.0.tar.gz

StartedAt: 2015-08-24 00:51:18 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:57:06 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 348.6 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 hiReadsProcessor_1.3.0.tar.gz
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* 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 ‘1.3.0’
* 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/38s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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’
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’
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.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 ‘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 ... [72s/52s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
isuSites           9.915  4.484   5.787
otuSites           9.006  3.996   6.137
vpairwiseAlignSeqs 4.006  2.195   3.735
* 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
  ‘/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	0.13	0.01	0.14
addListNameToReads	0.512	0.015	0.527
annotateSites	0.000	0.000	0.001
blatSeqs	0.001	0.000	0.001
chunkize	0.061	0.000	0.062
clusterSites	0	0	0
crossOverCheck	0.169	0.001	0.170
dereplicateReads	0.055	0.000	0.055
doRCtest	0.059	0.019	1.262
extractFeature	1.625	0.866	0.225
extractSeqs	0.875	0.041	0.974
findAndTrimSeq	1.289	0.081	1.372
findBarcodes	0.366	0.001	0.370
findIntegrations	0.000	0.001	0.000
findLTRs	0	0	0
findLinkers	0	0	0
findPrimers	0.001	0.000	0.001
findVector	0.001	0.001	0.001
getIntegrationSites	0.788	0.009	0.812
getSectorsForSamples	0.126	0.008	0.134
getSonicAbund	0.047	0.026	1.915
isuSites	9.915	4.484	5.787
otuSites	9.006	3.996	6.137
pairUpAlignments	0	0	0
pairwiseAlignSeqs	3.493	1.502	3.956
primerIDAlignSeqs	2.981	0.966	2.931
pslCols	0.001	0.001	0.002
pslToRangedObject	0.086	0.009	0.095
read.BAMasPSL	0.001	0.000	0.000
read.SeqFolder	2.607	0.045	3.070
read.blast8	0.000	0.000	0.001
read.psl	0.132	0.009	0.147
read.sampleInfo	2.769	0.008	2.753
read.seqsFromSector	0.000	0.000	0.001
removeReadsWithNs	0.048	0.001	0.048
replicateReads	0.089	0.001	0.091
sampleSummary	1.049	0.017	1.069
splitByBarcode	0.058	0.001	0.058
splitSeqsToFiles	0.001	0.000	0.001
startgfServer	0.001	0.000	0.001
trimSeqs	0.046	0.000	0.047
vpairwiseAlignSeqs	4.006	2.195	3.735
write.listedDNAStringSet	0	0	0
write.psl	0.030	0.006	0.038