Back to Multiple platform build/check report for BioC 3.8
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

CHECK report for hiReadsProcessor on merida1

This page was generated on 2019-04-16 11:57:53 -0400 (Tue, 16 Apr 2019).

Package 727/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.18.0
Nirav V Malani
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/hiReadsProcessor
Branch: RELEASE_3_8
Last Commit: c231665
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: hiReadsProcessor
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiReadsProcessor_1.18.0.tar.gz
StartedAt: 2019-04-16 00:34:30 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:39:20 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 290.0 seconds
RetCode: 0
Status:  OK 
CheckDir: hiReadsProcessor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiReadsProcessor_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.18.0’
* 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 ... 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 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 : <anonymous>: no visible binding for global variable
  ‘queryHits’
clusterSites: no visible binding for global variable ‘clusteredValue’
clusterSites: no visible binding for global variable
  ‘clusteredValue.freq’
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>: no visible global function
  definition for ‘IRanges’
findBarcodes: no visible global function definition for ‘metadata<-’
findBarcodes: no visible global function definition for ‘metadata’
findIntegrations: no visible global function definition for
  ‘fasta.info’
findIntegrations : <anonymous>: no visible global function definition
  for ‘IRanges’
findVector : <anonymous>: no visible global function definition for
  ‘IRanges’
pairUpAlignments : <anonymous>: no visible binding for global variable
  ‘queryHits’
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’
splitSeqsToFiles: no visible global function definition for
  ‘fasta.info’
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 detectCores
  fasta.info matches mclapply metadata metadata<- misMatches
  qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.



Installation output

hiReadsProcessor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hiReadsProcessor
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘hiReadsProcessor’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hiReadsProcessor)

Tests output


Example timings

hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings

nameusersystemelapsed
addFeature0.2750.0070.284
addListNameToReads0.3940.0100.409
annotateSites0.0000.0010.000
blatSeqs000
chunkize0.0330.0020.036
clusterSites0.4150.0080.427
crossOverCheck0.2200.0070.227
dereplicateReads0.0260.0000.026
doRCtest0.1900.0930.272
extractFeature0.1890.0480.241
extractSeqs1.2650.2081.485
findAndTrimSeq1.5890.0441.647
findBarcodes0.6390.0010.643
findIntegrations0.0000.0000.001
findLTRs000
findLinkers000
findPrimers000
findVector0.0010.0000.000
getIntegrationSites1.6220.0111.654
getSectorsForSamples0.1320.0050.137
getSonicAbund0.3520.0990.458
isuSites2.8010.0192.847
otuSites3.0110.0073.037
pairUpAlignments000
pairwiseAlignSeqs2.2560.7612.876
primerIDAlignSeqs2.8050.4223.164
pslCols0.0010.0010.001
pslToRangedObject0.2380.0060.247
read.BAMasPSL000
read.SeqFolder1.3080.0861.409
read.blast80.0000.0000.001
read.psl0.0000.0000.001
read.sampleInfo1.1980.0081.212
read.seqsFromSector000
removeReadsWithNs0.0220.0010.022
replicateReads0.0390.0010.041
sampleSummary0.6400.0160.666
splitByBarcode0.0260.0000.027
splitSeqsToFiles0.2130.0060.220
startgfServer000
trimSeqs0.0380.0010.039
vpairwiseAlignSeqs2.0500.7962.691
write.listedDNAStringSet0.0010.0010.000
write.psl0.0330.0080.042