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This page was generated on 2022-06-27 11:09:57 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hiReadsProcessor on nebbiolo1


To the developers/maintainers of the hiReadsProcessor package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiReadsProcessor.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 902/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.32.0  (landing page)
Nirav V Malani
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/hiReadsProcessor
git_branch: RELEASE_3_15
git_last_commit: 2107a54
git_last_commit_date: 2022-04-26 11:21:09 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hiReadsProcessor
Version: 1.32.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.32.0.tar.gz
StartedAt: 2022-06-26 20:15:25 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:19:28 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 243.0 seconds
RetCode: 0
Status:   OK  
CheckDir: hiReadsProcessor.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.32.0’
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.



Installation output

hiReadsProcessor.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL hiReadsProcessor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘hiReadsProcessor’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hiReadsProcessor)

Tests output


Example timings

hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings

nameusersystemelapsed
addFeature0.1780.0240.202
addListNameToReads0.2820.0120.293
annotateSites000
blatSeqs000
chunkize0.0260.0040.030
clusterSites0.310.000.31
crossOverCheck0.1010.0040.104
dereplicateReads0.0420.0000.042
doRCtest1.8600.0992.195
extractFeature0.1640.1040.121
extractSeqs0.3180.0560.374
findAndTrimSeq1.3900.1241.515
findBarcodes0.9980.0081.006
findIntegrations000
findLTRs000
findLinkers000
findPrimers0.0000.0000.001
findVector0.0000.0010.000
getIntegrationSites2.1400.0432.183
getSectorsForSamples0.1300.0000.266
getSonicAbund0.3550.1750.574
isuSites3.7020.1163.817
otuSites3.9380.0404.197
pairUpAlignments0.0010.0000.000
pairwiseAlignSeqs2.4210.6503.113
primerIDAlignSeqs3.1860.3253.391
pslCols000
pslToRangedObject0.1910.0000.191
read.BAMasPSL0.0010.0000.000
read.SeqFolder1.0520.0361.259
read.blast80.0000.0000.001
read.psl0.0000.0000.001
read.sampleInfo0.8020.0180.820
read.seqsFromSector0.0000.0000.001
removeReadsWithNs0.0180.0000.018
replicateReads0.0370.0000.037
sampleSummary0.5080.0080.515
splitByBarcode0.0190.0070.027
splitSeqsToFiles0.1270.0040.132
startgfServer0.0000.0000.001
trimSeqs0.0200.0030.024
vpairwiseAlignSeqs2.1360.4772.400
write.listedDNAStringSet0.0000.0000.001
write.psl0.0250.0000.025