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This page was generated on 2025-09-22 11:37 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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

Package 987/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.44.0  (landing page)
Nirav V Malani
Snapshot Date: 2025-09-18 13:40 -0400 (Thu, 18 Sep 2025)
git_url: https://git.bioconductor.org/packages/hiReadsProcessor
git_branch: RELEASE_3_21
git_last_commit: 2a9fd2b
git_last_commit_date: 2025-04-15 10:33:28 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for hiReadsProcessor on nebbiolo1

To the developers/maintainers of the hiReadsProcessor package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: hiReadsProcessor
Version: 1.44.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings hiReadsProcessor_1.44.0.tar.gz
StartedAt: 2025-09-22 00:00:20 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 00:05:26 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 306.5 seconds
RetCode: 0
Status:   OK  
CheckDir: hiReadsProcessor.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings hiReadsProcessor_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.44.0’
* 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 code 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 : <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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotateSites.Rd: SerialParam, doAnnotation
  blatSeqs.Rd: BiocParallel, SerialParam
  clusterSites.Rd: BiocParallel, SerialParam
  doRCtest.Rd: vcountPattern, BiocParallel, SerialParam
  findAndRemoveVector.Rd: BiocParallel, SerialParam, MulticoreParam,
    SnowParam
  findAndTrimSeq.Rd: vmatchPattern, pairwiseAlignment, MulticoreParam,
    SnowParam
  findIntegrations.Rd: BiocParallel, SerialParam, MulticoreParam,
    SnowParam
  findLTRs.Rd: BiocParallel, SerialParam, pairwiseAlignment,
    MulticoreParam, SnowParam
  findLinkers.Rd: BiocParallel, SerialParam, pairwiseAlignment,
    MulticoreParam, SnowParam
  findPrimers.Rd: vmatchPattern, pairwiseAlignment, SerialParam,
    MulticoreParam, SnowParam
  findVector.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
  getSonicAbund.Rd: sonicLength, BiocParallel, SerialParam
  isuSites.Rd: BiocParallel, SerialParam
  otuSites.Rd: BiocParallel, SerialParam
  pairUpAlignments.Rd: BiocParallel, SerialParam
  pairwiseAlignSeqs.Rd: pairwiseAlignment, BiocParallel, SerialParam,
    MulticoreParam, SnowParam
  primerIDAlignSeqs.Rd: pairwiseAlignment
  read.blast8.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
  read.psl.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
  troubleshootLinkers.Rd: BiocParallel, SerialParam, pairwiseAlignment,
    MulticoreParam, SnowParam
  vpairwiseAlignSeqs.Rd: vmatchPattern, BiocParallel, SerialParam,
    MulticoreParam, SnowParam
  write.listedDNAStringSet.Rd: BiocParallel, SerialParam,
    writeXStringSet, MulticoreParam, SnowParam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.


Installation output

hiReadsProcessor.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL hiReadsProcessor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘hiReadsProcessor’ ...
** this is package ‘hiReadsProcessor’ version ‘1.44.0’
** 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
addFeature0.1720.0190.190
addListNameToReads0.2460.0030.249
annotateSites000
blatSeqs0.0010.0000.000
chunkize0.0270.0000.027
clusterSites0.2840.0010.284
crossOverCheck0.0930.0000.093
dereplicateReads0.0380.0010.038
doRCtest3.5870.1333.738
extractFeature0.1330.0940.124
extractSeqs0.3450.0290.374
findAndTrimSeq1.1760.1661.341
findBarcodes0.8910.0020.893
findIntegrations0.0010.0000.000
findLTRs000
findLinkers000
findPrimers0.0000.0000.001
findVector000
getIntegrationSites2.0840.0022.092
getSectorsForSamples0.0800.0060.086
getSonicAbund0.2990.1760.440
isuSites3.5860.2263.813
otuSites4.2770.0684.346
pairUpAlignments000
pairwiseAlignSeqs2.6150.9083.318
primerIDAlignSeqs3.8580.6794.446
pslCols0.0010.0000.001
pslToRangedObject0.1610.0020.163
read.BAMasPSL0.0010.0000.000
read.SeqFolder0.9110.0450.956
read.blast8000
read.psl000
read.sampleInfo0.9040.0510.955
read.seqsFromSector000
removeReadsWithNs0.0190.0010.019
replicateReads0.0470.0010.048
sampleSummary0.5970.1590.755
splitByBarcode0.0300.0090.039
splitSeqsToFiles0.1280.0210.150
startgfServer000
trimSeqs0.0240.0010.026
vpairwiseAlignSeqs2.1301.1683.118
write.listedDNAStringSet000
write.psl0.0190.0000.019