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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 963/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.43.0  (landing page)
Nirav V Malani
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/hiReadsProcessor
git_branch: devel
git_last_commit: b964203
git_last_commit_date: 2024-10-29 09:54:10 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.43.0
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_1.43.0.tar.gz
StartedAt: 2024-12-23 22:53:39 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:58:35 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 296.5 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_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/hiReadsProcessor.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.43.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
isuSites 4.881  0.454   5.338
* 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

##############################################################################
##############################################################################
###
### 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’ ...
** 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
addFeature0.1700.0190.189
addListNameToReads0.2320.0360.268
annotateSites000
blatSeqs000
chunkize0.0260.0050.032
clusterSites0.3170.0390.360
crossOverCheck0.0880.0000.088
dereplicateReads0.0340.0010.035
doRCtest3.9890.1554.164
extractFeature0.1350.1380.128
extractSeqs0.3370.0390.377
findAndTrimSeq1.3050.1601.465
findBarcodes1.0030.0031.006
findIntegrations000
findLTRs000
findLinkers000
findPrimers0.0010.0000.000
findVector0.0000.0010.001
getIntegrationSites1.9650.0041.969
getSectorsForSamples0.0810.0070.088
getSonicAbund0.3950.2070.551
isuSites4.8810.4545.338
otuSites4.4660.0034.470
pairUpAlignments000
pairwiseAlignSeqs2.2710.7672.850
primerIDAlignSeqs3.6090.4343.969
pslCols0.0000.0010.001
pslToRangedObject0.1880.0030.191
read.BAMasPSL000
read.SeqFolder0.9790.0200.999
read.blast8000
read.psl0.0000.0010.001
read.sampleInfo0.9110.0050.916
read.seqsFromSector0.0010.0000.000
removeReadsWithNs0.0190.0010.020
replicateReads0.0410.0000.041
sampleSummary0.5660.0230.589
splitByBarcode0.0270.0000.027
splitSeqsToFiles0.1230.0040.126
startgfServer000
trimSeqs0.0260.0000.025
vpairwiseAlignSeqs2.1470.7872.754
write.listedDNAStringSet000
write.psl0.0270.0010.028