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This page was generated on 2024-03-28 11:32:22 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 964/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.38.0  (landing page)
Nirav V Malani
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/hiReadsProcessor
git_branch: RELEASE_3_18
git_last_commit: d60e18c
git_last_commit_date: 2023-10-24 10:00:50 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for hiReadsProcessor on kjohnson1


To the developers/maintainers of the hiReadsProcessor package:
- 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: 1.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hiReadsProcessor_1.38.0.tar.gz
StartedAt: 2024-03-27 16:03:35 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 16:08:58 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 323.1 seconds
RetCode: 0
Status:   OK  
CheckDir: hiReadsProcessor.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hiReadsProcessor_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/hiReadsProcessor.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.38.0’
* 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-3.18-bioc-mac-arm64/meat/hiReadsProcessor.Rcheck/00check.log’
for details.



Installation output

hiReadsProcessor.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
addFeature0.2150.0070.223
addListNameToReads0.3120.0160.331
annotateSites000
blatSeqs000
chunkize0.0280.0040.032
clusterSites0.3360.0260.363
crossOverCheck0.1330.0060.140
dereplicateReads0.0350.0000.036
doRCtest4.1480.1214.244
extractFeature0.1460.0280.173
extractSeqs0.3580.0650.424
findAndTrimSeq1.2770.2711.548
findBarcodes1.0500.0021.052
findIntegrations000
findLTRs0.0000.0000.001
findLinkers0.0000.0010.000
findPrimers000
findVector000
getIntegrationSites2.1420.0082.151
getSectorsForSamples0.1200.0020.121
getSonicAbund0.3710.2250.585
isuSites4.1130.2804.397
otuSites4.8730.0164.908
pairUpAlignments000
pairwiseAlignSeqs2.3071.0573.259
primerIDAlignSeqs3.4110.5063.869
pslCols0.0010.0000.001
pslToRangedObject0.1780.0060.184
read.BAMasPSL0.0000.0010.001
read.SeqFolder0.8410.0250.869
read.blast8000
read.psl0.0010.0000.000
read.sampleInfo0.8690.0120.881
read.seqsFromSector000
removeReadsWithNs0.0170.0010.017
replicateReads0.0390.0010.040
sampleSummary0.6070.0130.620
splitByBarcode0.0260.0010.026
splitSeqsToFiles0.1310.0050.135
startgfServer0.0000.0000.001
trimSeqs0.0230.0010.024
vpairwiseAlignSeqs2.2070.8062.924
write.listedDNAStringSet000
write.psl0.0270.0050.032