Multiple platform build/check report for BioC 3.22 - CHECK results for R453Plus1Toolbox on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4764
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4586
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4529
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4554
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 R453Plus1Toolbox on lconway

To the developers/maintainers of the R453Plus1Toolbox package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R453Plus1Toolbox.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: R453Plus1Toolbox

Version: 1.59.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.59.0.tar.gz

StartedAt: 2025-09-16 23:11:18 -0400 (Tue, 16 Sep 2025)

EndedAt: 2025-09-16 23:18:21 -0400 (Tue, 16 Sep 2025)

EllapsedTime: 423.7 seconds

RetCode: 0

Status: OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.59.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.59.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘R453Plus1Toolbox’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.annotateVariants_MapperSet: no visible binding for global variable
  ‘Hsapiens’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.getEnsemblInfo: no visible binding for global variable ‘cds_length’
.getEnsemblInfo: no visible binding for global variable
  ‘ensembl_transcript_id’
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
.plotVariants: no visible binding for global variable ‘mutation’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
annotateVariants,MapperSet-BSgenome: no visible binding for global
  variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
  variable ‘Hsapiens’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
detectBreakpoints,list: no visible binding for global variable
  ‘Hsapiens’
subset,AVASet: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
  Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse
  cds_length ensembl_transcript_id mutation referenceSeqID
* 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:
  AVASet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class
  Breakpoints-class.Rd: PairwiseAlignmentsSingleSubject-class,
    AlignedRead-class
  MapperSet-class.Rd: eSet-class, VersionedBiobase-class,
    Versioned-class
  alignShortReads.Rd: matchPDict, DNAStringSet, AlignedRead
  ava2vcf.Rd: VCF-class, writeVcf
  baseFrequency.Rd: DNAStringSet, ShortRead, alphabetFrequency
  baseQualityHist.Rd: QualityScaledDNAStringSet, ShortReadQ
  baseQualityStats.Rd: QualityScaledDNAStringSet, ShortReadQ
  complexity.dust.Rd: DNAStringSet, ShortRead
  complexity.entropy.Rd: DNAStringSet, ShortRead
  coverageOnTarget.Rd: scanBam
  demultiplexReads.Rd: DNAStringSet
  detectBreakpoints.Rd: scanBam, IRanges,
    PairwiseAlignmentsSingleSubject, AlignedRead
  dinucleotideOddsRatio.Rd: DNAStringSet, ShortRead
  featureDataAmp.Rd: AnnotatedDataFrame
  filterChimericReads.Rd: scanBam
  gcContent.Rd: DNAStringSet, ShortRead
  gcContentHist.Rd: DNAStringSet, ShortRead
  gcPerPosition.Rd: DNAStringSet, ShortRead
  getAlignedReads.Rd: DNAStringSet
  htmlReport.Rd: fData
  nucleotideCharts.Rd: DNAStringSet, ShortRead
  positionQualityBoxplot.Rd: QualityScaledDNAStringSet, ShortReadQ
  readLengthHist.Rd: DNAStringSet, ShortRead
  readLengthStats.Rd: DNAStringSet, ShortRead
  readsOnTarget.Rd: scanBam
  removeLinker.Rd: DNAStringSet, pairwiseAlignment
  sequenceQualityHist.Rd: QualityScaledDNAStringSet, ShortReadQ
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 6.226  0.164   6.442
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

Installation output

R453Plus1Toolbox.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R453Plus1Toolbox
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** this is package ‘R453Plus1Toolbox’ version ‘1.59.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readSFF.c -o readSFF.o
readSFF.c:27:7: warning: variable 'block_count' set but not used [-Wunused-but-set-variable]
  int block_count;
      ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c writeSFF.c -o writeSFF.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R453Plus1Toolbox)

Tests output

Example timings

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings

name	user	system	elapsed
AVASet-class	0.187	0.016	0.207
AVASet	0.147	0.011	0.160
AnnotatedVariants-class	0.001	0.000	0.001
MapperSet-class	0.020	0.014	0.034
MapperSet	0.006	0.002	0.008
SFFContainer-class	0.001	0.001	0.001
SFFRead-class	0.001	0.000	0.001
alignShortReads	2.387	0.025	2.435
annotateVariants	0.001	0.000	0.001
assayDataAmp	0.003	0.003	0.006
ava2vcf	0.268	0.004	0.273
avaSetExample	0.014	0.004	0.017
avaSetFiltered	0.018	0.003	0.022
avaSetFiltered_annot	0.002	0.003	0.005
breakpoints	0.003	0.002	0.005
calculateTiTv	0.009	0.003	0.013
captureArray	0.001	0.002	0.003
coverageOnTarget	0.202	0.005	0.210
demultiplexReads	0.090	0.003	0.092
detectBreakpoints	0.786	0.053	0.846
fDataAmp	0.013	0.004	0.017
featureDataAmp	0.016	0.006	0.023
filterChimericReads	3.728	0.041	3.787
genomeSequencerMIDs	0.024	0.002	0.025
getAlignedReads	0.070	0.005	0.077
getVariantPercentages	0.023	0.003	0.027
htmlReport	2.211	0.314	2.571
mapperSetExample	0.006	0.003	0.009
mergeBreakpoints	6.226	0.164	6.442
mutationInfo	0.002	0.002	0.003
plotAmpliconCoverage	0	0	0
plotChimericReads	3.453	0.025	3.499
plotVariants	0.003	0.001	0.004
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.094	0.003	0.098
readsOnTarget	0.053	0.002	0.056
referenceSequences	0.007	0.003	0.010
regions	0.002	0.002	0.004
removeLinker	0.023	0.001	0.024
sequenceCaptureLinkers	0.004	0.000	0.003
setVariantFilter	0.040	0.005	0.046
variants	0.001	0.001	0.003
writeSFF	0.026	0.000	0.027