Multiple platform build/check report for BioC 3.21 - CHECK results for R453Plus1Toolbox on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4749
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4461
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4411
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4366
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4241
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 kunpeng2

To the developers/maintainers of the R453Plus1Toolbox package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: R453Plus1Toolbox

Version: 1.57.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R453Plus1Toolbox_1.57.0.tar.gz

StartedAt: 2024-12-09 09:01:39 -0000 (Mon, 09 Dec 2024)

EndedAt: 2024-12-09 09:09:44 -0000 (Mon, 09 Dec 2024)

EllapsedTime: 485.1 seconds

RetCode: 0

Status: OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R453Plus1Toolbox_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.57.0’
* 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: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    extdata   2.8Mb
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 7.062  0.055   7.152
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

Installation output

R453Plus1Toolbox.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL R453Plus1Toolbox
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c readSFF.c -o readSFF.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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	0.239	0.004	0.250
AVASet	0.179	0.000	0.179
AnnotatedVariants-class	0.001	0.000	0.001
MapperSet-class	0.019	0.004	0.023
MapperSet	0.006	0.000	0.006
SFFContainer-class	0.001	0.000	0.001
SFFRead-class	0.001	0.000	0.001
alignShortReads	2.760	0.039	2.808
annotateVariants	0.001	0.000	0.001
assayDataAmp	0.004	0.000	0.004
ava2vcf	0.289	0.000	0.291
avaSetExample	0.013	0.000	0.013
avaSetFiltered	0.02	0.00	0.02
avaSetFiltered_annot	0.000	0.002	0.002
breakpoints	0.002	0.001	0.004
calculateTiTv	0.009	0.000	0.010
captureArray	0.000	0.001	0.001
coverageOnTarget	0.231	0.002	0.233
demultiplexReads	0.087	0.000	0.088
detectBreakpoints	0.784	0.059	0.896
fDataAmp	0.014	0.002	0.016
featureDataAmp	0.015	0.000	0.015
filterChimericReads	4.411	0.056	4.478
genomeSequencerMIDs	0.025	0.004	0.029
getAlignedReads	0.065	0.004	0.071
getVariantPercentages	0.020	0.011	0.031
htmlReport	2.957	0.068	3.032
mapperSetExample	0.006	0.000	0.006
mergeBreakpoints	7.062	0.055	7.152
mutationInfo	0.002	0.000	0.002
plotAmpliconCoverage	0	0	0
plotChimericReads	2.949	0.024	2.979
plotVariants	0.003	0.000	0.002
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.125	0.000	0.127
readsOnTarget	0.068	0.000	0.068
referenceSequences	0.008	0.000	0.007
regions	0.002	0.000	0.003
removeLinker	0.025	0.000	0.025
sequenceCaptureLinkers	0.005	0.000	0.006
setVariantFilter	0.052	0.000	0.052
variants	0.003	0.000	0.002
writeSFF	0.036	0.000	0.037