Hans-Ulrich Klein
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox |
| git_branch: devel |
| git_last_commit: 8d481bd |
| git_last_commit_date: 2024-10-29 09:35:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 1638/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.57.0 (landing page) Hans-Ulrich Klein
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| 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: 2024-12-24 10:11:14 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 10:19:24 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 490.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 6 |
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### Running command:
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### /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
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck/00install.out’ for details.
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
'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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
.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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Warning: program compiled against libxml 212 using older 211
* 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 7.13 0.12 7.273
* 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: 6 WARNINGs, 7 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.
R453Plus1Toolbox.Rcheck/00install.out
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### Running command:
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### /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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:27:7: warning: variable ‘block_count’ set but not used [-Wunused-but-set-variable]
27 | int block_count;
| ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c writeSFF.c -o writeSFF.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (R453Plus1Toolbox)
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings
| name | user | system | elapsed | |
| AVASet-class | 0.241 | 0.008 | 0.253 | |
| AVASet | 0.173 | 0.020 | 0.196 | |
| AnnotatedVariants-class | 0.001 | 0.000 | 0.002 | |
| MapperSet-class | 0.020 | 0.004 | 0.025 | |
| MapperSet | 0.005 | 0.000 | 0.006 | |
| SFFContainer-class | 0 | 0 | 0 | |
| SFFRead-class | 0.001 | 0.000 | 0.000 | |
| alignShortReads | 2.843 | 0.060 | 2.920 | |
| annotateVariants | 0.002 | 0.000 | 0.001 | |
| assayDataAmp | 0.004 | 0.000 | 0.004 | |
| ava2vcf | 0.293 | 0.000 | 0.294 | |
| avaSetExample | 0.013 | 0.000 | 0.013 | |
| avaSetFiltered | 0.02 | 0.00 | 0.02 | |
| avaSetFiltered_annot | 0.002 | 0.000 | 0.001 | |
| breakpoints | 0.003 | 0.000 | 0.004 | |
| calculateTiTv | 0.009 | 0.000 | 0.010 | |
| captureArray | 0.000 | 0.002 | 0.002 | |
| coverageOnTarget | 0.237 | 0.006 | 0.245 | |
| demultiplexReads | 0.094 | 0.000 | 0.094 | |
| detectBreakpoints | 0.815 | 0.080 | 0.899 | |
| fDataAmp | 0.017 | 0.000 | 0.017 | |
| featureDataAmp | 0.015 | 0.000 | 0.016 | |
| filterChimericReads | 4.573 | 0.052 | 4.636 | |
| genomeSequencerMIDs | 0.036 | 0.000 | 0.036 | |
| getAlignedReads | 0.076 | 0.000 | 0.078 | |
| getVariantPercentages | 0.030 | 0.000 | 0.031 | |
| htmlReport | 2.915 | 0.079 | 3.012 | |
| mapperSetExample | 0.006 | 0.000 | 0.006 | |
| mergeBreakpoints | 7.130 | 0.120 | 7.273 | |
| mutationInfo | 0.003 | 0.000 | 0.003 | |
| plotAmpliconCoverage | 0 | 0 | 0 | |
| plotChimericReads | 2.963 | 0.164 | 3.132 | |
| plotVariants | 0.003 | 0.000 | 0.003 | |
| plotVariationFrequency | 0 | 0 | 0 | |
| qualityReportSFF | 0 | 0 | 0 | |
| readSFF | 0.110 | 0.012 | 0.124 | |
| readsOnTarget | 0.062 | 0.008 | 0.070 | |
| referenceSequences | 0.008 | 0.000 | 0.008 | |
| regions | 0.003 | 0.000 | 0.003 | |
| removeLinker | 0.025 | 0.000 | 0.025 | |
| sequenceCaptureLinkers | 0.006 | 0.000 | 0.006 | |
| setVariantFilter | 0.048 | 0.004 | 0.053 | |
| variants | 0.003 | 0.000 | 0.003 | |
| writeSFF | 0.035 | 0.004 | 0.039 | |