| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:08:24 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the R453Plus1Toolbox package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1524/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.45.0 (landing page) Hans-Ulrich Klein
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: R453Plus1Toolbox |
| Version: 1.45.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.45.0.tar.gz |
| StartedAt: 2022-03-17 19:59:40 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:04:33 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 292.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.45.0'
* 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 whether package 'R453Plus1Toolbox' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
R 2.0Mb
extdata 2.5Mb
* 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 ... 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/R453Plus1Toolbox/libs/x64/R453Plus1Toolbox.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mergeBreakpoints 6.03 0.13 6.16
* 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: 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.
R453Plus1Toolbox.Rcheck/00install.out
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL R453Plus1Toolbox
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'R453Plus1Toolbox' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
int block_count;
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c writeSFF.c -o writeSFF.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'R453Plus1Toolbox'
finding HTML links ... done
AVASet-class html
finding level-2 HTML links ... done
AVASet html
AnnotatedVariants-class html
Breakpoints-class html
MapperSet-class html
MapperSet html
SFFContainer-class html
SFFRead-class html
alignShortReads html
annotateVariants html
assayDataAmp html
ava2vcf html
avaSetExample html
avaSetFiltered html
avaSetFiltered_annot html
baseFrequency html
baseQualityHist html
baseQualityStats html
breakpoints html
calculateTiTv html
captureArray html
complexity.dust html
complexity.entropy html
convertCigar html
coverageOnTarget html
demultiplexReads html
detectBreakpoints html
dinucleotideOddsRatio html
fDataAmp html
featureDataAmp html
filterChimericReads html
flowgramBarplot html
gcContent html
gcContentHist html
gcPerPosition html
genomeSequencerMIDs html
getAlignedReads html
getAminoAbbr html
getVariantPercentages html
homopolymerHist html
htmlReport html
mapperSetExample html
mergeBreakpoints html
mutationInfo html
nucleotideCharts html
plotAmpliconCoverage html
plotChimericReads html
plotVariants html
plotVariationFrequency html
positionQualityBoxplot html
qualityReportSFF html
readLengthHist html
readLengthStats html
readSFF html
readsOnTarget html
referenceSequences html
regions html
removeLinker html
sequenceCaptureLinkers html
sequenceQualityHist html
setVariantFilter html
sff2fastq html
variants html
writeSFF html
** 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 (R453Plus1Toolbox)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'soGGi' is missing or broken
done
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings
| name | user | system | elapsed | |
| AVASet-class | 0.17 | 0.07 | 0.23 | |
| AVASet | 0.17 | 0.00 | 0.18 | |
| AnnotatedVariants-class | 0 | 0 | 0 | |
| MapperSet-class | 0.02 | 0.03 | 0.05 | |
| MapperSet | 0.02 | 0.00 | 0.01 | |
| SFFContainer-class | 0 | 0 | 0 | |
| SFFRead-class | 0 | 0 | 0 | |
| alignShortReads | 1.78 | 0.00 | 1.79 | |
| annotateVariants | 0 | 0 | 0 | |
| assayDataAmp | 0.00 | 0.01 | 0.01 | |
| ava2vcf | 0.17 | 0.00 | 0.17 | |
| avaSetExample | 0 | 0 | 0 | |
| avaSetFiltered | 0.02 | 0.00 | 0.01 | |
| avaSetFiltered_annot | 0 | 0 | 0 | |
| breakpoints | 0.02 | 0.00 | 0.02 | |
| calculateTiTv | 0 | 0 | 0 | |
| captureArray | 0.00 | 0.02 | 0.02 | |
| coverageOnTarget | 0.12 | 0.02 | 0.14 | |
| demultiplexReads | 0.05 | 0.00 | 0.04 | |
| detectBreakpoints | 0.54 | 0.06 | 0.61 | |
| fDataAmp | 0.02 | 0.00 | 0.02 | |
| featureDataAmp | 0.03 | 0.00 | 0.03 | |
| filterChimericReads | 2.85 | 0.12 | 2.97 | |
| genomeSequencerMIDs | 0.01 | 0.00 | 0.01 | |
| getAlignedReads | 0.05 | 0.00 | 0.05 | |
| getVariantPercentages | 0.01 | 0.02 | 0.03 | |
| htmlReport | 2.58 | 0.26 | 2.91 | |
| mapperSetExample | 0.02 | 0.00 | 0.01 | |
| mergeBreakpoints | 6.03 | 0.13 | 6.16 | |
| mutationInfo | 0.00 | 0.01 | 0.02 | |
| plotAmpliconCoverage | 0 | 0 | 0 | |
| plotChimericReads | 1.84 | 0.00 | 1.84 | |
| plotVariants | 0.02 | 0.00 | 0.01 | |
| plotVariationFrequency | 0 | 0 | 0 | |
| qualityReportSFF | 0 | 0 | 0 | |
| readSFF | 0.06 | 0.00 | 0.07 | |
| readsOnTarget | 0.03 | 0.02 | 0.04 | |
| referenceSequences | 0.02 | 0.00 | 0.02 | |
| regions | 0.00 | 0.02 | 0.02 | |
| removeLinker | 0.01 | 0.00 | 0.01 | |
| sequenceCaptureLinkers | 0 | 0 | 0 | |
| setVariantFilter | 0.05 | 0.01 | 0.06 | |
| variants | 0 | 0 | 0 | |
| writeSFF | 0.03 | 0.00 | 0.03 | |