| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:21 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1583/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.48.0 (landing page) Hans-Ulrich Klein
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: R453Plus1Toolbox |
| Version: 1.48.0 |
| 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_1.48.0.tar.gz |
| StartedAt: 2023-04-10 22:04:51 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:10:23 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 331.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.48.0’
* 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
* 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 ... 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 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 5.323 0.125 5.461
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.
R453Plus1Toolbox.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R453Plus1Toolbox
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c writeSFF.c -o writeSFF.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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)
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings
| name | user | system | elapsed | |
| AVASet-class | 0.144 | 0.008 | 0.153 | |
| AVASet | 0.097 | 0.006 | 0.103 | |
| AnnotatedVariants-class | 0.001 | 0.001 | 0.001 | |
| MapperSet-class | 0.017 | 0.019 | 0.037 | |
| MapperSet | 0.005 | 0.002 | 0.008 | |
| SFFContainer-class | 0.001 | 0.001 | 0.002 | |
| SFFRead-class | 0.001 | 0.001 | 0.002 | |
| alignShortReads | 1.991 | 0.014 | 2.013 | |
| annotateVariants | 0.001 | 0.001 | 0.002 | |
| assayDataAmp | 0.004 | 0.002 | 0.006 | |
| ava2vcf | 0.218 | 0.010 | 0.237 | |
| avaSetExample | 0.009 | 0.002 | 0.012 | |
| avaSetFiltered | 0.018 | 0.003 | 0.021 | |
| avaSetFiltered_annot | 0.002 | 0.003 | 0.004 | |
| breakpoints | 0.004 | 0.002 | 0.005 | |
| calculateTiTv | 0.006 | 0.002 | 0.009 | |
| captureArray | 0.001 | 0.002 | 0.003 | |
| coverageOnTarget | 0.163 | 0.007 | 0.171 | |
| demultiplexReads | 0.063 | 0.006 | 0.069 | |
| detectBreakpoints | 0.621 | 0.059 | 0.684 | |
| fDataAmp | 0.012 | 0.004 | 0.016 | |
| featureDataAmp | 0.013 | 0.004 | 0.016 | |
| filterChimericReads | 3.666 | 0.044 | 3.721 | |
| genomeSequencerMIDs | 0.020 | 0.001 | 0.021 | |
| getAlignedReads | 0.057 | 0.004 | 0.061 | |
| getVariantPercentages | 0.025 | 0.003 | 0.028 | |
| htmlReport | 1.982 | 0.197 | 2.217 | |
| mapperSetExample | 0.004 | 0.002 | 0.005 | |
| mergeBreakpoints | 5.323 | 0.125 | 5.461 | |
| mutationInfo | 0.002 | 0.002 | 0.003 | |
| plotAmpliconCoverage | 0.000 | 0.001 | 0.000 | |
| plotChimericReads | 2.677 | 0.012 | 2.693 | |
| plotVariants | 0.002 | 0.001 | 0.003 | |
| plotVariationFrequency | 0.000 | 0.000 | 0.001 | |
| qualityReportSFF | 0 | 0 | 0 | |
| readSFF | 0.084 | 0.002 | 0.087 | |
| readsOnTarget | 0.049 | 0.002 | 0.051 | |
| referenceSequences | 0.005 | 0.001 | 0.007 | |
| regions | 0.002 | 0.001 | 0.004 | |
| removeLinker | 0.025 | 0.001 | 0.026 | |
| sequenceCaptureLinkers | 0.004 | 0.000 | 0.005 | |
| setVariantFilter | 0.033 | 0.004 | 0.037 | |
| variants | 0.002 | 0.002 | 0.004 | |
| writeSFF | 0.032 | 0.000 | 0.032 | |