| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:45 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1568/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.49.0 (landing page) Hans-Ulrich Klein
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: R453Plus1Toolbox |
| Version: 1.49.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.49.0.tar.gz |
| StartedAt: 2022-12-29 02:36:23 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:41:33 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 310.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.49.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/R453Plus1Toolbox.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.49.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-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 nor [v]sprintf. 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 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 7.72 0.08 7.8
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.
R453Plus1Toolbox.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL R453Plus1Toolbox
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'R453Plus1Toolbox' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writeSFF.c -o writeSFF.o
gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs/x64
** 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
** 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 | 0.89 | 0.00 | 0.89 | |
| AVASet | 0.13 | 0.02 | 0.14 | |
| AnnotatedVariants-class | 0 | 0 | 0 | |
| MapperSet-class | 0.00 | 0.03 | 0.03 | |
| MapperSet | 0 | 0 | 0 | |
| SFFContainer-class | 0 | 0 | 0 | |
| SFFRead-class | 0 | 0 | 0 | |
| alignShortReads | 1.70 | 0.02 | 1.80 | |
| annotateVariants | 0 | 0 | 0 | |
| assayDataAmp | 0 | 0 | 0 | |
| ava2vcf | 0.17 | 0.01 | 0.19 | |
| avaSetExample | 0.02 | 0.00 | 0.01 | |
| avaSetFiltered | 0.01 | 0.00 | 0.02 | |
| avaSetFiltered_annot | 0.00 | 0.02 | 0.02 | |
| breakpoints | 0 | 0 | 0 | |
| calculateTiTv | 0.02 | 0.00 | 0.01 | |
| captureArray | 0.02 | 0.00 | 0.02 | |
| coverageOnTarget | 0.14 | 0.01 | 0.15 | |
| demultiplexReads | 0.06 | 0.00 | 0.07 | |
| detectBreakpoints | 0.61 | 0.04 | 0.64 | |
| fDataAmp | 0.01 | 0.00 | 0.01 | |
| featureDataAmp | 0.03 | 0.00 | 0.03 | |
| filterChimericReads | 3.24 | 0.06 | 3.30 | |
| genomeSequencerMIDs | 0.01 | 0.00 | 0.02 | |
| getAlignedReads | 0.05 | 0.00 | 0.05 | |
| getVariantPercentages | 0.03 | 0.00 | 0.03 | |
| htmlReport | 1.86 | 0.40 | 2.34 | |
| mapperSetExample | 0.02 | 0.00 | 0.02 | |
| mergeBreakpoints | 7.72 | 0.08 | 7.80 | |
| mutationInfo | 0.00 | 0.02 | 0.01 | |
| plotAmpliconCoverage | 0 | 0 | 0 | |
| plotChimericReads | 1.54 | 0.01 | 1.58 | |
| plotVariants | 0 | 0 | 0 | |
| plotVariationFrequency | 0 | 0 | 0 | |
| qualityReportSFF | 0 | 0 | 0 | |
| readSFF | 0.09 | 0.02 | 0.10 | |
| readsOnTarget | 0.07 | 0.00 | 0.07 | |
| referenceSequences | 0.01 | 0.00 | 0.01 | |
| regions | 0 | 0 | 0 | |
| removeLinker | 0.02 | 0.00 | 0.02 | |
| sequenceCaptureLinkers | 0.00 | 0.02 | 0.01 | |
| setVariantFilter | 0.04 | 0.00 | 0.05 | |
| variants | 0 | 0 | 0 | |
| writeSFF | 0.03 | 0.00 | 0.03 | |