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This page was generated on 2022-10-19 13:22:05 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 palomino3


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.

raw results

Package 1558/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.46.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox
git_branch: RELEASE_3_15
git_last_commit: 6f7b330
git_last_commit_date: 2022-04-26 11:06:14 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: R453Plus1Toolbox
Version: 1.46.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.46.0.tar.gz
StartedAt: 2022-10-19 03:14:16 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:21:06 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 409.5 seconds
RetCode: 0
Status:   OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.46.0'
* 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 ... 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-3.15-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 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 11.24   0.19   11.67
* 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-3.15-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.



Installation output

R453Plus1Toolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL R453Plus1Toolbox
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'R453Plus1Toolbox' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-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-3.15-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-3.15-bioc/R/bin/x64 -lR
installing to F:/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
** 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)

Tests output


Example timings

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class0.140.050.24
AVASet0.120.010.14
AnnotatedVariants-class000
MapperSet-class0.030.000.03
MapperSet0.000.020.02
SFFContainer-class000
SFFRead-class000
alignShortReads2.510.012.67
annotateVariants000
assayDataAmp0.000.020.02
ava2vcf0.320.010.33
avaSetExample0.010.000.01
avaSetFiltered0.030.000.03
avaSetFiltered_annot0.000.010.01
breakpoints000
calculateTiTv0.000.020.02
captureArray0.020.000.01
coverageOnTarget0.170.000.18
demultiplexReads0.060.020.07
detectBreakpoints0.820.150.97
fDataAmp0.010.000.02
featureDataAmp0.020.000.02
filterChimericReads3.900.144.05
genomeSequencerMIDs0.030.000.03
getAlignedReads0.080.000.09
getVariantPercentages0.020.010.03
htmlReport3.650.634.47
mapperSetExample0.000.010.02
mergeBreakpoints11.24 0.1911.67
mutationInfo0.010.000.02
plotAmpliconCoverage000
plotChimericReads3.490.033.53
plotVariants0.010.000.01
plotVariationFrequency000
qualityReportSFF000
readSFF0.140.000.14
readsOnTarget0.050.000.05
referenceSequences000
regions0.020.000.02
removeLinker0.010.000.01
sequenceCaptureLinkers0.020.000.02
setVariantFilter0.060.000.06
variants0.020.000.02
writeSFF0.040.000.04