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This page was generated on 2022-06-24 11:07:02 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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 1539/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.47.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox
git_branch: master
git_last_commit: 79327f0
git_last_commit_date: 2022-04-26 11:06:14 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: R453Plus1Toolbox
Version: 1.47.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.47.0.tar.gz
StartedAt: 2022-06-24 04:48:07 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:54:17 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 370.2 seconds
RetCode: 0
Status:   OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 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 '1.47.0'
* 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-3.16-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 9.11   0.15    9.28
* 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-3.16-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.



Installation output

R453Plus1Toolbox.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/R453Plus1Toolbox_1.47.0.tar.gz && rm -rf R453Plus1Toolbox.buildbin-libdir && mkdir R453Plus1Toolbox.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.47.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL R453Plus1Toolbox_1.47.0.zip && rm R453Plus1Toolbox_1.47.0.tar.gz R453Plus1Toolbox_1.47.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  686k  100  686k    0     0  5751k      0 --:--:-- --:--:-- --:--:-- 5771k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'R453Plus1Toolbox' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/R453Plus1Toolbox.buildbin-libdir/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
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.47.0.zip
* DONE (R453Plus1Toolbox)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'R453Plus1Toolbox' successfully unpacked and MD5 sums checked

Tests output


Example timings

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class0.200.000.22
AVASet0.140.030.17
AnnotatedVariants-class000
MapperSet-class0.020.020.03
MapperSet0.000.010.01
SFFContainer-class000
SFFRead-class000
alignShortReads2.210.002.28
annotateVariants0.020.000.02
assayDataAmp000
ava2vcf0.190.030.22
avaSetExample0.000.020.01
avaSetFiltered0.010.000.02
avaSetFiltered_annot0.000.020.01
breakpoints000
calculateTiTv0.000.020.02
captureArray0.000.010.01
coverageOnTarget0.190.020.22
demultiplexReads0.090.000.10
detectBreakpoints0.710.110.81
fDataAmp0.010.010.03
featureDataAmp0.020.000.01
filterChimericReads2.970.143.11
genomeSequencerMIDs0.020.000.02
getAlignedReads0.050.020.06
getVariantPercentages0.040.000.04
htmlReport3.100.583.80
mapperSetExample0.010.000.02
mergeBreakpoints9.110.159.28
mutationInfo0.000.020.01
plotAmpliconCoverage000
plotChimericReads2.020.032.05
plotVariants000
plotVariationFrequency000
qualityReportSFF000
readSFF0.080.020.09
readsOnTarget0.040.000.05
referenceSequences000
regions0.020.000.01
removeLinker0.010.000.02
sequenceCaptureLinkers0.020.000.01
setVariantFilter0.050.000.05
variants000
writeSFF0.030.000.03