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This page was generated on 2022-12-01 11:06:49 -0500 (Thu, 01 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4203
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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 nebbiolo1


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 1566/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.49.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-11-30 14:00:15 -0500 (Wed, 30 Nov 2022)
git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox
git_branch: master
git_last_commit: 7b302c5
git_last_commit_date: 2022-11-01 11:05:23 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available

Summary

Package: R453Plus1Toolbox
Version: 1.49.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings R453Plus1Toolbox_1.49.0.tar.gz
StartedAt: 2022-11-30 22:58:33 -0500 (Wed, 30 Nov 2022)
EndedAt: 2022-11-30 23:05:46 -0500 (Wed, 30 Nov 2022)
EllapsedTime: 432.7 seconds
RetCode: 0
Status:   OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings R453Plus1Toolbox_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 5.458  0.223   5.682
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.



Installation output

R453Plus1Toolbox.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL R453Plus1Toolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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)

Tests output


Example timings

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class1.2020.0361.239
AVASet0.1140.0040.117
AnnotatedVariants-class0.0010.0000.001
MapperSet-class0.0190.0120.031
MapperSet0.0040.0000.004
SFFContainer-class0.0010.0000.001
SFFRead-class0.0000.0000.001
alignShortReads2.2310.0482.287
annotateVariants0.0010.0000.001
assayDataAmp0.0030.0010.005
ava2vcf0.2160.0020.218
avaSetExample0.0120.0000.012
avaSetFiltered0.0170.0000.017
avaSetFiltered_annot0.0020.0000.001
breakpoints0.0000.0040.004
calculateTiTv0.0020.0060.009
captureArray0.0000.0010.002
coverageOnTarget0.1870.0040.192
demultiplexReads0.0720.0040.076
detectBreakpoints0.6450.0640.709
fDataAmp0.0140.0000.014
featureDataAmp0.0130.0000.013
filterChimericReads3.8650.1283.993
genomeSequencerMIDs0.0200.0000.019
getAlignedReads0.0460.0040.051
getVariantPercentages0.0160.0080.023
htmlReport2.0970.0842.161
mapperSetExample0.0050.0000.005
mergeBreakpoints5.4580.2235.682
mutationInfo0.0020.0000.003
plotAmpliconCoverage0.0000.0010.001
plotChimericReads1.9930.0031.997
plotVariants0.0030.0000.003
plotVariationFrequency000
qualityReportSFF0.0010.0000.000
readSFF0.0880.0000.087
readsOnTarget0.0400.0080.048
referenceSequences0.0070.0000.007
regions0.0030.0000.002
removeLinker0.0260.0040.029
sequenceCaptureLinkers0.0040.0000.004
setVariantFilter0.0380.0000.038
variants0.0020.0000.002
writeSFF0.0310.0000.030