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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1649/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.56.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox
git_branch: RELEASE_3_20
git_last_commit: bf27f3f
git_last_commit_date: 2024-10-29 09:35:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for R453Plus1Toolbox on kjohnson1

To the developers/maintainers of the R453Plus1Toolbox package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: R453Plus1Toolbox
Version: 1.56.0
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_1.56.0.tar.gz
StartedAt: 2024-12-21 05:51:36 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 05:58:37 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 421.3 seconds
RetCode: 0
Status:   OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

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### Running 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_1.56.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.56.0’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 5.925  0.098   6.068
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.


Installation output

R453Plus1Toolbox.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R453Plus1Toolbox
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c writeSFF.c -o writeSFF.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.4-arm64/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)

Tests output


Example timings

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class0.1830.0130.198
AVASet0.1270.0080.135
AnnotatedVariants-class0.0010.0000.001
MapperSet-class0.0200.0150.036
MapperSet0.0050.0030.009
SFFContainer-class0.0000.0010.001
SFFRead-class0.0000.0010.001
alignShortReads2.8040.0152.821
annotateVariants0.0010.0000.001
assayDataAmp0.0060.0030.008
ava2vcf0.2230.0040.227
avaSetExample0.0120.0030.016
avaSetFiltered0.0170.0030.021
avaSetFiltered_annot0.0020.0030.004
breakpoints0.0050.0030.008
calculateTiTv0.0090.0040.013
captureArray0.0010.0030.004
coverageOnTarget0.1850.0030.189
demultiplexReads0.0810.0020.083
detectBreakpoints0.6910.0440.741
fDataAmp0.0150.0040.020
featureDataAmp0.0140.0040.019
filterChimericReads3.6190.0293.652
genomeSequencerMIDs0.0190.0010.020
getAlignedReads0.0650.0060.073
getVariantPercentages0.0260.0050.031
htmlReport1.9320.2682.215
mapperSetExample0.0060.0030.008
mergeBreakpoints5.9250.0986.068
mutationInfo0.0020.0030.006
plotAmpliconCoverage000
plotChimericReads2.1650.0212.211
plotVariants0.0020.0010.003
plotVariationFrequency0.0000.0010.001
qualityReportSFF0.0010.0000.000
readSFF0.1070.0070.115
readsOnTarget0.0540.0040.058
referenceSequences0.0090.0040.013
regions0.0030.0030.006
removeLinker0.0290.0030.031
sequenceCaptureLinkers0.0040.0000.005
setVariantFilter0.0440.0100.053
variants0.0020.0030.006
writeSFF0.0350.0020.037