Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1315/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifbreakR 2.20.0 (landing page) Simon Gert Coetzee
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the motifbreakR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifbreakR.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. |
Package: motifbreakR |
Version: 2.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifbreakR_2.20.0.tar.gz |
StartedAt: 2024-12-21 02:06:36 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 02:17:47 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 671.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: motifbreakR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifbreakR_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifbreakR.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 ‘motifbreakR/DESCRIPTION’ ... OK * this is package ‘motifbreakR’ version ‘2.20.0’ * package encoding: UTF-8 * 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 ‘motifbreakR’ 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 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 Package in Depends field not imported from: 'MotifDb' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE biomartToGranges: no visible binding for global variable 'chr_name' biomartToGranges: no visible binding for global variable 'chrom_start' biomartToGranges: no visible binding for global variable 'chrom_end' biomartToGranges: no visible binding for global variable 'SNP_id' biomartToGranges: no visible binding for global variable 'REF' biomartToGranges: no visible binding for global variable 'ALT' calculatePvalue: no visible binding for global variable 'Refpvalue' calculatePvalue: no visible binding for global variable 'Altpvalue' convertPeakFile: no visible binding for global variable 'chr' convertPeakFile: no visible binding for global variable 'name' Undefined global functions or variables: ALT Altpvalue REF Refpvalue SNP_id chr chr_name chrom_end chrom_start name * checking Rd files ... NOTE checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: 'example.pvalue' All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE Note: found 12 marked UTF-8 strings * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed snps.from.rsid 112.016 9.236 126.248 calculatePvalue 56.307 0.740 57.150 motifbreakR 10.287 0.224 10.516 * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘SNPlocs.Hsapiens.dbSNP142.GRCh37’ * 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: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifbreakR.Rcheck/00check.log’ for details.
motifbreakR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifbreakR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘motifbreakR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading See system.file("LICENSE", package="MotifDb") for use restrictions. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location See system.file("LICENSE", package="MotifDb") for use restrictions. ** testing if installed package can be loaded from final location See system.file("LICENSE", package="MotifDb") for use restrictions. ** testing if installed package keeps a record of temporary installation path * DONE (motifbreakR)
motifbreakR.Rcheck/motifbreakR-Ex.timings
name | user | system | elapsed | |
calculatePvalue | 56.307 | 0.740 | 57.150 | |
encodemotif | 0.091 | 0.004 | 0.095 | |
example.results | 0.090 | 0.005 | 0.095 | |
exportMBbed | 0.058 | 0.005 | 0.062 | |
exportMBtable | 0.058 | 0.004 | 0.063 | |
factorbook | 0.015 | 0.003 | 0.018 | |
findSupportingRemapPeaks | 0.022 | 0.003 | 0.025 | |
hocomoco | 0.032 | 0.003 | 0.035 | |
homer | 0.020 | 0.003 | 0.023 | |
motifbreakR | 10.287 | 0.224 | 10.516 | |
motifbreakR_motif | 0.118 | 0.003 | 0.122 | |
plotMB | 0.054 | 0.004 | 0.059 | |
shiny_motifbreakR | 0.202 | 0.018 | 0.227 | |
snps.from.file | 1.769 | 0.103 | 1.888 | |
snps.from.rsid | 112.016 | 9.236 | 126.248 | |