Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1308/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifbreakR 2.21.0 (landing page) Simon Gert Coetzee
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: motifbreakR |
Version: 2.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifbreakR_2.21.0.tar.gz |
StartedAt: 2024-12-23 09:49:22 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 10:03:42 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 860.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: motifbreakR.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifbreakR_2.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/motifbreakR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘motifbreakR/DESCRIPTION’ ... OK * this is package ‘motifbreakR’ version ‘2.21.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/motifbreakR.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: calculatePvalue.Rd: TFMsc2pv findSupportingRemapPeaks.Rd: MotifDb, associateTranscriptionFactors motifbreakR.Rd: TFMPvalue-package, TFMsc2pv shiny_motifbreakR.Rd: shinyAppDir snps.from.file.Rd: useEnsembl snps.from.rsid.Rd: useEnsembl Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 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 181.049 13.897 226.329 calculatePvalue 58.807 0.658 59.554 motifbreakR 14.526 0.300 14.858 * 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: 5 WARNINGs, 8 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/motifbreakR.Rcheck/00check.log’ for details.
motifbreakR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL motifbreakR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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. Warning: program compiled against libxml 212 using older 211 No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools' ** 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. Warning: program compiled against libxml 212 using older 211 No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools' ** testing if installed package can be loaded from final location See system.file("LICENSE", package="MotifDb") for use restrictions. Warning: program compiled against libxml 212 using older 211 No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools' ** testing if installed package keeps a record of temporary installation path * DONE (motifbreakR)
motifbreakR.Rcheck/motifbreakR-Ex.timings
name | user | system | elapsed | |
calculatePvalue | 58.807 | 0.658 | 59.554 | |
encodemotif | 0.068 | 0.004 | 0.071 | |
example.results | 0.111 | 0.000 | 0.111 | |
exportMBbed | 0.057 | 0.012 | 0.069 | |
exportMBtable | 0.068 | 0.000 | 0.069 | |
factorbook | 0.014 | 0.000 | 0.014 | |
findSupportingRemapPeaks | 0.019 | 0.000 | 0.019 | |
hocomoco | 0.025 | 0.000 | 0.025 | |
homer | 0.018 | 0.000 | 0.017 | |
motifbreakR | 14.526 | 0.300 | 14.858 | |
motifbreakR_motif | 0.082 | 0.004 | 0.087 | |
plotMB | 0.071 | 0.000 | 0.071 | |
shiny_motifbreakR | 0.202 | 0.016 | 0.229 | |
snps.from.file | 2.358 | 0.056 | 2.448 | |
snps.from.rsid | 181.049 | 13.897 | 226.329 | |