Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1185/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEDIPS 1.58.0 (landing page) Lukas Chavez
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MEDIPS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEDIPS.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: MEDIPS |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEDIPS_1.58.0.tar.gz |
StartedAt: 2024-11-19 23:44:58 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:53:12 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 494.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MEDIPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEDIPS_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MEDIPS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MEDIPS’ version ‘1.58.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘MEDIPS’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MEDIPS.CpGenrich: no visible global function definition for ‘seqlevels’ MEDIPS.CpGenrich: no visible global function definition for ‘seqlengths’ MEDIPS.CpGenrich: no visible global function definition for ‘GRangesList’ MEDIPS.CpGenrich : <anonymous>: no visible global function definition for ‘seqnames’ MEDIPS.CpGenrich: no visible global function definition for ‘new’ MEDIPS.addCNV: no visible global function definition for ‘seqnames’ MEDIPS.correlation: no visible global function definition for ‘pdf’ MEDIPS.correlation: no visible global function definition for ‘dev.off’ MEDIPS.couplingVector: no visible global function definition for ‘new’ MEDIPS.createROIset: no visible global function definition for ‘seqnames’ MEDIPS.createROIset: no visible global function definition for ‘seqlengths’ MEDIPS.createROIset: no visible global function definition for ‘new’ MEDIPS.createSet: no visible global function definition for ‘seqnames’ MEDIPS.createSet: no visible global function definition for ‘seqlengths’ MEDIPS.createSet: no visible global function definition for ‘seqlevels’ MEDIPS.createSet: no visible global function definition for ‘new’ MEDIPS.diffMeth: no visible global function definition for ‘p.adjust’ MEDIPS.exportWIG: no visible global function definition for ‘seqnames’ MEDIPS.mergeSets: no visible global function definition for ‘new’ MEDIPS.meth: no visible global function definition for ‘seqnames’ MEDIPS.plotCalibrationPlot: no visible global function definition for ‘seqnames’ MEDIPS.plotCalibrationPlot: no visible global function definition for ‘points’ MEDIPS.plotSeqCoverage: no visible global function definition for ‘pie’ MEDIPS.plotSeqCoverage: no visible global function definition for ‘hist’ MEDIPS.saturation: no visible global function definition for ‘seqlevels’ MEDIPS.saturation: no visible global function definition for ‘seqlengths’ MEDIPS.selectROIs: no visible global function definition for ‘elementMetadata<-’ MEDIPS.selectROIs: no visible global function definition for ‘elementMetadata’ MEDIPS.selectROIs: no visible global function definition for ‘findOverlaps’ MEDIPS.selectROIs: no visible global function definition for ‘values’ MEDIPS.selectROIs: no visible global function definition for ‘seqnames’ MEDIPS.seqCoverage: no visible global function definition for ‘seqlevels’ MEDIPS.seqCoverage: no visible global function definition for ‘seqlengths’ MEDIPS.setAnnotation: no visible global function definition for ‘findOverlaps’ MEDIPS.setAnnotation: no visible global function definition for ‘values’ getGRange: no visible global function definition for ‘qpois’ getGRange: no visible global function definition for ‘seqlengths’ getGRange: no visible global function definition for ‘countMatches’ getGRange: no visible global function definition for ‘strand<-’ getMObjectFromWIG: no visible global function definition for ‘seqlengths’ getMObjectFromWIG: no visible global function definition for ‘values’ getMObjectFromWIG: no visible global function definition for ‘runLength’ getMObjectFromWIG: no visible global function definition for ‘seqnames’ getMObjectFromWIG: no visible global function definition for ‘runValue’ getMObjectFromWIG: no visible global function definition for ‘new’ getPairedGRange: no visible global function definition for ‘sd’ getPairedGRange: no visible global function definition for ‘qpois’ getPairedGRange: no visible global function definition for ‘seqlengths’ getPairedGRange: no visible global function definition for ‘countMatches’ getPairedGRange: no visible global function definition for ‘strand<-’ matSd: no visible binding for global variable ‘sd’ matTtest: no visible binding for global variable ‘sd’ matTtest: no visible global function definition for ‘pt’ Undefined global functions or variables: GRangesList countMatches dev.off elementMetadata elementMetadata<- findOverlaps hist new p.adjust pdf pie points pt qpois runLength runValue sd seqlengths seqlevels seqnames strand<- values Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "hist", "pie", "points") importFrom("methods", "new") importFrom("stats", "p.adjust", "pt", "qpois", "sd") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 MEDIPS.meth 25.316 1.491 26.878 MEDIPS.addCNV 15.478 0.467 16.009 MEDIPS.plotSaturation 4.578 0.441 5.029 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck/00check.log’ for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MEDIPS’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’ ** testing if installed package keeps a record of temporary installation path * DONE (MEDIPS)
MEDIPS.Rcheck/MEDIPS-Ex.timings
name | user | system | elapsed | |
COUPLINGset-class | 0.001 | 0.000 | 0.001 | |
MEDIPS.CpGenrich | 0.040 | 0.005 | 0.046 | |
MEDIPS.addCNV | 15.478 | 0.467 | 16.009 | |
MEDIPS.correlation | 1.145 | 0.127 | 1.276 | |
MEDIPS.couplingVector | 2.609 | 0.088 | 2.705 | |
MEDIPS.createROIset | 0.964 | 0.050 | 1.018 | |
MEDIPS.createSet | 1.017 | 0.046 | 1.068 | |
MEDIPS.exportWIG | 1.844 | 0.072 | 1.929 | |
MEDIPS.getAnnotation | 0 | 0 | 0 | |
MEDIPS.mergeFrames | 0.003 | 0.000 | 0.003 | |
MEDIPS.mergeSets | 0.682 | 0.017 | 0.703 | |
MEDIPS.meth | 25.316 | 1.491 | 26.878 | |
MEDIPS.plotCalibrationPlot | 2.339 | 0.204 | 2.551 | |
MEDIPS.plotSaturation | 4.578 | 0.441 | 5.029 | |
MEDIPS.plotSeqCoverage | 2.333 | 0.111 | 2.451 | |
MEDIPS.saturation | 4.379 | 0.393 | 4.780 | |
MEDIPS.selectROIs | 1.163 | 0.023 | 1.190 | |
MEDIPS.selectSig | 1.857 | 0.135 | 1.996 | |
MEDIPS.seqCoverage | 2.281 | 0.157 | 2.441 | |
MEDIPS.setAnnotation | 1.914 | 0.104 | 2.025 | |
MEDIPSroiSet-class | 0.000 | 0.000 | 0.001 | |
MEDIPSset-class | 0.000 | 0.000 | 0.001 | |