Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1163/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEDIPS 1.57.0 (landing page) Lukas Chavez
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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: 1.57.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEDIPS_1.57.0.tar.gz |
StartedAt: 2024-07-16 01:29:21 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 01:35:37 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 375.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MEDIPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEDIPS_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MEDIPS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MEDIPS' version '1.57.0' * 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 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 42.78 2.16 44.70 MEDIPS.addCNV 23.16 0.55 23.71 MEDIPS.plotSaturation 5.87 0.55 6.44 MEDIPS.couplingVector 6.07 0.12 6.20 MEDIPS.saturation 5.11 0.76 5.87 * 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MEDIPS.Rcheck/00check.log' for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 | 0 | 0 | |
MEDIPS.CpGenrich | 0.06 | 0.00 | 0.08 | |
MEDIPS.addCNV | 23.16 | 0.55 | 23.71 | |
MEDIPS.correlation | 1.45 | 0.08 | 1.53 | |
MEDIPS.couplingVector | 6.07 | 0.12 | 6.20 | |
MEDIPS.createROIset | 1.21 | 0.05 | 1.27 | |
MEDIPS.createSet | 1.25 | 0.05 | 1.29 | |
MEDIPS.exportWIG | 3.40 | 0.06 | 3.44 | |
MEDIPS.getAnnotation | 0 | 0 | 0 | |
MEDIPS.mergeFrames | 0 | 0 | 0 | |
MEDIPS.mergeSets | 1.00 | 0.03 | 1.03 | |
MEDIPS.meth | 42.78 | 2.16 | 44.70 | |
MEDIPS.plotCalibrationPlot | 3.91 | 0.29 | 4.22 | |
MEDIPS.plotSaturation | 5.87 | 0.55 | 6.44 | |
MEDIPS.plotSeqCoverage | 4.35 | 0.13 | 4.47 | |
MEDIPS.saturation | 5.11 | 0.76 | 5.87 | |
MEDIPS.selectROIs | 0.96 | 0.17 | 1.12 | |
MEDIPS.selectSig | 2.07 | 0.28 | 2.36 | |
MEDIPS.seqCoverage | 4.42 | 0.19 | 4.59 | |
MEDIPS.setAnnotation | 3.16 | 0.49 | 3.64 | |
MEDIPSroiSet-class | 0 | 0 | 0 | |
MEDIPSset-class | 0 | 0 | 0 | |