Back to Multiple platform build/check report for BioC 3.20: simplified long |
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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 334/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chipseq 1.55.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the chipseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chipseq.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: chipseq |
Version: 1.55.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipseq_1.55.0.tar.gz |
StartedAt: 2024-07-15 22:38:51 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 22:42:16 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 204.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: chipseq.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipseq_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/chipseq.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 'chipseq/DESCRIPTION' ... OK * this is package 'chipseq' version '1.55.0' * 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 'chipseq' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'BiocGenerics' 'IRanges' 'GenomicRanges' 'ShortRead' A package should be listed in only one of these fields. * 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 .genomicContext: no visible global function definition for 'transcripts' .genomicContext: no visible global function definition for 'cdsBy' .genomicContext: no visible global function definition for 'threeUTRsByTranscript' .genomicContext: no visible global function definition for 'fiveUTRsByTranscript' .genomicContext: no visible global function definition for 'intronsByTranscript' .nearestTss: no visible global function definition for 'transcripts' .nearestTss: no visible global function definition for 'seqlevels<-' .nearestTss: no visible global function definition for 'seqlevels' applyPosByChrAndStrand: no visible global function definition for 'seqnames' correlation.estimate: no visible binding for global variable 'mu' correlation.estimate: no visible binding for global variable 'corr' correlationProfile : <anonymous>: no visible global function definition for 'subseq' coverage.estimate: no visible binding for global variable 'mu' coverage.estimate: no visible binding for global variable 'covered' islandDepthPlot: no visible binding for global variable 'depth' islandDepthPlot : <anonymous>: no visible global function definition for 'panel.lines' islandDepthPlot : <anonymous>: no visible global function definition for 'panel.xyplot' laneSubsample: no visible global function definition for 'seqnames' laneSubsample: no visible global function definition for 'GRangesList' subsetSummary: no visible global function definition for 'seqlengths' subsetSummary: no visible global function definition for 'GRanges' subsetSummary: no visible global function definition for 'seqnames' subsetSummary: no visible global function definition for 'seqlengths<-' diffPeakSummary,RleViewsList-RleViewsList: no visible global function definition for 'GRanges' estimate.mean.fraglen,GRanges: no visible global function definition for 'seqnames' peakSummary,RleViewsList: no visible global function definition for 'GRanges' Undefined global functions or variables: GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript intronsByTranscript mu panel.lines panel.xyplot seqlengths seqlengths<- seqlevels seqlevels<- seqnames subseq threeUTRsByTranscript transcripts * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'densityCorr' and siglist 'GenomicRanges' generic 'densityCorr' and siglist 'list' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'estimate.mean.fraglen.Rd': densityCorr Code: function(x, ...) Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width = seqLen * 2L, seqLen = 100L, maxDist = 500L, ...) Argument names in docs not in code: shift center width seqLen maxDist Mismatches in argument names: Position: 2 Code: ... Docs: shift * 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/chipseq/libs/x64/chipseq.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed diffPeakSummary 6.67 0.17 6.86 * 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: 2 WARNINGs, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/chipseq.Rcheck/00check.log' for details.
chipseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL chipseq ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'chipseq' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlesumprod.c -o rlesumprod.o gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-chipseq/00new/chipseq/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chipseq)
chipseq.Rcheck/chipseq-Ex.timings
name | user | system | elapsed | |
chipseqFilter | 0.25 | 0.07 | 0.32 | |
coverageplot | 0.06 | 0.00 | 0.06 | |
cstest | 0.12 | 0.04 | 0.17 | |
diffPeakSummary | 6.67 | 0.17 | 6.86 | |
estimate.mean.fraglen | 2.44 | 0.27 | 2.70 | |
islandDepthPlot | 0.72 | 0.13 | 0.84 | |
laneSubsample | 0.36 | 0.01 | 0.38 | |
peakCutoff | 0.70 | 0.08 | 0.78 | |