Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the exomePeak2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/exomePeak2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 605/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
exomePeak2 1.4.2 (landing page) Zhen Wei
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: exomePeak2 |
Version: 1.4.2 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings exomePeak2_1.4.2.tar.gz |
StartedAt: 2021-10-14 22:58:46 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:10:13 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 687.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: exomePeak2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings exomePeak2_1.4.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'exomePeak2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'exomePeak2' version '1.4.2' * 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 whether package 'exomePeak2' 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 GLM_inference : <anonymous>: no visible global function definition for 'median' Results,SummarizedExomePeak: no visible global function definition for 'glm_M' estimateSeqDepth,SummarizedExomePeak : <anonymous>: no visible global function definition for 'median' exomePeakCalling,MeripBamFileList: no visible global function definition for 'metadata' exomePeakCalling,MeripBamFileList: no visible global function definition for '%over%' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'GC_idx' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'Log2FC' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'Label' plotReadsGC,SummarizedExomePeak: no visible binding for global variable 'GC_cont' plotReadsGC,SummarizedExomePeak: no visible binding for global variable 'value' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'samples' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'size_factors' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'Estimation_Methods' Undefined global functions or variables: %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M median metadata samples size_factors value Consider adding importFrom("stats", "median") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed exomePeak2 70.53 0.31 71.56 exomePeakCalling-methods 45.06 0.15 45.69 SummarizedExomePeak-class 24.60 1.69 28.12 glmM-methods 6.09 0.00 6.30 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed exomePeak2 78.75 0.16 78.91 exomePeakCalling-methods 44.22 0.06 44.28 SummarizedExomePeak-class 26.63 1.06 27.72 glmM-methods 6.03 0.00 6.03 glmDM-methods 5.30 0.00 5.30 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.13-bioc/meat/exomePeak2.Rcheck/00check.log' for details.
exomePeak2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/exomePeak2_1.4.2.tar.gz && rm -rf exomePeak2.buildbin-libdir && mkdir exomePeak2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomePeak2.buildbin-libdir exomePeak2_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL exomePeak2_1.4.2.zip && rm exomePeak2_1.4.2.tar.gz exomePeak2_1.4.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 39 2229k 39 885k 0 0 1975k 0 0:00:01 --:--:-- 0:00:01 1977k 100 2229k 100 2229k 0 0 2982k 0 --:--:-- --:--:-- --:--:-- 2981k install for i386 * installing *source* package 'exomePeak2' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'exomePeak2' finding HTML links ... done GC_content_over_grl html GCsizeFactors-methods html GLM_inference html LibraryType-methods html MeripBamFileList-class html finding level-2 HTML links ... done Parameter-methods html Results-methods html SummarizedExomePeak-class html call_peaks_with_GLM html convertTxDb html ctest html decision_deseq2 html disj_background html estimateSeqDepth-methods html exomePeak2 html exomePeak2Results-methods html exomePeakCalling-methods html exome_bins_from_txdb html exonPlot html exons_by_unique_gene html exportResults-methods html flank_on_exons html glmDM-methods html glmM-methods html mclust_bg html normalizeGC-methods html plotExonLength-methods html plotLfcGC-methods html plotReadsGC-methods html plotSizeFactors-methods html quiet html reads_five_POS html reads_five_POS_rev html reduce_peaks html remove_introns html replace_bg html scanMeripBAM html sort_sep html split_by_name html ** 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 install for x64 * installing *source* package 'exomePeak2' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'exomePeak2' as exomePeak2_1.4.2.zip * DONE (exomePeak2) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'exomePeak2' successfully unpacked and MD5 sums checked
exomePeak2.Rcheck/examples_i386/exomePeak2-Ex.timings
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exomePeak2.Rcheck/examples_x64/exomePeak2-Ex.timings
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