Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MesKit package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MesKit.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 1074/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.2.0 (landing page) Mengni Liu
| 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: MesKit |
Version: 1.2.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MesKit_1.2.0.tar.gz |
StartedAt: 2021-10-15 01:33:16 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:45:18 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 722.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MesKit.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MesKit_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MesKit.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 'MesKit/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MesKit' version '1.2.0' * 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 'MesKit' can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: extdata 4.9Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 calJSI : processJSI: no visible binding for global variable 'CCF' cna2gene: no visible global function definition for 'genes' cna2gene: no visible binding for global variable 'org.Hs.eg.db' cna2gene: no visible binding for global variable 'seqnames' cna2gene: no visible binding for global variable 'Chromosome' cna2gene: no visible binding for global variable 'Hugo_Symbol' cna2gene: no visible binding for global variable 'Start_Position' cna2gene: no visible binding for global variable 'End_Position' cna2gene: no visible binding for global variable 'i.End_Position' cna2gene: no visible binding for global variable 'i.Start_Position' cna2gene: no visible binding for global variable 'Patient_ID' cna2gene: no visible binding for global variable 'Tumor_Sample_Barcode' cna2gene: no visible binding for global variable 'seg_id' cna2gene: no visible binding for global variable 'overlap_width' copyNumberFilter: no visible binding for global variable 'Patient_ID' drawVAFCombine: no visible binding for global variable 'V' drawVAFCombineVline: no visible binding for global variable 'V' fitSignatures : processFitSig: no visible binding for global variable 'Branch' fitSignatures : processFitSig: no visible binding for global variable 'Original' fitSignatures : processFitSig: no visible binding for global variable 'Reconstructed' mutCluster : processVafcluster_sample: no visible binding for global variable 'cluster' plotCNA: no visible binding for global variable 'Cytoband' plotCNA: no visible binding for global variable 'Cytoband_pos' plotCNA: no visible binding for global variable 'gene_id' plotCNA: no visible binding for global variable 'gene_pos' plotCNA: no visible binding for global variable 'Hugo_Symbol' plotTree: no visible binding for global variable 'is.match' plotTree: no visible binding for global variable 'x' plotTree: no visible binding for global variable 'y' plotTree: no visible binding for global variable 'xend' plotTree: no visible binding for global variable 'yend' Undefined global functions or variables: Branch CCF Chromosome Cytoband Cytoband_pos End_Position Hugo_Symbol Original Patient_ID Reconstructed Start_Position Tumor_Sample_Barcode V cluster gene_id gene_pos genes i.End_Position i.Start_Position is.match org.Hs.eg.db overlap_width seg_id seqnames x xend y yend * 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 cna2gene 19.55 0.69 20.61 getBinaryMatrix 12.00 0.20 12.21 getTree 12.16 0.03 12.18 calFst 11.18 0.43 12.24 getTreeMethod 10.98 0.02 10.99 getCCFMatrix 10.94 0.02 10.93 getPhyloTreePatient 10.85 0.01 10.86 getPhyloTreeRef 10.70 0.07 10.75 getPhyloTreeTsbLabel 10.75 0.01 10.77 getMutBranches 10.50 0.17 10.70 getBootstrapValue 10.59 0.06 10.64 getPhyloTree 10.40 0.07 10.45 getBranchType 10.33 0.06 10.39 mutHeatmap 9.14 0.05 9.16 compareCCF 8.00 1.09 9.08 plotMutSigProfile 8.81 0.19 8.99 calJSI 8.13 0.05 8.15 compareTree 7.11 0.77 7.87 calNeiDist 7.37 0.03 7.41 mutCluster 6.99 0.09 7.06 mutTrunkBranch 6.61 0.08 6.68 fitSignatures 5.77 0.14 5.91 triMatrix 5.75 0.11 5.86 ccfAUC 5.71 0.03 5.72 plotPhyloTree 5.11 0.01 5.12 plotMutProfile 5.06 0.02 5.08 testNeutral 5.03 0.03 5.07 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cna2gene 17.44 0.42 17.84 calFst 11.01 0.21 11.22 getBootstrapValue 9.42 0.04 9.45 getBranchType 9.38 0.00 9.36 getTreeMethod 9.27 0.03 9.30 getPhyloTreeRef 9.25 0.02 9.27 getPhyloTreeTsbLabel 9.14 0.02 9.15 getBinaryMatrix 9.12 0.01 9.14 getTree 9.03 0.01 9.05 getCCFMatrix 9.01 0.01 9.02 plotMutSigProfile 8.83 0.11 8.94 getMutBranches 8.88 0.01 8.88 getPhyloTree 8.74 0.01 8.74 getPhyloTreePatient 8.72 0.00 8.70 compareCCF 7.39 0.33 7.71 calJSI 7.11 0.06 7.17 calNeiDist 7.05 0.00 7.04 triMatrix 6.95 0.10 7.05 mutHeatmap 6.80 0.02 6.82 ccfAUC 6.42 0.01 6.43 compareTree 5.97 0.09 6.06 mutTrunkBranch 5.55 0.05 5.59 mutCluster 5.56 0.03 5.59 fitSignatures 5.30 0.11 5.41 plotMutProfile 5.08 0.00 5.06 plotPhyloTree 5.07 0.00 5.08 * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MesKit.Rcheck/00check.log' for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MesKit_1.2.0.tar.gz && rm -rf MesKit.buildbin-libdir && mkdir MesKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MesKit.buildbin-libdir MesKit_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MesKit_1.2.0.zip && rm MesKit_1.2.0.tar.gz MesKit_1.2.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1799k 100 1799k 0 0 2674k 0 --:--:-- --:--:-- --:--:-- 2677k install for i386 * installing *source* package 'MesKit' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MesKit' finding HTML links ... done Maf-class html MafList-class html calFst html calJSI html calNeiDist html ccfAUC html classifyMut html cna2gene html compareCCF html compareTree html fitSignatures html getBinaryMatrix html getBootstrapValue html getBranchType html getCCFMatrix html getMafData html getMafPatient html getMafRef html getMutBranches html getNonSyn_vc html getPhyloTree html getPhyloTreePatient html getPhyloTreeRef html getPhyloTreeTsbLabel html getSampleInfo html getTree html getTreeMethod html mathScore html mutCluster html mutHeatmap html mutTrunkBranch html phyloTree-class html phyloTreeList-class html plotCNA html plotMutProfile html plotMutSigProfile html plotPhyloTree html readMaf html readSegment html runMesKit html subMaf html testNeutral html triMatrix 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 'MesKit' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MesKit' as MesKit_1.2.0.zip * DONE (MesKit) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'MesKit' successfully unpacked and MD5 sums checked
MesKit.Rcheck/examples_i386/MesKit-Ex.timings
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MesKit.Rcheck/examples_x64/MesKit-Ex.timings
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