Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:38:25 -0400 (Wed, 16 Oct 2019).
Package 1237/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
PPInfer 1.10.0 Dongmin Jung
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: PPInfer |
Version: 1.10.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PPInfer_1.10.0.tar.gz |
StartedAt: 2019-10-16 06:04:58 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 06:15:41 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 643.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PPInfer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PPInfer_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PPInfer.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PPInfer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PPInfer' version '1.10.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'biomaRt', 'fgsea', 'kernlab', 'ggplot2', 'igraph', 'STRINGdb', 'yeastExpData' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'PPInfer' 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 ORA: no visible global function definition for 'txtProgressBar' ORA: no visible global function definition for 'fisher.test' ORA: no visible global function definition for 'setTxtProgressBar' ORA: no visible global function definition for 'p.adjust' ORA.barplot: no visible global function definition for 'p.adjust' enrich.net: no visible global function definition for 'stack' enrich.net: no visible global function definition for 'adjustcolor' enrich.net :: no visible global function definition for 'adjustcolor' enrich.net: no visible binding for global variable 'legend' net.infer: no visible global function definition for 'na.omit' net.infer.ST: no visible global function definition for 'na.omit' ppi.infer.human: no visible global function definition for 'na.omit' ppi.infer.mouse: no visible global function definition for 'na.omit' Undefined global functions or variables: adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar stack txtProgressBar Consider adding importFrom("grDevices", "adjustcolor") importFrom("graphics", "legend") importFrom("stats", "fisher.test", "na.omit", "p.adjust") importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar") 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed ppi.infer.human 64.17 1.17 103.72 ppi.infer.mouse 36.66 1.35 94.75 ORA.barplot 0.61 0.03 22.99 ORA 0.21 0.03 24.09 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed ppi.infer.human 42.97 1.86 89.17 ppi.infer.mouse 34.39 2.13 65.75 ORA.barplot 0.73 0.02 23.12 ORA 0.17 0.03 22.58 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PPInfer.Rcheck/00check.log' for details.
PPInfer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PPInfer_1.10.0.tar.gz && rm -rf PPInfer.buildbin-libdir && mkdir PPInfer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PPInfer.buildbin-libdir PPInfer_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PPInfer_1.10.0.zip && rm PPInfer_1.10.0.tar.gz PPInfer_1.10.0.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 272k 100 272k 0 0 4035k 0 --:--:-- --:--:-- --:--:-- 4471k install for i386 * installing *source* package 'PPInfer' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PPInfer' finding HTML links ... done GSEA.barplot html ORA html ORA.barplot html PPInfer-package html enrich.net html net.infer html net.infer.ST html net.kernel html ppi.infer.human html ppi.infer.mouse html self.train.kernel html ** building package indices ** installing vignettes 'PPInfer.Rnw' ** 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 'PPInfer' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'PPInfer' as PPInfer_1.10.0.zip * DONE (PPInfer) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'PPInfer' successfully unpacked and MD5 sums checked
PPInfer.Rcheck/examples_i386/PPInfer-Ex.timings
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PPInfer.Rcheck/examples_x64/PPInfer-Ex.timings
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