Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the PPInfer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PPInfer.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 1420/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PPInfer 1.18.0 (landing page) Dongmin Jung
| 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: PPInfer |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PPInfer_1.18.0.tar.gz |
StartedAt: 2021-10-14 11:04:36 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:12:26 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 470.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PPInfer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PPInfer_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/PPInfer.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PPInfer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PPInfer’ version ‘1.18.0’ * 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 for sufficient/correct file permissions ... 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 * 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 : <anonymous>: 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ppi.infer.human 35.224 2.472 173.704 ppi.infer.mouse 27.581 1.621 103.582 ORA.barplot 2.029 0.121 16.563 ORA 1.761 0.211 16.368 * 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/PPInfer.Rcheck/00check.log’ for details.
PPInfer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL PPInfer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘PPInfer’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (PPInfer)
PPInfer.Rcheck/PPInfer-Ex.timings
name | user | system | elapsed | |
GSEA.barplot | 3.268 | 0.070 | 3.338 | |
ORA | 1.761 | 0.211 | 16.368 | |
ORA.barplot | 2.029 | 0.121 | 16.563 | |
enrich.net | 1.891 | 0.036 | 1.913 | |
net.infer | 1.700 | 0.004 | 1.705 | |
net.infer.ST | 0.068 | 0.004 | 0.071 | |
net.kernel | 0.024 | 0.000 | 0.024 | |
ppi.infer.human | 35.224 | 2.472 | 173.704 | |
ppi.infer.mouse | 27.581 | 1.621 | 103.582 | |
self.train.kernel | 0.059 | 0.000 | 0.060 | |