Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for pathifier on machv2

This page was generated on 2020-10-17 11:59:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pathifier PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1270/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathifier 1.26.0
Assif Yitzhaky
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pathifier
Branch: RELEASE_3_11
Last Commit: 7b2240c
Last Changed Date: 2020-04-27 14:35:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pathifier
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathifier_1.26.0.tar.gz
StartedAt: 2020-10-17 03:46:44 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:48:05 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 80.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pathifier.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathifier_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathifier.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathifier’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pathifier’ 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
.getpathway: no visible global function definition for ‘var’
.samplings_stdev: no visible binding for global variable ‘sd’
.score_pathway: no visible binding for global variable ‘sd’
.score_pathway: no visible global function definition for ‘aggregate’
.score_pathway: no visible global function definition for ‘dist’
quantify_pathways_deregulation: no visible binding for global variable
  ‘sd’
quantify_pathways_deregulation: no visible global function definition
  for ‘prcomp’
Undefined global functions or variables:
  aggregate dist prcomp sd var
Consider adding
  importFrom("stats", "aggregate", "dist", "prcomp", "sd", "var")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
pathifier-package              20.749  0.134  20.911
quantify_pathways_deregulation 18.611  0.091  18.772
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathifier.Rcheck/00check.log’
for details.



Installation output

pathifier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathifier
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pathifier’ ...
** using staged installation
** 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 (pathifier)

Tests output


Example timings

pathifier.Rcheck/pathifier-Ex.timings

nameusersystemelapsed
KEGG0.0210.0040.024
Sheffer0.0320.0040.038
pathifier-package20.749 0.13420.911
quantify_pathways_deregulation18.611 0.09118.772