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CHECK report for GeneGeneInteR on malbec2

This page was generated on 2019-04-09 11:46:29 -0400 (Tue, 09 Apr 2019).

Package 621/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.9.0
Mathieu Emily , Magalie Houee-Bigot
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneGeneInteR
Branch: master
Last Commit: dd25738
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: GeneGeneInteR
Version: 1.9.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.9.0.tar.gz
StartedAt: 2019-04-09 00:42:43 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:48:54 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 370.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneGeneInteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneGeneInteR’ version ‘1.9.0’
* 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 ‘GeneGeneInteR’ 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
CCA.test: no visible global function definition for 'as'
CLD.test: no visible global function definition for 'as'
GBIGM.test: no visible global function definition for 'as'
KCCA.test: no visible global function definition for 'as'
PCA.Std: no visible global function definition for 'as'
PLSPM.test: no visible global function definition for 'as'
imputeSnpMatrix: no visible global function definition for 'as'
snpMatrixScour: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GeneGeneInteR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GeneGeneInteR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (GeneGeneInteR)

Tests output


Example timings

GeneGeneInteR.Rcheck/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test1.8080.0281.844
CLD.test1.3480.0001.348
GBIGM.test4.1230.1164.241
GGI1.4660.0001.548
KCCA.test0.0010.0000.002
PCA.test0.0530.0000.053
PLSPM.test3.2700.0003.271
gates.test0.3650.0000.366
importFile0.5060.0000.507
imputeSnpMatrix1.0180.0001.019
minP.test0.6440.0000.651
plot.GGInetwork0.1320.0000.136
print.GGItest0.0190.0000.019
selectSnps0.0050.0000.005
snpMatrixScour0.0450.0000.046
summary.GGInetwork0.0040.0000.005
summary.GGItest0.0170.0000.017
tProd.test0.2870.0000.287
tTS.test0.4020.0000.402