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BioC 3.5: CHECK report for GeneGeneInteR on malbec2

This page was generated on 2017-10-18 14:17:55 -0400 (Wed, 18 Oct 2017).

Package 514/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.2.0
Mathieu Emily , Magalie Houee-Bigot
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GeneGeneInteR
Branch: RELEASE_3_5
Last Commit: bee4f0e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneGeneInteR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GeneGeneInteR_1.2.0.tar.gz
StartedAt: 2017-10-17 23:26:19 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:31:52 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 332.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GeneGeneInteR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GeneGeneInteR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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-3.5-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.


GeneGeneInteR.Rcheck/00install.out:

* installing *source* package ‘GeneGeneInteR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneGeneInteR)

GeneGeneInteR.Rcheck/GeneGeneInteR-Ex.timings:

nameusersystemelapsed
CCA.test0.5240.0040.543
CLD.test0.9080.0000.909
GBIGM.test2.9720.0162.992
GGI1.6880.0041.694
KCCA.test0.0000.0000.002
PCA.test0.540.000.54
PLSPM.test2.7560.0082.778
gates.test0.3000.0040.305
importFile0.5360.0040.539
imputeSnpMatrix0.9560.0040.960
minP.test0.5520.0000.555
plot.GGInetwork1.3480.0001.448
print.GGItest0.0520.0040.056
selectSnps0.0040.0000.006
snpMatrixScour0.0320.0000.031
summary.GGInetwork0.0040.0000.006
summary.GGItest0.0160.0000.018
tProd.test0.3640.0000.362
tTS.test0.3760.0000.379