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BioC 3.5: CHECK report for GeneGeneInteR on oaxaca

This page was generated on 2017-03-04 16:52:56 -0500 (Sat, 04 Mar 2017).

Package 496/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.1.1
Mathieu Emily , Magalie Houee-Bigot
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneGeneInteR
Last Changed Rev: 124771 / Revision: 127142
Last Changed Date: 2016-12-03 09:57:18 -0500 (Sat, 03 Dec 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: GeneGeneInteR
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneGeneInteR_1.1.1.tar.gz
StartedAt: 2017-03-04 03:19:27 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 03:26:07 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 399.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneGeneInteR_1.1.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneGeneInteR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/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
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
* DONE (GeneGeneInteR)

GeneGeneInteR.Rcheck/GeneGeneInteR-Ex.timings:

nameusersystemelapsed
CCA.test0.7860.0510.856
CLD.test1.3440.0531.397
GBIGM.test3.5780.0423.622
GGI1.8550.0391.914
KCCA.test0.0010.0010.003
PCA.test0.5340.0020.537
PLSPM.test3.8930.0333.953
gates.test0.9730.0040.977
importFile0.5240.0030.528
imputeSnpMatrix0.8260.0140.856
minP.test0.6910.0020.711
plot.GGInetwork1.8620.0281.943
print.GGItest0.0920.0010.093
selectSnps0.0080.0000.008
snpMatrixScour0.0460.0000.046
summary.GGInetwork0.0090.0010.009
summary.GGItest0.0280.0010.028
tProd.test0.5370.0290.567
tTS.test0.4990.0120.511