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BioC 3.5: CHECK report for GeneGeneInteR on tokay2

This page was generated on 2017-10-18 14:26:17 -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: rm -rf GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && mkdir GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.2.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.2.0.tar.gz
StartedAt: 2017-10-17 23:59:12 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-18 00:07:39 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 506.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && mkdir GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.2.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneGeneInteR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneGeneInteR.Rcheck/00check.log'
for details.


GeneGeneInteR.Rcheck/00install.out:

install for i386

* 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

install for x64

* installing *source* package 'GeneGeneInteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneGeneInteR' as GeneGeneInteR_1.2.0.zip
* DONE (GeneGeneInteR)

GeneGeneInteR.Rcheck/examples_i386/GeneGeneInteR-Ex.timings:

nameusersystemelapsed
CCA.test0.500.050.55
CLD.test1.800.001.84
GBIGM.test2.880.082.95
GGI1.250.031.28
KCCA.test000
PCA.test0.290.000.30
PLSPM.test2.540.012.56
gates.test0.310.020.33
importFile0.420.000.42
imputeSnpMatrix0.550.080.62
minP.test0.900.001.13
plot.GGInetwork1.000.111.11
print.GGItest0.070.000.06
selectSnps0.010.000.02
snpMatrixScour0.000.030.03
summary.GGInetwork0.020.000.01
summary.GGItest0.030.000.04
tProd.test0.360.010.37
tTS.test0.350.000.34

GeneGeneInteR.Rcheck/examples_x64/GeneGeneInteR-Ex.timings:

nameusersystemelapsed
CCA.test0.770.010.84
CLD.test1.480.001.52
GBIGM.test4.390.004.39
GGI1.970.001.99
KCCA.test000
PCA.test0.40.00.4
PLSPM.test3.170.023.19
gates.test0.40.00.5
importFile0.570.020.60
imputeSnpMatrix0.630.000.62
minP.test1.620.031.67
plot.GGInetwork1.280.001.28
print.GGItest0.070.010.08
selectSnps000
snpMatrixScour0.030.000.04
summary.GGInetwork0.020.000.02
summary.GGItest0.030.000.03
tProd.test0.500.020.52
tTS.test0.50.00.5