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BioC 3.6: CHECK report for GeneGeneInteR on tokay1

This page was generated on 2017-08-16 13:36:39 -0400 (Wed, 16 Aug 2017).

Package 521/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.3.0
Mathieu Emily , Magalie Houee-Bigot
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneGeneInteR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneGeneInteR
Version: 1.3.0
Command: rm -rf GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && mkdir GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.3.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.3.0.tar.gz
StartedAt: 2017-08-15 23:40:11 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:48:17 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 485.6 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.3.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneGeneInteR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.3.0'
* 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-3.6-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
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'GeneGeneInteR' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'GeneGeneInteR' as GeneGeneInteR_1.3.0.zip
* DONE (GeneGeneInteR)

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

nameusersystemelapsed
CCA.test0.500.030.53
CLD.test1.490.001.50
GBIGM.test2.970.113.08
GGI1.300.031.32
KCCA.test000
PCA.test0.340.000.34
PLSPM.test2.850.062.94
gates.test0.390.000.39
importFile0.420.020.44
imputeSnpMatrix0.720.040.76
minP.test0.730.000.82
plot.GGInetwork1.020.071.08
print.GGItest0.050.000.04
selectSnps0.010.000.02
snpMatrixScour0.030.000.03
summary.GGInetwork000
summary.GGItest0.020.000.01
tProd.test0.360.000.36
tTS.test0.400.000.41

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

nameusersystemelapsed
CCA.test0.820.010.86
CLD.test1.430.001.43
GBIGM.test3.300.023.31
GGI1.760.011.83
KCCA.test0.020.000.01
PCA.test0.450.000.46
PLSPM.test3.770.023.78
gates.test0.590.000.64
importFile0.640.020.66
imputeSnpMatrix2.470.002.46
minP.test0.780.010.85
plot.GGInetwork1.300.021.31
print.GGItest0.110.000.11
selectSnps0.010.000.02
snpMatrixScour0.070.000.12
summary.GGInetwork000
summary.GGItest0.030.000.03
tProd.test0.580.010.59
tTS.test0.560.000.56