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BioC 3.5: CHECK report for OGSA on tokay2

This page was generated on 2017-10-18 14:25:01 -0400 (Wed, 18 Oct 2017).

Package 914/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGSA 1.6.0
Michael F. Ochs
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/OGSA
Branch: RELEASE_3_5
Last Commit: 3fc54db
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: OGSA
Version: 1.6.0
Command: rm -rf OGSA.buildbin-libdir OGSA.Rcheck && mkdir OGSA.buildbin-libdir OGSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OGSA.buildbin-libdir OGSA_1.6.0.tar.gz >OGSA.Rcheck\00install.out 2>&1 && cp OGSA.Rcheck\00install.out OGSA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OGSA.buildbin-libdir --install="check:OGSA-install.out" --force-multiarch --no-vignettes --timings OGSA_1.6.0.tar.gz
StartedAt: 2017-10-18 01:47:05 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:51:23 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 258.0 seconds
RetCode: 0
Status:  OK  
CheckDir: OGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OGSA.buildbin-libdir OGSA.Rcheck && mkdir OGSA.buildbin-libdir OGSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OGSA.buildbin-libdir OGSA_1.6.0.tar.gz >OGSA.Rcheck\00install.out 2>&1 && cp OGSA.Rcheck\00install.out OGSA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OGSA.buildbin-libdir --install="check:OGSA-install.out" --force-multiarch --no-vignettes --timings OGSA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/OGSA.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 'OGSA/DESCRIPTION' ... OK
* this is package 'OGSA' version '1.6.0'
* 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 'OGSA' 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
copaStat: no visible binding for global variable 'median'
copaStat: no visible binding for global variable 'mad'
copaStat: no visible binding for global variable 'IQR'
copaStat: no visible binding for global variable 'quantile'
expressionSetPheno: no visible global function definition for 'relevel'
outCallTib: no visible binding for global variable 'median'
outCallTib: no visible binding for global variable 'mad'
outCallTib: no visible binding for global variable 'IQR'
outCallTib: no visible binding for global variable 'quantile'
outCallTibE: no visible binding for global variable 'median'
outCallTibE: no visible binding for global variable 'mad'
outCallTibE: no visible binding for global variable 'IQR'
outCallTibE: no visible binding for global variable 'quantile'
outCount: no visible binding for global variable 'median'
outCount: no visible binding for global variable 'mad'
outCount: no visible binding for global variable 'IQR'
outCount: no visible binding for global variable 'quantile'
outMap: no visible global function definition for 'pdf'
outMap: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  IQR dev.off mad median pdf quantile relevel
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "IQR", "mad", "median", "quantile", "relevel")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
          user system elapsed
copaStat 71.25   0.58   71.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
copaStat 84.09    0.5   84.61
* 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/OGSA.Rcheck/00check.log'
for details.


OGSA.Rcheck/00install.out:


install for i386

* installing *source* package 'OGSA' ...
** 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 'OGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OGSA' as OGSA_1.6.0.zip
* DONE (OGSA)

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

nameusersystemelapsed
copaInt2.410.012.42
copaIntE2.330.022.34
copaStat71.25 0.5871.83
expressionSetDataSet0.190.000.18
expressionSetPheno0.080.000.08
outCallRank1.090.031.13
outCallRankE1.090.001.09
outCallTib1.930.001.92
outCallTibE2.110.002.11
outCount2.180.002.19
outMap2.100.012.11
outRank1.590.021.61
testGScogps000

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

nameusersystemelapsed
copaInt2.700.042.75
copaIntE2.740.022.75
copaStat84.09 0.5084.61
expressionSetDataSet0.200.020.22
expressionSetPheno0.080.000.08
outCallRank1.190.001.19
outCallRankE1.340.001.34
outCallTib2.550.012.56
outCallTibE2.910.022.92
outCount2.540.002.55
outMap2.630.012.64
outRank1.520.001.51
testGScogps000