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BioC 3.2: CHECK report for GGBase on moscato1

This page was generated on 2016-04-23 10:16:36 -0700 (Sat, 23 Apr 2016).

Package 437/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGBase 3.32.0
VJ Carey
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GGBase
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GGBase
Version: 3.32.0
Command: rm -rf GGBase.buildbin-libdir GGBase.Rcheck && mkdir GGBase.buildbin-libdir GGBase.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGBase.buildbin-libdir GGBase_3.32.0.tar.gz >GGBase.Rcheck\00install.out 2>&1 && cp GGBase.Rcheck\00install.out GGBase-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GGBase.buildbin-libdir --install="check:GGBase-install.out" --force-multiarch --no-vignettes --timings GGBase_3.32.0.tar.gz
StartedAt: 2016-04-23 02:56:25 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:05:41 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 555.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GGBase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GGBase.buildbin-libdir GGBase.Rcheck && mkdir GGBase.buildbin-libdir GGBase.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGBase.buildbin-libdir GGBase_3.32.0.tar.gz >GGBase.Rcheck\00install.out 2>&1 && cp GGBase.Rcheck\00install.out GGBase-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GGBase.buildbin-libdir --install="check:GGBase-install.out" --force-multiarch --no-vignettes --timings GGBase_3.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GGBase.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.32.0'
* 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 'GGBase' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/GGBase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'snpStats' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [98s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
MAFfilter 4.79   0.20   41.12
plot_EvG  4.30   0.08   46.94
** running examples for arch 'x64' ... [21s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'MAFfilter.R' [12s]
  Running 'make.R' [13s]
  Running 'plot_EvG.R' [27s]
 [52s] OK
** running tests for arch 'x64' ...
  Running 'MAFfilter.R' [54s]
  Running 'make.R' [15s]
  Running 'plot_EvG.R' [16s]
 [85s] 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 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/GGBase.Rcheck/00check.log'
for details.


GGBase.Rcheck/00install.out:


install for i386

* installing *source* package 'GGBase' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5

install for x64

* installing *source* package 'GGBase' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.32.0.zip
* DONE (GGBase)

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

nameusersystemelapsed
MAFfilter 4.79 0.2041.12
clipPCs000
externalize000
make_smlSet3.420.093.51
plot_EvG 4.30 0.0846.94
rsid-class000
smlSet-class000

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

nameusersystemelapsed
MAFfilter4.180.264.76
clipPCs000
externalize0.020.000.02
make_smlSet4.130.064.19
plot_EvG4.180.074.44
rsid-class000
smlSet-class000