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BioC 3.2: CHECK report for BiocInstaller on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:30 -0400 (Tue, 27 Oct 2015).

Package 99/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocInstaller 1.20.0
Bioconductor Package Maintainer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiocInstaller
Last Changed Rev: 109595 / Revision: 109947
Last Changed Date: 2015-10-13 16:42:26 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  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: BiocInstaller
Version: 1.20.0
Command: rm -rf BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && mkdir BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocInstaller.buildbin-libdir BiocInstaller_1.20.0.tar.gz >BiocInstaller.Rcheck\00install.out 2>&1 && cp BiocInstaller.Rcheck\00install.out BiocInstaller-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocInstaller.buildbin-libdir --install="check:BiocInstaller-install.out" --force-multiarch --no-vignettes --timings BiocInstaller_1.20.0.tar.gz
StartedAt: 2015-10-27 00:03:22 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:03:53 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 30.9 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocInstaller.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && mkdir BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocInstaller.buildbin-libdir BiocInstaller_1.20.0.tar.gz >BiocInstaller.Rcheck\00install.out 2>&1 && cp BiocInstaller.Rcheck\00install.out BiocInstaller-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocInstaller.buildbin-libdir --install="check:BiocInstaller-install.out" --force-multiarch --no-vignettes --timings BiocInstaller_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/BiocInstaller.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocInstaller/DESCRIPTION' ... OK
* this is package 'BiocInstaller' version '1.20.0'
* 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 'BiocInstaller' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 'utils' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'utils:::.clean_up_dependencies'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.updateBiocInstallerFinish' '.updateFinish'
* 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 examples ...
** running examples for arch 'i386' ... [6s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
biocValid 4.52   0.67    5.42
** running examples for arch 'x64' ... [5s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'BiocInstaller_unit_tests.R' [2s]
 [2s] OK
** running tests for arch 'x64' ...
  Running 'BiocInstaller_unit_tests.R' [2s]
 [2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/BiocInstaller.Rcheck/00check.log'
for details.


BiocInstaller.Rcheck/00install.out:


install for i386

* installing *source* package 'BiocInstaller' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help

install for x64

* installing *source* package 'BiocInstaller' ...
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
* MD5 sums
packaged installation of 'BiocInstaller' as BiocInstaller_1.20.0.zip
* DONE (BiocInstaller)

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

nameusersystemelapsed
BiocUpgrade000
biocLite0.030.000.03
biocUpdatePackages000
biocValid4.520.675.42
biocVersion000
biocinstallRepos000
packageGroups0.080.000.08
useDevel000

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

nameusersystemelapsed
BiocUpgrade000
biocLite0.040.000.03
biocUpdatePackages000
biocValid4.290.244.77
biocVersion000
biocinstallRepos0.020.000.01
packageGroups0.080.000.08
useDevel000