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

This page was generated on 2015-10-27 17:28:00 -0400 (Tue, 27 Oct 2015).

Package 102/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.38.0
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/biocViews
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -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: biocViews
Version: 1.38.0
Command: rm -rf biocViews.buildbin-libdir biocViews.Rcheck && mkdir biocViews.buildbin-libdir biocViews.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biocViews.buildbin-libdir biocViews_1.38.0.tar.gz >biocViews.Rcheck\00install.out 2>&1 && cp biocViews.Rcheck\00install.out biocViews-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=biocViews.buildbin-libdir --install="check:biocViews-install.out" --force-multiarch --no-vignettes --timings biocViews_1.38.0.tar.gz
StartedAt: 2015-10-27 00:04:33 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:07:02 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 149.2 seconds
RetCode: 0
Status:  OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biocViews.buildbin-libdir biocViews.Rcheck && mkdir biocViews.buildbin-libdir biocViews.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biocViews.buildbin-libdir biocViews_1.38.0.tar.gz >biocViews.Rcheck\00install.out 2>&1 && cp biocViews.Rcheck\00install.out biocViews-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=biocViews.buildbin-libdir --install="check:biocViews-install.out" --force-multiarch --no-vignettes --timings biocViews_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/biocViews.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 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.38.0'
* 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 'biocViews' can be installed ... OK
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/unitTests/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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
Unexported objects imported by ':::' calls:
  'tools:::.build_news_db_from_package_NEWS_Rd'
  'tools:::.build_repository_package_db'
  'tools:::.get_standard_repository_db_fields'
  'tools:::.news_reader_default' 'tools:::.split_dependencies'
  'tools:::vignetteInfo'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getChildren: no visible binding for global variable 'biocViewsVocab'
getPackageNEWS : getNews: no visible binding for global variable
  'Version'
getReverseDepends : <anonymous>: no visible binding for global variable
  'Package'
validate_bioc_views: no visible binding for global variable
  'biocViewsVocab'
htmlDoc,BiocView: no visible binding for global variable 'stylesheet'
* 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' ... [13s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
recommendPackages 6.81   2.16    8.98
** running examples for arch 'x64' ... [11s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
recommendPackages 5.28   1.54    6.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [42s]
 [42s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [32s]
 [33s] 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: 4 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/biocViews.Rcheck/00check.log'
for details.


biocViews.Rcheck/00install.out:


install for i386

* installing *source* package 'biocViews' ...
** R
** data
** 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 'biocViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.38.0.zip
* DONE (biocViews)

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

nameusersystemelapsed
PackageDetail-class0.060.000.06
biocViews-package0.030.000.03
biocViewsVocab000
getBiocSubViews1.500.021.51
getBiocViews1.400.031.44
getCurrentbiocViews000
getSubTerms0.10.00.1
recommendPackages6.812.168.98
validation_tests000

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

nameusersystemelapsed
PackageDetail-class0.10.00.1
biocViews-package0.040.020.06
biocViewsVocab0.000.010.02
getBiocSubViews1.490.021.50
getBiocViews1.260.001.26
getCurrentbiocViews0.020.000.02
getSubTerms0.160.000.15
recommendPackages5.281.546.83
validation_tests000