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BioC 3.4: CHECK report for ArrayExpress on moscato1

This page was generated on 2016-09-21 03:42:37 -0700 (Wed, 21 Sep 2016).

Package 57/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.33.0
Ugis Sarkans
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpress
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayExpress
Version: 1.33.0
Command: rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.33.0.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.33.0.tar.gz
StartedAt: 2016-09-20 03:59:54 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:05:28 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 333.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.33.0.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.33.0'
* 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 'ArrayExpress' 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ae2bioc: no visible global function definition for 'new'
extract.zip : <anonymous>: no visible global function definition for
  'unzip'
getAE : <anonymous>: no visible global function definition for
  'download.file'
getAE: no visible global function definition for 'download.file'
getDataColsForAE1: no visible global function definition for
  'read.table'
preparePhenoDataFor2channel: no visible global function definition for
  'new'
queryAE: no visible global function definition for 'download.file'
readDerivedDataFiles: no visible global function definition for
  'read.table'
readDerivedDataFiles: no visible global function definition for 'new'
readDerivedDataMatrixFile: no visible global function definition for
  'read.table'
readDerivedDataMatrixFile: no visible global function definition for
  'new'
readExperimentData: no visible global function definition for 'new'
readFeatures: no visible global function definition for 'read.table'
readFeatures: no visible global function definition for 'new'
readPhenoData: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file new read.table unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "read.table", "unzip")
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 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
ArrayExpress 9.72   0.72   39.47
getAE        7.20   0.58   41.56
queryAE      2.99   0.05    7.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ArrayExpress 9.67   0.56   27.98
queryAE      3.44   0.01    7.66
getAE        2.93   0.29   11.96
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.


ArrayExpress.Rcheck/00install.out:


install for i386

* installing *source* package 'ArrayExpress' ...
** R
** 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 'ArrayExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.33.0.zip
* DONE (ArrayExpress)

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

nameusersystemelapsed
ArrayExpress 9.72 0.7239.47
ae2bioc000
getAE 7.20 0.5841.56
procset000
queryAE2.990.057.91

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

nameusersystemelapsed
ArrayExpress 9.67 0.5627.98
ae2bioc000
getAE 2.93 0.2911.96
procset000
queryAE3.440.017.66