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BioC 3.4: CHECK report for GEOquery on moscato1

This page was generated on 2016-09-21 03:41:42 -0700 (Wed, 21 Sep 2016).

Package 506/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOquery 2.39.3
Sean Davis
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GEOquery
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 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: GEOquery
Version: 2.39.3
Command: rm -rf GEOquery.buildbin-libdir GEOquery.Rcheck && mkdir GEOquery.buildbin-libdir GEOquery.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOquery.buildbin-libdir GEOquery_2.39.3.tar.gz >GEOquery.Rcheck\00install.out 2>&1 && cp GEOquery.Rcheck\00install.out GEOquery-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GEOquery.buildbin-libdir --install="check:GEOquery-install.out" --force-multiarch --no-vignettes --timings GEOquery_2.39.3.tar.gz
StartedAt: 2016-09-20 09:22:19 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:33:17 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 657.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GEOquery.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GEOquery.buildbin-libdir GEOquery.Rcheck && mkdir GEOquery.buildbin-libdir GEOquery.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOquery.buildbin-libdir GEOquery_2.39.3.tar.gz >GEOquery.Rcheck\00install.out 2>&1 && cp GEOquery.Rcheck\00install.out GEOquery-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GEOquery.buildbin-libdir --install="check:GEOquery-install.out" --force-multiarch --no-vignettes --timings GEOquery_2.39.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GEOquery.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 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.39.3'
* 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 'GEOquery' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.8Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
* 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
* 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 'limma' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Biobase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'GEOquery/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
    packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")

See section 'Good practice' in '?.onAttach'.

GDS2MA: no visible binding for global variable 'MA'
fastTabRead: no visible global function definition for 'read.table'
fastTabRead: no visible global function definition for 'read.delim'
getAndParseGSEMatrices: no visible global function definition for
  'download.file'
getDirListing: no visible global function definition for 'read.table'
getGEOSuppFiles: no visible global function definition for
  'download.file'
getGEOfile: no visible global function definition for 'download.file'
getGSEDataTables : <anonymous>: no visible global function definition
  for 'read.delim'
parseGSEMatrix: no visible global function definition for 'read.table'
parseGSEMatrix: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  MA download.file read.delim read.table
Consider adding
  importFrom("utils", "download.file", "read.delim", "read.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getGSEDataTables  0.2   0.06    5.68
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/GEOquery.Rcheck/00check.log'
for details.


GEOquery.Rcheck/00install.out:


install for i386

* installing *source* package 'GEOquery' ...
** 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 'GEOquery' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOquery' as GEOquery_2.39.3.zip
* DONE (GEOquery)

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

nameusersystemelapsed
GDS2MA000
getGEO000
getGEOSuppFiles000
getGEOfile000
getGSEDataTables0.250.033.89

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

nameusersystemelapsed
GDS2MA000
getGEO000
getGEOSuppFiles000
getGEOfile000
getGSEDataTables0.200.065.68