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BioC 3.4: CHECK report for GEOsearch on moscato1

This page was generated on 2016-09-21 03:47:33 -0700 (Wed, 21 Sep 2016).

Package 507/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOsearch 1.3.2
Zhicheng Ji
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GEOsearch
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GEOsearch
Version: 1.3.2
Command: rm -rf GEOsearch.buildbin-libdir GEOsearch.Rcheck && mkdir GEOsearch.buildbin-libdir GEOsearch.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOsearch.buildbin-libdir GEOsearch_1.3.2.tar.gz >GEOsearch.Rcheck\00install.out 2>&1 && cp GEOsearch.Rcheck\00install.out GEOsearch-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GEOsearch.buildbin-libdir --install="check:GEOsearch-install.out" --force-multiarch --no-vignettes --timings GEOsearch_1.3.2.tar.gz
StartedAt: 2016-09-20 09:24:44 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:27:58 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 193.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GEOsearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GEOsearch.buildbin-libdir GEOsearch.Rcheck && mkdir GEOsearch.buildbin-libdir GEOsearch.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOsearch.buildbin-libdir GEOsearch_1.3.2.tar.gz >GEOsearch.Rcheck\00install.out 2>&1 && cp GEOsearch.Rcheck\00install.out GEOsearch-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GEOsearch.buildbin-libdir --install="check:GEOsearch-install.out" --force-multiarch --no-vignettes --timings GEOsearch_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GEOsearch.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 'GEOsearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOsearch' version '1.3.2'
* 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 'GEOsearch' can be installed ... OK
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
KeyWordFreq: no visible global function definition for 'data'
KeyWordFreq: no visible global function definition for 'p.adjust'
KeyWordFreq : <anonymous>: no visible global function definition for
  'fisher.test'
TermAlias: no visible global function definition for 'data'
TermAlias: no visible binding for global variable 'database'
TermAlias : <anonymous>: no visible binding for global variable
  'database'
TermAlias : <anonymous>: no visible global function definition for
  'keys'
TermAlias : <anonymous>: no visible binding for global variable 'db'
TermAlias : <anonymous>: no visible global function definition for
  'select'
Undefined global functions or variables:
  data database db fisher.test keys p.adjust select
Consider adding
  importFrom("stats", "fisher.test", "p.adjust")
  importFrom("utils", "data")
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 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' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
TermAlias   7.41   0.06   16.54
KeyWordFreq 0.97   0.13   30.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
TermAlias 7.94   0.22   16.34
* 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 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/GEOsearch.Rcheck/00check.log'
for details.


GEOsearch.Rcheck/00install.out:


install for i386

* installing *source* package 'GEOsearch' ...
** 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 'GEOsearch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOsearch' as GEOsearch_1.3.2.zip
* DONE (GEOsearch)

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

nameusersystemelapsed
GEOSearchTerm0.260.092.77
GEOSearchUI000
KeyWordFreq 0.97 0.1330.48
SampleDetail0.700.144.20
TermAlias 7.41 0.0616.54

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

nameusersystemelapsed
GEOSearchTerm0.360.050.95
GEOSearchUI0.010.000.02
KeyWordFreq1.250.091.70
SampleDetail0.920.242.82
TermAlias 7.94 0.2216.34