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BioC 3.5: CHECK report for AGDEX on tokay2

This page was generated on 2017-08-16 13:21:18 -0400 (Wed, 16 Aug 2017).

Package 30/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AGDEX 1.24.0
Cuilan lani Gao
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AGDEX
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AGDEX
Version: 1.24.0
Command: rm -rf AGDEX.buildbin-libdir AGDEX.Rcheck && mkdir AGDEX.buildbin-libdir AGDEX.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AGDEX.buildbin-libdir AGDEX_1.24.0.tar.gz >AGDEX.Rcheck\00install.out 2>&1 && cp AGDEX.Rcheck\00install.out AGDEX-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AGDEX.buildbin-libdir --install="check:AGDEX-install.out" --force-multiarch --no-vignettes --timings AGDEX_1.24.0.tar.gz
StartedAt: 2017-08-15 21:55:56 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:58:00 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 123.2 seconds
RetCode: 0
Status:  OK  
CheckDir: AGDEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AGDEX.buildbin-libdir AGDEX.Rcheck && mkdir AGDEX.buildbin-libdir AGDEX.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AGDEX.buildbin-libdir AGDEX_1.24.0.tar.gz >AGDEX.Rcheck\00install.out 2>&1 && cp AGDEX.Rcheck\00install.out AGDEX-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AGDEX.buildbin-libdir --install="check:AGDEX-install.out" --force-multiarch --no-vignettes --timings AGDEX_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/AGDEX.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AGDEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AGDEX' version '1.24.0'
* 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 'AGDEX' 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.
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'GSEABase'
  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
agdex: no visible global function definition for 'exprs'
agdex: no visible global function definition for 'qnorm'
agdex: no visible global function definition for 'pnorm'
agdex: no visible global function definition for 'sampleNames'
agdex: no visible global function definition for 'pData'
agdex.scatterplot: no visible global function definition for 'plot'
agdex.scatterplot: no visible global function definition for 'points'
agdex.scatterplot: no visible global function definition for 'lines'
agdex.scatterplot: no visible global function definition for 'prcomp'
agdex.scatterplot: no visible global function definition for 'abline'
gsc.to.index.list: no visible global function definition for 'geneIds'
prep.dex.set: no visible global function definition for 'exprs'
prep.dex.set: no visible global function definition for 'pData'
read.agdex.gset.details: no visible global function definition for
  'read.table'
read.agdex.gset.list: no visible global function definition for
  'read.table'
read.agdex.result: no visible global function definition for
  'read.table'
read.enrich.gset.list: no visible global function definition for
  'read.table'
read.gset.collection: no visible global function definition for
  'read.table'
read.gset.collection: no visible global function definition for
  'GeneSet'
read.gset.collection: no visible global function definition for
  'geneIds<-'
read.gset.collection: no visible global function definition for
  'GeneSetCollection'
write.agdex.gset.details: no visible global function definition for
  'write.table'
write.agdex.result: no visible global function definition for
  'write.table'
write.gset.list.result: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
  plot pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "pnorm", "prcomp", "qnorm")
  importFrom("utils", "read.table", "write.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 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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/AGDEX.Rcheck/00check.log'
for details.


AGDEX.Rcheck/00install.out:


install for i386

* installing *source* package 'AGDEX' ...
** 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 'AGDEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AGDEX' as AGDEX_1.24.0.zip
* DONE (AGDEX)

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

nameusersystemelapsed
agdex0.800.030.82
agdex.scatterplot0.030.000.03
get.gset.result.details0.110.000.11
gset.data000
human.data0.010.020.03
make.dex.set.object0.050.020.06
map.data000
mouse.data0.010.010.03
read.agdex.gset.details000
read.agdex.result000
write.agdex.gset.details0.050.000.05
write.agdex.result0.010.000.01

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

nameusersystemelapsed
agdex1.090.041.14
agdex.scatterplot0.020.020.03
get.gset.result.details0.160.000.16
gset.data000
human.data0.010.000.01
make.dex.set.object0.050.030.08
map.data000
mouse.data0.020.020.03
read.agdex.gset.details000
read.agdex.result000
write.agdex.gset.details0.050.000.04
write.agdex.result0.020.010.04