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BioC 2.14: CHECK report for tRanslatome on moscato2

This page was generated on 2014-10-08 08:55:38 -0700 (Wed, 08 Oct 2014).

Package 787/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.2.0
Toma Tebaldi , Erik Dassi
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/tRanslatome
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: tRanslatome
Version: 1.2.0
Command: rm -rf tRanslatome.buildbin-libdir && mkdir tRanslatome.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tRanslatome.buildbin-libdir tRanslatome_1.2.0.tar.gz >tRanslatome-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=tRanslatome.buildbin-libdir --install="check:tRanslatome-install.out" --force-multiarch --no-vignettes --timings tRanslatome_1.2.0.tar.gz
StartedAt: 2014-10-08 05:47:06 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 05:52:05 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 298.9 seconds
RetCode: 0
Status:  OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf tRanslatome.buildbin-libdir && mkdir tRanslatome.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tRanslatome.buildbin-libdir tRanslatome_1.2.0.tar.gz >tRanslatome-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=tRanslatome.buildbin-libdir --install="check:tRanslatome-install.out" --force-multiarch --no-vignettes --timings tRanslatome_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/tRanslatome.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tRanslatome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tRanslatome' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma' 'sigPathway' 'samr' 'anota' 'DESeq' 'edgeR' 'RankProd'
  'topGO' 'org.Hs.eg.db' 'GOSemSim' 'Heatplus' 'gplots' 'plotrix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'tRanslatome' 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 ... NOTE
Packages in Depends field not imported from:
  'DESeq' 'GOSemSim' 'Heatplus' 'RankProd' 'anota' 'edgeR' 'gplots'
  'limma' 'methods' 'org.Hs.eg.db' 'plotrix' 'samr' 'sigPathway'
  'topGO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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' ... [32s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOEnrichment 18.01   0.03   18.05
** running examples for arch 'x64' ... [36s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOEnrichment 20.06   0.01    20.1
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/tRanslatome.Rcheck/00check.log'
for details.

tRanslatome.Rcheck/00install.out:


install for i386

* installing *source* package 'tRanslatome' ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

install for x64

* installing *source* package 'tRanslatome' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'tRanslatome' as tRanslatome_1.2.0.zip
* DONE (tRanslatome)

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

nameusersystemelapsed
CVplot0.080.000.07
DEGs000
DEGs.table0.170.030.20
EnrichedSets000
FC.threshold0.060.000.06
GOComparison1.100.001.14
GOEnrichment18.01 0.0318.05
GOsets000
GOsims000
Heatmap0.080.020.10
Histogram0.050.010.06
IdentityPlot0.040.000.05
MAplot0.060.000.06
Radar0.060.020.08
RegulatoryEnrichment2.200.032.23
SDplot0.080.000.08
Scatterplot0.080.000.08
SimilarityPlot0.060.000.06
TranslatomeDataset000
average.similarity.scores0.060.000.06
computeDEGs0.460.000.45
enriched.table0.060.000.06
getConditionA0.050.010.06
getConditionB0.040.000.05
getConditionC0.060.000.06
getConditionD0.070.000.06
getConditionLabels0.060.000.07
getDEGs0.060.000.06
getDEGsMethod0.060.000.06
getDataType0.050.000.05
getExprMatrix0.110.020.12
getLevelLabels0.060.000.07
identity.matrix0.070.000.06
label.condition0.040.000.05
label.level.DEGs0.060.000.06
label.level.enriched0.080.000.08
newTranslatomeDataset0.060.000.06
significance.threshold0.050.000.04
similarity.matrix0.050.000.05
tRanslatomeSampleData0.050.020.06

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

nameusersystemelapsed
CVplot0.060.020.08
DEGs000
DEGs.table0.120.030.15
EnrichedSets000
FC.threshold0.050.000.05
GOComparison1.230.021.24
GOEnrichment20.06 0.0120.10
GOsets000
GOsims000
Heatmap0.090.000.09
Histogram0.060.000.06
IdentityPlot0.050.020.06
MAplot0.060.000.06
Radar0.060.010.08
RegulatoryEnrichment2.730.002.73
SDplot0.070.000.06
Scatterplot0.060.000.06
SimilarityPlot0.030.020.04
TranslatomeDataset0.020.000.02
average.similarity.scores0.040.000.05
computeDEGs0.530.010.55
enriched.table0.060.000.06
getConditionA0.060.000.06
getConditionB0.050.000.05
getConditionC0.060.000.06
getConditionD0.060.000.06
getConditionLabels0.050.000.05
getDEGs0.040.000.04
getDEGsMethod0.050.020.07
getDataType0.060.000.06
getExprMatrix0.100.000.09
getLevelLabels0.050.000.04
identity.matrix0.060.000.07
label.condition0.060.000.06
label.level.DEGs0.040.020.05
label.level.enriched0.050.000.05
newTranslatomeDataset0.060.000.06
significance.threshold0.060.000.06
similarity.matrix0.060.000.07
tRanslatomeSampleData0.050.000.04