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BioC 3.4: CHECK report for SMITE on moscato1

This page was generated on 2016-09-21 03:48:00 -0700 (Wed, 21 Sep 2016).

Package 1131/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.1.3
Neil Ari Wijetunga , Andrew Damon Johnston
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SMITE
Last Changed Rev: 120886 / Revision: 121152
Last Changed Date: 2016-09-12 19:09:01 -0700 (Mon, 12 Sep 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: SMITE
Version: 1.1.3
Command: rm -rf SMITE.buildbin-libdir SMITE.Rcheck && mkdir SMITE.buildbin-libdir SMITE.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.1.3.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.1.3.tar.gz
StartedAt: 2016-09-20 16:46:13 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:51:49 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 335.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SMITE.buildbin-libdir SMITE.Rcheck && mkdir SMITE.buildbin-libdir SMITE.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.1.3.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/SMITE.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 'SMITE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMITE' version '1.1.3'
* 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 'SMITE' 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 ... 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' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
convertGeneIds 2.77   0.14    5.14
** 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: OK

SMITE.Rcheck/00install.out:


install for i386

* installing *source* package 'SMITE' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'SMITE'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SMITE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SMITE' as SMITE_1.1.3.zip
* DONE (SMITE)

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.110.010.12
SMITE-package0.480.030.51
addShadowText000
annotateExpression0.490.000.48
annotateModification000
convertGeneIds2.770.145.14
curated_expression0.060.000.06
extractExpression0.190.000.19
extractGOseq0.030.020.04
extractModification1.050.011.06
extractModules0.050.000.05
extractScores0.070.000.08
genes_for_conversiontest1.130.001.12
hg19_gene_bed0.180.000.19
highScores0.030.020.05
histone_h3k4me10.100.020.11
makePvalueAnnotation1.000.000.99
makePvalueObject0.110.000.11
methylationdata0.070.000.08
normalizePval0.050.000.04
plotCompareScores0.450.000.46
plotDensityPval0.080.000.07
plotModule0.040.000.05
removeModification0.110.000.11
runBioNet0.050.000.05
runGOseq0.050.000.04
runSpinglass1.040.011.64
scorePval0.050.000.05
stoufferTest000
test_annotation_score_data0.110.000.11

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.090.000.09
SMITE-package0.440.000.43
addShadowText000
annotateExpression0.250.000.25
annotateModification000
convertGeneIds3.340.133.78
curated_expression0.060.000.06
extractExpression0.180.000.19
extractGOseq0.040.010.05
extractModification1.320.021.34
extractModules0.060.000.06
extractScores0.070.000.06
genes_for_conversiontest1.710.031.75
hg19_gene_bed0.140.000.15
highScores0.020.030.04
histone_h3k4me10.080.010.10
makePvalueAnnotation0.700.020.71
makePvalueObject0.080.010.09
methylationdata0.060.020.08
normalizePval0.050.000.05
plotCompareScores1.140.001.14
plotDensityPval0.110.000.11
plotModule0.060.000.06
removeModification0.110.000.11
runBioNet0.060.000.06
runGOseq0.070.000.07
runSpinglass0.90.00.9
scorePval0.050.000.05
stoufferTest000
test_annotation_score_data0.090.000.09