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BioC 3.6: CHECK report for SMITE on tokay1

This page was generated on 2017-08-16 13:35:43 -0400 (Wed, 16 Aug 2017).

Package 1261/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.5.1
Neil Ari Wijetunga
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SMITE
Last Changed Rev: 131894 / Revision: 131943
Last Changed Date: 2017-08-10 18:09:05 -0400 (Thu, 10 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SMITE
Version: 1.5.1
Command: rm -rf SMITE.buildbin-libdir SMITE.Rcheck && mkdir SMITE.buildbin-libdir SMITE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.5.1.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.5.1.tar.gz
StartedAt: 2017-08-16 02:34:29 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:40:58 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 388.9 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 && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.5.1.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SMITE.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 'SMITE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMITE' version '1.5.1'
* 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
** 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
** 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_1.5.1.zip
* DONE (SMITE)

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.120.020.14
SMITE-package0.480.010.50
addShadowText0.020.000.02
annotateExpression0.230.000.23
annotateModification000
convertGeneIds2.280.142.42
curated_expression0.060.000.06
extractExpression0.270.050.31
extractGOseq0.050.000.05
extractModification1.760.081.84
extractModules0.060.000.07
extractScores0.050.000.04
genes_for_conversiontest1.020.001.02
hg19_gene_bed0.150.000.16
highScores0.030.010.04
histone_h3k4me10.10.00.1
makePvalueAnnotation0.870.040.90
makePvalueObject0.080.000.08
methylationdata0.080.000.08
normalizePval0.060.000.06
plotCompareScores1.580.011.60
plotDensityPval0.090.000.09
plotModule0.030.020.05
removeModification0.080.010.09
runBioNet0.030.020.05
runGOseq0.070.000.06
runSpinglass0.750.010.76
scorePval0.040.000.05
stoufferTest000
test_annotation_score_data0.140.000.14

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.110.000.11
SMITE-package0.420.030.46
addShadowText0.010.000.02
annotateExpression0.290.020.29
annotateModification000
convertGeneIds2.980.143.13
curated_expression0.050.020.06
extractExpression0.310.010.33
extractGOseq0.050.000.05
extractModification2.470.032.50
extractModules0.030.020.04
extractScores0.040.000.05
genes_for_conversiontest1.020.011.03
hg19_gene_bed0.120.000.13
highScores0.040.020.04
histone_h3k4me10.100.000.11
makePvalueAnnotation1.880.011.89
makePvalueObject0.140.000.14
methylationdata0.050.000.05
normalizePval0.030.000.03
plotCompareScores1.300.021.32
plotDensityPval0.060.010.07
plotModule0.050.000.05
removeModification0.060.000.06
runBioNet0.030.020.05
runGOseq0.070.000.06
runSpinglass0.860.000.86
scorePval0.030.010.05
stoufferTest000
test_annotation_score_data0.120.000.12