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BioC 3.5: CHECK report for SMITE on tokay2

This page was generated on 2017-08-16 13:25:21 -0400 (Wed, 16 Aug 2017).

Package 1236/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.4.1
Neil Ari Wijetunga
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/SMITE
Last Changed Rev: 131580 / Revision: 131943
Last Changed Date: 2017-07-25 23:22:00 -0400 (Tue, 25 Jul 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: SMITE
Version: 1.4.1
Command: rm -rf SMITE.buildbin-libdir SMITE.Rcheck && mkdir SMITE.buildbin-libdir SMITE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.4.1.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.4.1.tar.gz
StartedAt: 2017-08-16 03:00:16 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:07:11 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 414.6 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SMITE.buildbin-libdir SMITE_1.4.1.tar.gz >SMITE.Rcheck\00install.out 2>&1 && cp SMITE.Rcheck\00install.out SMITE-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SMITE.buildbin-libdir --install="check:SMITE-install.out" --force-multiarch --no-vignettes --timings SMITE_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-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 '1.4.1'
* 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_1.4.1.zip
* DONE (SMITE)

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.080.050.13
SMITE-package0.610.010.62
addShadowText000
annotateExpression0.370.030.41
annotateModification000
convertGeneIds2.50.22.7
curated_expression0.100.020.11
extractExpression0.420.010.44
extractGOseq0.010.040.05
extractModification1.690.041.73
extractModules0.030.020.05
extractScores0.030.010.05
genes_for_conversiontest1.050.001.04
hg19_gene_bed0.170.000.18
highScores0.030.000.03
histone_h3k4me10.080.010.10
makePvalueAnnotation0.960.020.96
makePvalueObject0.070.020.10
methylationdata0.100.010.11
normalizePval0.050.000.05
plotCompareScores1.290.021.31
plotDensityPval0.100.010.11
plotModule0.060.000.06
removeModification0.060.020.08
runBioNet0.060.000.07
runGOseq0.080.000.07
runSpinglass1.890.051.94
scorePval0.060.000.06
stoufferTest000
test_annotation_score_data0.200.020.22

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.120.000.13
SMITE-package0.430.050.47
addShadowText000
annotateExpression0.330.020.35
annotateModification000
convertGeneIds3.750.173.92
curated_expression0.050.000.04
extractExpression0.360.010.38
extractGOseq0.030.000.03
extractModification2.110.052.16
extractModules0.040.020.06
extractScores0.070.010.08
genes_for_conversiontest1.090.001.09
hg19_gene_bed0.140.000.14
highScores0.030.000.03
histone_h3k4me10.080.000.08
makePvalueAnnotation1.530.031.56
makePvalueObject0.060.000.06
methylationdata0.070.020.08
normalizePval0.030.000.03
plotCompareScores1.220.081.29
plotDensityPval0.070.000.06
plotModule0.040.010.06
removeModification0.060.020.08
runBioNet0.040.000.03
runGOseq0.040.000.05
runSpinglass0.860.000.86
scorePval0.060.000.06
stoufferTest000
test_annotation_score_data0.110.000.11