Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for SMITE on tokay2

This page was generated on 2017-10-18 14:25:36 -0400 (Wed, 18 Oct 2017).

Package 1235/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.4.1
Neil Ari Wijetunga
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/SMITE
Branch: RELEASE_3_5
Last Commit: 77699c7
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: 2017-10-18 03:07:10 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:13:58 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 407.8 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 3.4.2 Patched (2017-10-07 r73498)
* 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.Igraph0.170.020.18
SMITE-package0.510.040.57
addShadowText000
annotateExpression0.250.020.27
annotateModification000
convertGeneIds2.030.012.04
curated_expression0.060.000.07
extractExpression0.280.040.31
extractGOseq0.050.000.05
extractModification2.000.062.06
extractModules0.060.000.06
extractScores0.050.000.05
genes_for_conversiontest0.920.000.92
hg19_gene_bed0.190.010.22
highScores0.060.000.06
histone_h3k4me10.110.000.11
makePvalueAnnotation0.910.020.92
makePvalueObject0.110.000.11
methylationdata0.080.000.08
normalizePval0.040.000.05
plotCompareScores1.500.091.59
plotDensityPval0.080.000.08
plotModule0.050.000.05
removeModification0.080.030.10
runBioNet0.060.000.07
runGOseq0.060.000.06
runSpinglass0.910.000.91
scorePval0.040.000.04
stoufferTest000
test_annotation_score_data0.140.000.14

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

nameusersystemelapsed
Reactome.Symbol.Igraph0.110.000.11
SMITE-package0.610.020.63
addShadowText0.000.010.01
annotateExpression0.270.020.28
annotateModification000
convertGeneIds2.510.112.63
curated_expression0.050.000.04
extractExpression0.250.060.31
extractGOseq0.040.000.03
extractModification2.140.002.14
extractModules0.040.000.05
extractScores0.030.000.03
genes_for_conversiontest0.970.000.97
hg19_gene_bed0.210.000.20
highScores0.040.000.05
histone_h3k4me10.090.010.11
makePvalueAnnotation1.660.001.65
makePvalueObject0.090.000.10
methylationdata0.070.000.06
normalizePval0.030.020.05
plotCompareScores1.250.031.28
plotDensityPval0.070.000.08
plotModule0.040.000.03
removeModification0.060.000.06
runBioNet0.050.000.05
runGOseq0.030.000.03
runSpinglass101
scorePval0.050.020.07
stoufferTest000
test_annotation_score_data0.220.000.21