Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SMITE on tokay1

This page was generated on 2020-04-15 12:26:06 -0400 (Wed, 15 Apr 2020).

Package 1619/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.14.0
Neil Ari Wijetunga
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SMITE
Branch: RELEASE_3_10
Last Commit: c3867a6
Last Changed Date: 2019-10-29 13:09:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SMITE
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SMITE_1.14.0.tar.gz
StartedAt: 2020-04-15 06:44:55 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:51:05 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 369.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SMITE_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SMITE.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.14.0'
* 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
* 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 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 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


Installation output

SMITE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SMITE_1.14.0.tar.gz && rm -rf SMITE.buildbin-libdir && mkdir SMITE.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SMITE.buildbin-libdir SMITE_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SMITE_1.14.0.zip && rm SMITE_1.14.0.tar.gz SMITE_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  3 2950k    3  112k    0     0   654k      0  0:00:04 --:--:--  0:00:04  666k
100 2950k  100 2950k    0     0  11.1M      0 --:--:-- --:--:-- --:--:-- 11.2M

install for i386

* installing *source* package 'SMITE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SMITE'
    finding HTML links ... done
    Reactome.Symbol.Igraph                  html  
    SMITE-package                           html  
    addShadowText                           html  
    annotateExpression                      html  
    annotateModification                    html  
    convertGeneIds                          html  
    curated_expression                      html  
    extractExpression                       html  
    extractGOseq                            html  
    extractModification                     html  
    extractModules                          html  
    extractScores                           html  
    genes_for_conversiontest                html  
    hg19_gene_bed                           html  
    highScores                              html  
    histone_h3k4me1                         html  
    makePvalueAnnotation                    html  
    makePvalueObject                        html  
    methylationdata                         html  
    normalizePval                           html  
    plotCompareScores                       html  
    plotDensityPval                         html  
    plotModule                              html  
    removeModification                      html  
    runBioNet                               html  
    runGOseq                                html  
    runSpinglass                            html  
    scorePval                               html  
    stoufferTest                            html  
    test_annotation_score_data              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SMITE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SMITE' as SMITE_1.14.0.zip
* DONE (SMITE)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SMITE' successfully unpacked and MD5 sums checked

Tests output


Example timings

SMITE.Rcheck/examples_i386/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.170.040.20
SMITE-package0.520.030.55
addShadowText000
annotateExpression0.250.060.32
annotateModification000
convertGeneIds2.430.162.58
curated_expression0.060.000.06
extractExpression0.180.010.19
extractGOseq0.040.020.06
extractModification1.960.122.08
extractModules0.040.000.05
extractScores0.030.020.05
genes_for_conversiontest1.350.011.35
hg19_gene_bed0.250.000.25
highScores0.070.000.06
histone_h3k4me10.070.020.10
makePvalueAnnotation0.820.010.82
makePvalueObject0.130.000.13
methylationdata0.110.020.12
normalizePval0.070.000.08
plotCompareScores0.550.020.56
plotDensityPval0.080.000.08
plotModule0.060.010.08
removeModification0.100.000.09
runBioNet0.120.000.13
runGOseq0.250.000.25
runSpinglass0.530.000.53
scorePval0.120.000.13
stoufferTest000
test_annotation_score_data0.110.000.11

SMITE.Rcheck/examples_x64/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.10.00.1
SMITE-package0.340.030.37
addShadowText0.000.020.02
annotateExpression0.190.000.18
annotateModification000
convertGeneIds1.360.151.52
curated_expression0.040.000.05
extractExpression0.160.000.15
extractGOseq0.050.000.05
extractModification1.730.021.75
extractModules0.050.000.05
extractScores0.050.000.04
genes_for_conversiontest0.710.000.72
hg19_gene_bed0.140.000.14
highScores0.050.000.05
histone_h3k4me10.050.010.06
makePvalueAnnotation0.640.000.64
makePvalueObject0.060.000.06
methylationdata0.060.000.07
normalizePval0.040.020.04
plotCompareScores0.480.030.52
plotDensityPval0.110.000.11
plotModule0.050.000.05
removeModification0.060.000.06
runBioNet0.030.020.05
runGOseq0.190.010.20
runSpinglass0.50.00.5
scorePval0.040.000.05
stoufferTest000
test_annotation_score_data0.080.000.07