Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-01-17 13:07:03 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SMITE on tokay2


To the developers/maintainers of the SMITE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMITE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1823/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.22.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: RELEASE_3_14
git_last_commit: 6979357
git_last_commit_date: 2021-10-26 12:25:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SMITE_1.22.0.tar.gz
StartedAt: 2022-01-17 04:03:09 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 04:09:05 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 356.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SMITE_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SMITE.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.22.0'
* 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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/SMITE_1.22.0.tar.gz && rm -rf SMITE.buildbin-libdir && mkdir SMITE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SMITE.buildbin-libdir SMITE_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SMITE_1.22.0.zip && rm SMITE_1.22.0.tar.gz SMITE_1.22.0.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
 27 2952k   27  803k    0     0  3108k      0 --:--:-- --:--:-- --:--:-- 3104k
100 2952k  100 2952k    0     0  5189k      0 --:--:-- --:--:-- --:--:-- 5188k

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_1.22.0.zip
* DONE (SMITE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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.Igraph0.130.020.14
SMITE-package0.650.040.71
addShadowText0.010.000.02
annotateExpression0.210.020.22
annotateModification000
convertGeneIds1.580.221.79
curated_expression0.060.000.07
extractExpression0.150.030.18
extractGOseq0.050.000.05
extractModification1.720.011.73
extractModules0.050.000.05
extractScores0.030.000.03
genes_for_conversiontest0.800.020.81
hg19_gene_bed0.150.000.16
highScores0.030.000.03
histone_h3k4me10.10.00.1
makePvalueAnnotation0.810.020.82
makePvalueObject0.080.000.08
methylationdata0.060.010.08
normalizePval0.030.020.05
plotCompareScores0.340.000.34
plotDensityPval0.940.000.94
plotModule0.060.010.08
removeModification0.160.000.15
runBioNet0.060.000.07
runGOseq0.070.000.06
runSpinglass0.460.100.56
scorePval0.040.000.03
stoufferTest000
test_annotation_score_data0.070.010.10

SMITE.Rcheck/examples_x64/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.100.000.09
SMITE-package0.310.030.35
addShadowText000
annotateExpression0.140.030.17
annotateModification000
convertGeneIds1.570.131.71
curated_expression0.080.000.07
extractExpression0.220.010.24
extractGOseq0.050.000.05
extractModification1.860.052.21
extractModules0.030.000.04
extractScores0.050.000.04
genes_for_conversiontest0.810.000.82
hg19_gene_bed0.110.020.12
highScores0.040.000.05
histone_h3k4me10.070.000.06
makePvalueAnnotation0.770.000.76
makePvalueObject0.060.000.06
methylationdata0.060.000.07
normalizePval0.030.000.03
plotCompareScores0.380.000.37
plotDensityPval0.080.000.08
plotModule0.030.000.03
removeModification0.060.000.06
runBioNet0.030.000.04
runGOseq0.050.000.04
runSpinglass0.450.010.47
scorePval0.060.000.06
stoufferTest000
test_annotation_score_data0.080.000.08