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

This page was generated on 2022-01-21 13:07:08 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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: 2022-01-20 01:55:04 -0500 (Thu, 20 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: 2022-01-21 03:07:13 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 03:13:01 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 348.1 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
 32 2952k   32  955k    0     0  2214k      0  0:00:01 --:--:--  0:00:01 2212k
100 2952k  100 2952k    0     0  3867k      0 --:--:-- --:--:-- --:--:-- 3869k

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.Igraph0.090.020.11
SMITE-package0.390.030.42
addShadowText000
annotateExpression0.120.030.15
annotateModification000
convertGeneIds1.540.091.63
curated_expression0.040.020.06
extractExpression0.170.000.17
extractGOseq0.040.000.03
extractModification1.480.111.60
extractModules0.030.000.04
extractScores0.030.000.03
genes_for_conversiontest0.730.000.73
hg19_gene_bed0.130.030.16
highScores0.030.000.03
histone_h3k4me10.080.020.09
makePvalueAnnotation0.700.010.72
makePvalueObject0.080.000.08
methylationdata0.060.000.06
normalizePval0.030.000.03
plotCompareScores0.300.020.32
plotDensityPval0.760.000.76
plotModule0.040.000.03
removeModification0.060.010.08
runBioNet0.030.000.03
runGOseq0.030.000.03
runSpinglass0.360.050.40
scorePval0.030.000.04
stoufferTest000
test_annotation_score_data0.060.000.06

SMITE.Rcheck/examples_x64/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.070.030.10
SMITE-package0.500.020.51
addShadowText000
annotateExpression0.220.010.23
annotateModification000
convertGeneIds1.580.161.74
curated_expression0.110.000.11
extractExpression0.250.010.26
extractGOseq0.040.000.05
extractModification1.830.021.85
extractModules0.030.000.03
extractScores0.040.000.03
genes_for_conversiontest0.750.000.75
hg19_gene_bed0.120.000.13
highScores0.030.000.03
histone_h3k4me10.060.000.06
makePvalueAnnotation0.720.010.73
makePvalueObject0.070.000.07
methylationdata0.040.000.04
normalizePval0.020.020.03
plotCompareScores0.330.010.34
plotDensityPval0.060.000.06
plotModule0.030.000.03
removeModification0.060.000.07
runBioNet0.030.000.03
runGOseq0.040.000.03
runSpinglass0.440.000.44
scorePval0.060.000.06
stoufferTest000
test_annotation_score_data0.080.000.08