Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:01 -0400 (Fri, 17 Sep 2021).

CHECK results for compEpiTools on tokay2

To the developers/maintainers of the compEpiTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compEpiTools.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 370/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.26.0  (landing page)
Kamal Kishore
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/compEpiTools
git_branch: RELEASE_3_13
git_last_commit: cefdb04
git_last_commit_date: 2021-05-19 12:06:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: compEpiTools
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compEpiTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compEpiTools_1.26.0.tar.gz
StartedAt: 2021-09-16 21:30:30 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 21:40:17 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 586.8 seconds
RetCode: 0
Status:   OK  
CheckDir: compEpiTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compEpiTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compEpiTools_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/compEpiTools.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.26.0'
* 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 'compEpiTools' 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 ... NOTE
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
stallingIndex : getBound: no visible global function definition for
  'start<-'
stallingIndex : getBound: no visible global function definition for
  'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres : <anonymous>: no visible global function definition for
  'ggplot'
topGOres : <anonymous>: no visible global function definition for 'aes'
topGOres : <anonymous>: no visible binding for global variable
  'Significant'
topGOres : <anonymous>: no visible binding for global variable 'P_val'
topGOres : <anonymous>: no visible global function definition for
  'geom_bar'
topGOres : <anonymous>: no visible global function definition for
  'coord_flip'
topGOres : <anonymous>: no visible global function definition for
  'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
  'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRcoverageSummit,GRanges: no visible global function definition for
  'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
  'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
  'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
  'start<-'
getPromoterClass,TxDb: no visible global function definition for
  'stopCluster'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
matchEnhancers,GRanges: no visible global function definition for
  'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges P_val Significant aes coord_flip distanceToNearest end<-
  geom_bar ggplot reduce seqlengths seqlengths<- start<- stopCluster
  trim txdb ylab
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
topGOres                 24.28   0.81   25.10
makeGtfFromDb             4.14   0.23   11.64
heatmapPlot               3.39   0.58    5.28
getPromoterClass-methods  0.98   0.08   18.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
topGOres                 28.09   0.09   28.19
getPromoterClass-methods  0.82   0.06   17.76
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.



Installation output

compEpiTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/compEpiTools_1.26.0.tar.gz && rm -rf compEpiTools.buildbin-libdir && mkdir compEpiTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compEpiTools.buildbin-libdir compEpiTools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL compEpiTools_1.26.0.zip && rm compEpiTools_1.26.0.tar.gz compEpiTools_1.26.0.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
  2 2068k    2 45687    0     0   292k      0  0:00:07 --:--:--  0:00:07  293k
 86 2068k   86 1779k    0     0  1549k      0  0:00:01  0:00:01 --:--:-- 1550k
100 2068k  100 2068k    0     0  1577k      0  0:00:01  0:00:01 --:--:-- 1577k

install for i386

* installing *source* package 'compEpiTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
  converting help for package 'compEpiTools'
    finding HTML links ... done
    GR2fasta-methods                        html  
    GRanges2ucsc-methods                    html  
    GRangesInPromoters-methods              html  
    GRannotate-methods                      html  
    GRannotateSimple                        html  
    GRbaseCoverage-methods                  html  
    GRcoverage-methods                      html  
    GRcoverageSummit-methods                html  
    GRenrichment-methods                    html  
    GRmidpoint-methods                      html  
    GRsetwidth                              html  
    TSS                                     html  
    compEpiTools-package                    html  
    countOverlapsInBins-methods             html  
    distanceFromTSS-methods                 html  
    enhancers                               html  
    findLncRNA                              html  
    getPromoterClass-methods                html  
    finding level-2 HTML links ... done

    heatmapData                             html  
    heatmapPlot                             html  
    makeGtfFromDb                           html  
    matchEnhancers                          html  
    overlapOfGRanges-methods                html  
    palette2d                               html  
    plotStallingIndex                       html  
    simplifyGOterms                         html  
    stallingIndex                           html  
    topGOres                                html  
    ucsc2GRanges                            html  
    unionMaxScore-methods                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.26.0.zip
* DONE (compEpiTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'compEpiTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

compEpiTools.Rcheck/examples_i386/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods0.430.030.47
GRanges2ucsc-methods0.010.000.01
GRangesInPromoters-methods3.100.113.21
GRannotate-methods3.950.114.06
GRannotateSimple0.640.070.70
GRbaseCoverage-methods0.130.000.13
GRcoverage-methods0.140.000.14
GRcoverageSummit-methods0.090.000.09
GRenrichment-methods0.080.010.10
GRmidpoint-methods0.030.000.03
GRsetwidth0.060.000.06
TSS1.440.141.58
countOverlapsInBins-methods0.140.000.14
distanceFromTSS-methods2.220.032.25
enhancers0.340.020.36
findLncRNA1.110.011.53
getPromoterClass-methods 0.98 0.0818.47
heatmapData2.240.022.25
heatmapPlot3.390.585.28
makeGtfFromDb 4.14 0.2311.64
matchEnhancers1.900.021.93
overlapOfGRanges-methods0.070.000.06
palette2d0.030.010.05
plotStallingIndex2.810.052.90
simplifyGOterms0.530.010.55
stallingIndex2.710.072.76
topGOres24.28 0.8125.10
ucsc2GRanges0.030.000.03
unionMaxScore-methods0.150.000.16

compEpiTools.Rcheck/examples_x64/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods0.450.010.47
GRanges2ucsc-methods000
GRangesInPromoters-methods3.180.023.21
GRannotate-methods3.960.034.00
GRannotateSimple0.650.010.67
GRbaseCoverage-methods0.130.000.12
GRcoverage-methods0.140.020.16
GRcoverageSummit-methods0.110.000.11
GRenrichment-methods0.090.000.09
GRmidpoint-methods0.060.000.07
GRsetwidth0.070.000.06
TSS1.450.041.50
countOverlapsInBins-methods0.170.000.17
distanceFromTSS-methods4.020.084.09
enhancers0.590.000.60
findLncRNA1.240.021.25
getPromoterClass-methods 0.82 0.0617.76
heatmapData1.930.021.94
heatmapPlot3.760.073.86
makeGtfFromDb4.240.184.41
matchEnhancers1.960.032.00
overlapOfGRanges-methods0.080.000.08
palette2d0.100.000.09
plotStallingIndex2.710.002.72
simplifyGOterms0.440.000.44
stallingIndex2.630.062.68
topGOres28.09 0.0928.19
ucsc2GRanges0.020.000.02
unionMaxScore-methods0.160.000.16