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This page was generated on 2021-09-18 12:06:07 -0400 (Sat, 18 Sep 2021).

CHECK results for GeneStructureTools on riesling1

To the developers/maintainers of the GeneStructureTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneStructureTools.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 719/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.13.0  (landing page)
Beth Signal
Snapshot Date: 2021-09-17 14:50:09 -0400 (Fri, 17 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: master
git_last_commit: b6fe688
git_last_commit_date: 2021-05-19 12:33:53 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneStructureTools
Version: 1.13.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneStructureTools_1.13.0.tar.gz
StartedAt: 2021-09-18 01:00:06 -0400 (Sat, 18 Sep 2021)
EndedAt: 2021-09-18 01:08:14 -0400 (Sat, 18 Sep 2021)
EllapsedTime: 487.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneStructureTools_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/GeneStructureTools.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 'GeneStructureTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneStructureTools' version '1.13.0'
* package encoding: UTF-8
* 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 'GeneStructureTools' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 15.47   0.89   16.36
whippetTranscriptChangeSummary     9.73   0.12   10.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 17.96   0.75   18.71
whippetTranscriptChangeSummary    11.27   0.17   11.83
replaceJunction                    4.75   0.08    5.05
* 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

GeneStructureTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GeneStructureTools_1.13.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.13.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.13.0.zip && rm GeneStructureTools_1.13.0.tar.gz GeneStructureTools_1.13.0.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
 41  986k   41  408k    0     0  1559k      0 --:--:-- --:--:-- --:--:-- 1559k
100  986k  100  986k    0     0  3204k      0 --:--:-- --:--:-- --:--:-- 3204k

install for i386

* installing *source* package 'GeneStructureTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneStructureTools'
    finding HTML links ... done
    DEXSeqIdsToGeneIds                      html  
    UTR2UTR53                               html  
    addBroadTypes                           html  
    addIntronInTranscript                   html  
    addSets                                 html  
    alternativeIntronUsage                  html  
    annotateGeneModel                       html  
    attrChangeAltSpliced                    html  
    coordinates-methods                     html  
    cumsumANDpad                            html  
    diffSplicingResults-methods             html  
    exonsToTranscripts                      html  
    filterGtfOverlap                        html  
    filterWhippetEvents                     html  
    findDEXexonType                         html  
    findExonContainingTranscripts           html  
    findIntronContainingTranscripts         html  
    findJunctionPairs                       html  
    formatWhippetEvents                     html  
    getOrfs                                 html  
    getUOrfs                                html  
    junctions-methods                       html  
    leafcutterTranscriptChangeSummary       html  
    makeGeneModel                           html  
    maxLocation                             html  
    orfDiff                                 html  
    orfSimilarity                           html  
    overlapTypes                            html  
    readCounts-methods                      html  
    readWhippetDIFFfiles                    html  
    readWhippetDataSet                      html  
    readWhippetJNCfiles                     html  
    readWhippetPSIfiles                     html  
    removeDuplicateTranscripts              html  
    removeSameExon                          html  
    removeVersion                           html  
    reorderExonNumbers                      html  
    replaceJunction                         html  
    skipExonInTranscript                    html  
    summariseExonTypes                      html  
    transcriptChangeSummary                 html  
    whippetDataSet-class                    html  
    whippetTranscriptChangeSummary          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 'GeneStructureTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneStructureTools' as GeneStructureTools_1.13.0.zip
* DONE (GeneStructureTools)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds000
UTR2UTR531.630.041.67
addBroadTypes0.190.000.19
addIntronInTranscript2.250.022.56
alternativeIntronUsage2.870.062.94
annotateGeneModel0.660.020.67
attrChangeAltSpliced1.000.041.30
coordinates-methods0.010.000.28
diffSplicingResults-methods0.020.030.30
exonsToTranscripts0.220.000.22
filterGtfOverlap0.220.000.21
filterWhippetEvents0.060.020.33
findDEXexonType1.670.001.67
findExonContainingTranscripts0.420.030.68
findIntronContainingTranscripts0.610.030.89
findJunctionPairs1.270.001.57
formatWhippetEvents0.010.000.05
getOrfs0.550.020.56
getUOrfs0.450.000.46
junctions-methods0.050.010.34
leafcutterTranscriptChangeSummary15.47 0.8916.36
makeGeneModel0.170.000.17
maxLocation000
orfDiff1.280.041.56
orfSimilarity0.020.000.02
overlapTypes1.610.001.61
readCounts-methods0.040.000.34
readWhippetDIFFfiles0.000.010.03
readWhippetDataSet0.050.020.36
readWhippetJNCfiles0.020.000.14
readWhippetPSIfiles0.000.000.13
removeDuplicateTranscripts0.230.000.23
removeSameExon0.190.000.19
removeVersion000
reorderExonNumbers0.190.010.20
replaceJunction3.450.003.79
skipExonInTranscript1.300.001.56
summariseExonTypes1.670.001.67
transcriptChangeSummary1.250.051.56
whippetTranscriptChangeSummary 9.73 0.1210.17

GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds000
UTR2UTR532.590.072.66
addBroadTypes0.190.000.19
addIntronInTranscript1.760.012.09
alternativeIntronUsage3.280.003.28
annotateGeneModel0.740.000.74
attrChangeAltSpliced1.090.031.37
coordinates-methods0.060.000.33
diffSplicingResults-methods0.070.020.30
exonsToTranscripts0.20.00.2
filterGtfOverlap0.220.000.22
filterWhippetEvents0.080.010.31
findDEXexonType1.860.001.86
findExonContainingTranscripts0.410.000.65
findIntronContainingTranscripts0.640.000.92
findJunctionPairs1.340.001.57
formatWhippetEvents0.010.000.03
getOrfs0.600.020.61
getUOrfs0.450.010.47
junctions-methods0.060.020.28
leafcutterTranscriptChangeSummary17.96 0.7518.71
makeGeneModel0.140.020.15
maxLocation000
orfDiff1.340.061.77
orfSimilarity000
overlapTypes1.720.001.72
readCounts-methods0.050.010.39
readWhippetDIFFfiles0.000.000.03
readWhippetDataSet0.030.020.37
readWhippetJNCfiles0.010.000.21
readWhippetPSIfiles0.020.020.14
removeDuplicateTranscripts0.280.000.28
removeSameExon0.20.00.2
removeVersion000
reorderExonNumbers0.210.010.22
replaceJunction4.750.085.05
skipExonInTranscript1.470.051.83
summariseExonTypes1.870.001.87
transcriptChangeSummary1.450.011.78
whippetTranscriptChangeSummary11.27 0.1711.83