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This page was generated on 2021-09-20 15:05:13 -0400 (Mon, 20 Sep 2021).

CHECK results for GeneStructureTools on tokay2

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 727/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.12.0  (landing page)
Beth Signal
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_13
git_last_commit: 1b05c47
git_last_commit_date: 2021-05-19 12:33:53 -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: GeneStructureTools
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
StartedAt: 2021-09-19 22:52:25 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 23:02:14 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 588.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.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:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-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 '1.12.0'
* 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 27.80   0.97   28.77
whippetTranscriptChangeSummary    19.11   0.05   20.02
replaceJunction                    6.06   0.13    7.22
alternativeIntronUsage             4.91   0.70    5.61
addIntronInTranscript              4.23   0.05    5.15
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 27.92   0.89   28.81
whippetTranscriptChangeSummary    16.41   0.04   17.13
alternativeIntronUsage             6.66   0.02    6.68
replaceJunction                    6.22   0.00    7.00
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneStructureTools_1.12.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.12.0.zip && rm GeneStructureTools_1.12.0.tar.gz GeneStructureTools_1.12.0.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
  4  987k    4 44338    0     0   212k      0  0:00:04 --:--:--  0:00:04  212k
 99  987k   99  985k    0     0   812k      0  0:00:01  0:00:01 --:--:--  812k
100  987k  100  987k    0     0   661k      0  0:00:01  0:00:01 --:--:--  662k

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_1.12.0.zip
* DONE (GeneStructureTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds000
UTR2UTR533.460.434.10
addBroadTypes0.280.000.28
addIntronInTranscript4.230.055.15
alternativeIntronUsage4.910.705.61
annotateGeneModel1.110.101.21
attrChangeAltSpliced1.890.012.59
coordinates-methods0.060.000.89
diffSplicingResults-methods0.070.020.84
exonsToTranscripts0.540.000.55
filterGtfOverlap0.410.060.47
filterWhippetEvents0.080.022.47
findDEXexonType3.560.083.69
findExonContainingTranscripts0.970.041.75
findIntronContainingTranscripts1.300.002.11
findJunctionPairs2.400.023.18
formatWhippetEvents0.030.000.13
getOrfs1.240.001.23
getUOrfs0.790.000.80
junctions-methods0.080.000.84
leafcutterTranscriptChangeSummary27.80 0.9728.77
makeGeneModel0.300.010.31
maxLocation000
orfDiff2.700.023.75
orfSimilarity000
overlapTypes3.210.003.20
readCounts-methods0.080.010.98
readWhippetDIFFfiles0.000.000.24
readWhippetDataSet0.110.021.01
readWhippetJNCfiles0.030.000.40
readWhippetPSIfiles0.000.000.38
removeDuplicateTranscripts0.50.00.5
removeSameExon0.340.000.34
removeVersion000
reorderExonNumbers0.390.040.44
replaceJunction6.060.137.22
skipExonInTranscript3.070.013.79
summariseExonTypes3.460.023.49
transcriptChangeSummary2.410.033.18
whippetTranscriptChangeSummary19.11 0.0520.02

GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.010.000.01
UTR2UTR534.640.094.74
addBroadTypes0.440.000.44
addIntronInTranscript3.620.004.42
alternativeIntronUsage6.660.026.68
annotateGeneModel1.280.001.28
attrChangeAltSpliced2.170.032.98
coordinates-methods0.060.000.91
diffSplicingResults-methods0.060.000.86
exonsToTranscripts0.520.010.53
filterGtfOverlap0.420.000.42
filterWhippetEvents0.110.000.78
findDEXexonType3.490.003.49
findExonContainingTranscripts0.950.001.73
findIntronContainingTranscripts1.260.022.08
findJunctionPairs2.610.023.34
formatWhippetEvents0.040.000.13
getOrfs1.170.011.18
getUOrfs0.760.020.79
junctions-methods0.070.000.81
leafcutterTranscriptChangeSummary27.92 0.8928.81
makeGeneModel0.20.00.2
maxLocation000
orfDiff2.560.033.30
orfSimilarity000
overlapTypes2.920.002.92
readCounts-methods0.070.000.79
readWhippetDIFFfiles0.00.00.1
readWhippetDataSet0.060.000.69
readWhippetJNCfiles0.050.000.36
readWhippetPSIfiles0.000.000.31
removeDuplicateTranscripts0.540.000.54
removeSameExon0.320.070.38
removeVersion000
reorderExonNumbers0.290.010.31
replaceJunction6.220.007.00
skipExonInTranscript2.630.003.33
summariseExonTypes2.890.002.89
transcriptChangeSummary2.500.023.15
whippetTranscriptChangeSummary16.41 0.0417.13