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CHECK report for GeneStructureTools on tokay1

This page was generated on 2020-04-15 12:30:01 -0400 (Wed, 15 Apr 2020).

Package 666/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.6.0
Beth Signal
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GeneStructureTools
Branch: RELEASE_3_10
Last Commit: 94b91cf
Last Changed Date: 2019-10-29 13:11:00 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneStructureTools
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GeneStructureTools_1.6.0.tar.gz
StartedAt: 2020-04-15 03:25:02 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:35:18 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 615.4 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GeneStructureTools_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GeneStructureTools.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 28.49   1.01   29.50
whippetTranscriptChangeSummary    13.06   0.00   13.66
replaceJunction                    5.00   0.05    5.63
UTR2UTR53                          4.38   0.64    5.36
addIntronInTranscript              3.03   0.23    5.64
orfDiff                            2.31   0.07    9.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 30.93   0.74   31.89
whippetTranscriptChangeSummary    15.69   0.04   16.56
replaceJunction                    4.64   0.00    7.03
junctions-methods                  0.01   0.01   10.65
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GeneStructureTools_1.6.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.6.0.zip && rm GeneStructureTools_1.6.0.tar.gz GeneStructureTools_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 64  987k   64  640k    0     0  2344k      0 --:--:-- --:--:-- --:--:-- 2370k
100  987k  100  987k    0     0  2625k      0 --:--:-- --:--:-- --:--:-- 2646k

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_1.6.0.zip
* DONE (GeneStructureTools)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.010.000.02
UTR2UTR534.380.645.36
addBroadTypes0.420.050.46
addIntronInTranscript3.030.235.64
alternativeIntronUsage4.940.005.00
annotateGeneModel1.280.001.29
attrChangeAltSpliced1.810.052.49
coordinates-methods0.050.010.68
diffSplicingResults-methods0.050.020.80
exonsToTranscripts0.470.010.48
filterGtfOverlap0.50.00.5
filterWhippetEvents0.040.020.69
findDEXexonType3.800.033.97
findExonContainingTranscripts0.610.001.14
findIntronContainingTranscripts0.730.001.33
findJunctionPairs1.330.001.89
formatWhippetEvents0.020.000.08
getOrfs0.820.000.83
getUOrfs0.580.020.59
junctions-methods0.030.000.64
leafcutterTranscriptChangeSummary28.49 1.0129.50
makeGeneModel0.300.030.33
maxLocation000
orfDiff2.310.079.47
orfSimilarity000
overlapTypes3.490.043.53
readCounts-methods0.030.021.22
readWhippetDIFFfiles0.010.000.07
readWhippetDataSet0.040.000.78
readWhippetJNCfiles0.010.000.34
readWhippetPSIfiles0.000.000.27
removeDuplicateTranscripts0.500.010.51
removeSameExon0.450.030.49
removeVersion000
reorderExonNumbers0.240.100.32
replaceJunction5.000.055.63
skipExonInTranscript2.110.012.72
summariseExonTypes3.370.023.39
transcriptChangeSummary2.070.012.62
whippetTranscriptChangeSummary13.06 0.0013.66

GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds000
UTR2UTR533.510.113.62
addBroadTypes0.240.000.24
addIntronInTranscript2.080.023.01
alternativeIntronUsage4.030.004.04
annotateGeneModel0.950.010.96
attrChangeAltSpliced1.720.032.86
coordinates-methods0.050.001.07
diffSplicingResults-methods0.030.021.50
exonsToTranscripts0.300.000.29
filterGtfOverlap0.290.000.30
filterWhippetEvents0.050.010.89
findDEXexonType3.280.043.31
findExonContainingTranscripts0.480.011.66
findIntronContainingTranscripts0.770.021.56
findJunctionPairs1.880.012.83
formatWhippetEvents0.010.000.20
getOrfs0.780.030.82
getUOrfs0.660.020.67
junctions-methods 0.01 0.0110.65
leafcutterTranscriptChangeSummary30.93 0.7431.89
makeGeneModel0.20.00.2
maxLocation000
orfDiff2.110.033.02
orfSimilarity000
overlapTypes2.830.022.84
readCounts-methods0.050.000.63
readWhippetDIFFfiles0.000.000.04
readWhippetDataSet0.010.030.69
readWhippetJNCfiles1.040.001.28
readWhippetPSIfiles0.010.000.30
removeDuplicateTranscripts0.30.00.3
removeSameExon0.300.000.29
removeVersion000
reorderExonNumbers0.250.000.25
replaceJunction4.640.007.03
skipExonInTranscript1.820.002.44
summariseExonTypes3.640.003.64
transcriptChangeSummary1.940.002.42
whippetTranscriptChangeSummary15.69 0.0416.56