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CHECK report for GeneStructureTools on tokay1

This page was generated on 2019-04-13 11:28:57 -0400 (Sat, 13 Apr 2019).

Package 610/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.2.1
Beth Signal
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneStructureTools
Branch: RELEASE_3_8
Last Commit: 2a83f22
Last Changed Date: 2019-01-04 13:34:13 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 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: 1.2.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz
StartedAt: 2019-04-13 02:31:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:45:09 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 847.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneStructureTools.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 18.47   0.71   19.17
whippetTranscriptChangeSummary     8.27   0.06   54.90
replaceJunction                    2.14   0.04   41.23
transcriptChangeSummary            1.12   0.02   73.72
skipExonInTranscript               0.86   0.03   55.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
leafcutterTranscriptChangeSummary 22.04   0.60   22.64
whippetTranscriptChangeSummary     9.66   0.03   11.33
addIntronInTranscript              1.33   0.02   72.33
* 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/3.8/bioc/src/contrib/GeneStructureTools_1.2.1.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.2.1.zip && rm GeneStructureTools_1.2.1.tar.gz GeneStructureTools_1.2.1.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
100  987k  100  987k    0     0  20.6M      0 --:--:-- --:--:-- --:--:-- 22.4M

install for i386

* installing *source* package 'GeneStructureTools' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'GeneStructureTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneStructureTools' as GeneStructureTools_1.2.1.zip
* DONE (GeneStructureTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.010.000.01
UTR2UTR531.720.553.07
addBroadTypes0.190.140.33
addIntronInTranscript2.340.133.61
alternativeIntronUsage3.240.033.30
annotateGeneModel0.700.060.76
attrChangeAltSpliced2.090.033.08
coordinates-methods0.040.000.98
diffSplicingResults-methods0.030.002.72
exonsToTranscripts0.260.000.27
filterGtfOverlap0.280.000.29
filterWhippetEvents0.000.001.84
findDEXexonType1.230.001.48
findExonContainingTranscripts0.360.001.36
findIntronContainingTranscripts0.520.021.43
findJunctionPairs1.000.022.01
formatWhippetEvents0.000.000.13
getOrfs0.970.000.96
getUOrfs0.860.030.90
junctions-methods0.030.011.04
leafcutterTranscriptChangeSummary18.47 0.7119.17
makeGeneModel0.220.030.25
maxLocation000
orfDiff1.210.034.61
orfSimilarity0.020.000.02
overlapTypes1.140.001.14
readCounts-methods0.050.013.59
readWhippetDIFFfiles0.010.000.13
readWhippetDataSet0.050.001.84
readWhippetJNCfiles0.030.000.66
readWhippetPSIfiles0.000.001.64
removeDuplicateTranscripts0.280.000.28
removeSameExon0.250.020.27
removeVersion000
reorderExonNumbers0.240.020.25
replaceJunction 2.14 0.0441.23
skipExonInTranscript 0.86 0.0355.19
summariseExonTypes1.140.001.14
transcriptChangeSummary 1.12 0.0273.72
whippetTranscriptChangeSummary 8.27 0.0654.90

GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds000
UTR2UTR531.200.011.22
addBroadTypes0.240.000.24
addIntronInTranscript 1.33 0.0272.33
alternativeIntronUsage2.650.012.67
annotateGeneModel0.630.000.62
attrChangeAltSpliced0.920.024.92
coordinates-methods0.010.021.71
diffSplicingResults-methods0.050.001.40
exonsToTranscripts0.250.000.25
filterGtfOverlap0.310.000.31
filterWhippetEvents0.050.002.67
findDEXexonType2.140.012.16
findExonContainingTranscripts0.380.032.61
findIntronContainingTranscripts0.540.023.89
findJunctionPairs0.960.003.33
formatWhippetEvents0.00.00.2
getOrfs0.850.000.85
getUOrfs0.560.010.58
junctions-methods0.050.002.42
leafcutterTranscriptChangeSummary22.04 0.6022.64
makeGeneModel0.210.000.20
maxLocation000
orfDiff1.250.012.89
orfSimilarity000
overlapTypes1.220.021.23
readCounts-methods0.020.011.72
readWhippetDIFFfiles0.000.000.38
readWhippetDataSet0.040.001.86
readWhippetJNCfiles0.000.000.84
readWhippetPSIfiles0.000.000.62
removeDuplicateTranscripts0.270.000.27
removeSameExon0.220.040.25
removeVersion000
reorderExonNumbers0.220.010.23
replaceJunction2.460.004.19
skipExonInTranscript1.020.002.74
summariseExonTypes1.330.001.32
transcriptChangeSummary1.170.052.66
whippetTranscriptChangeSummary 9.66 0.0311.33