Multiple platform build/check report for BioC 3.10 - CHECK report for GeneStructureTools on tokay1

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

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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

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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

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 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

name	user	system	elapsed
DEXSeqIdsToGeneIds	0.01	0.00	0.02
UTR2UTR53	4.38	0.64	5.36
addBroadTypes	0.42	0.05	0.46
addIntronInTranscript	3.03	0.23	5.64
alternativeIntronUsage	4.94	0.00	5.00
annotateGeneModel	1.28	0.00	1.29
attrChangeAltSpliced	1.81	0.05	2.49
coordinates-methods	0.05	0.01	0.68
diffSplicingResults-methods	0.05	0.02	0.80
exonsToTranscripts	0.47	0.01	0.48
filterGtfOverlap	0.5	0.0	0.5
filterWhippetEvents	0.04	0.02	0.69
findDEXexonType	3.80	0.03	3.97
findExonContainingTranscripts	0.61	0.00	1.14
findIntronContainingTranscripts	0.73	0.00	1.33
findJunctionPairs	1.33	0.00	1.89
formatWhippetEvents	0.02	0.00	0.08
getOrfs	0.82	0.00	0.83
getUOrfs	0.58	0.02	0.59
junctions-methods	0.03	0.00	0.64
leafcutterTranscriptChangeSummary	28.49	1.01	29.50
makeGeneModel	0.30	0.03	0.33
maxLocation	0	0	0
orfDiff	2.31	0.07	9.47
orfSimilarity	0	0	0
overlapTypes	3.49	0.04	3.53
readCounts-methods	0.03	0.02	1.22
readWhippetDIFFfiles	0.01	0.00	0.07
readWhippetDataSet	0.04	0.00	0.78
readWhippetJNCfiles	0.01	0.00	0.34
readWhippetPSIfiles	0.00	0.00	0.27
removeDuplicateTranscripts	0.50	0.01	0.51
removeSameExon	0.45	0.03	0.49
removeVersion	0	0	0
reorderExonNumbers	0.24	0.10	0.32
replaceJunction	5.00	0.05	5.63
skipExonInTranscript	2.11	0.01	2.72
summariseExonTypes	3.37	0.02	3.39
transcriptChangeSummary	2.07	0.01	2.62
whippetTranscriptChangeSummary	13.06	0.00	13.66

name	user	system	elapsed
DEXSeqIdsToGeneIds	0	0	0
UTR2UTR53	3.51	0.11	3.62
addBroadTypes	0.24	0.00	0.24
addIntronInTranscript	2.08	0.02	3.01
alternativeIntronUsage	4.03	0.00	4.04
annotateGeneModel	0.95	0.01	0.96
attrChangeAltSpliced	1.72	0.03	2.86
coordinates-methods	0.05	0.00	1.07
diffSplicingResults-methods	0.03	0.02	1.50
exonsToTranscripts	0.30	0.00	0.29
filterGtfOverlap	0.29	0.00	0.30
filterWhippetEvents	0.05	0.01	0.89
findDEXexonType	3.28	0.04	3.31
findExonContainingTranscripts	0.48	0.01	1.66
findIntronContainingTranscripts	0.77	0.02	1.56
findJunctionPairs	1.88	0.01	2.83
formatWhippetEvents	0.01	0.00	0.20
getOrfs	0.78	0.03	0.82
getUOrfs	0.66	0.02	0.67
junctions-methods	0.01	0.01	10.65
leafcutterTranscriptChangeSummary	30.93	0.74	31.89
makeGeneModel	0.2	0.0	0.2
maxLocation	0	0	0
orfDiff	2.11	0.03	3.02
orfSimilarity	0	0	0
overlapTypes	2.83	0.02	2.84
readCounts-methods	0.05	0.00	0.63
readWhippetDIFFfiles	0.00	0.00	0.04
readWhippetDataSet	0.01	0.03	0.69
readWhippetJNCfiles	1.04	0.00	1.28
readWhippetPSIfiles	0.01	0.00	0.30
removeDuplicateTranscripts	0.3	0.0	0.3
removeSameExon	0.30	0.00	0.29
removeVersion	0	0	0
reorderExonNumbers	0.25	0.00	0.25
replaceJunction	4.64	0.00	7.03
skipExonInTranscript	1.82	0.00	2.44
summariseExonTypes	3.64	0.00	3.64
transcriptChangeSummary	1.94	0.00	2.42
whippetTranscriptChangeSummary	15.69	0.04	16.56

CHECK report for GeneStructureTools on tokay1

Summary

Command output

Installation output

Tests output

Example timings