Bora Uyar
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/RCAS |
| Branch: RELEASE_3_11 |
| Last Commit: 4ce5df6 |
| Last Changed Date: 2020-04-27 14:59:40 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:33 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE RCAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1429/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCAS 1.14.0 Bora Uyar
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: RCAS |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RCAS_1.14.0.tar.gz |
| StartedAt: 2020-10-17 07:20:32 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:45:22 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1490.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCAS.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RCAS_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RCAS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCAS' version '1.14.0'
* 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 'RCAS' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
runMotifDiscovery 20.48 0.46 83.95
getMotifSummaryTable 20.22 0.39 91.50
calculateCoverageProfileList 17.79 1.27 19.07
getFeatureBoundaryCoverageMulti 17.54 0.42 17.96
calculateCoverageProfile 12.60 0.65 13.25
summarizeQueryRegions 11.52 0.22 11.74
summarizeQueryRegionsMulti 10.70 0.86 29.26
findDifferentialMotifs 10.83 0.31 38.88
getTxdbFeaturesFromGRanges 10.10 0.17 10.29
getTargetedGenesTable 9.60 0.14 9.73
plotFeatureBoundaryCoverage 8.16 0.08 8.23
getFeatureBoundaryCoverage 6.66 0.28 6.94
getFeatureBoundaryCoverageBin 6.62 0.16 6.78
createDB 3.59 0.09 41.23
getIntervalOverlapMatrix 1.17 0.11 17.68
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getMotifSummaryTable 23.91 0.72 97.13
runMotifDiscovery 21.16 0.48 66.06
getFeatureBoundaryCoverageMulti 15.16 0.41 15.59
calculateCoverageProfileList 14.51 0.51 15.03
calculateCoverageProfile 12.77 0.56 13.33
getTargetedGenesTable 10.17 0.32 10.50
summarizeQueryRegions 8.84 0.17 9.12
getTxdbFeaturesFromGRanges 8.41 0.24 8.64
summarizeQueryRegionsMulti 7.94 0.69 26.74
findDifferentialMotifs 8.02 0.10 43.84
getFeatureBoundaryCoverageBin 5.22 0.14 5.36
getFeatureBoundaryCoverage 4.76 0.22 13.53
createDB 4.03 0.09 40.95
runReportMetaAnalysis 1.23 0.52 6.53
getIntervalOverlapMatrix 0.92 0.06 21.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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
RCAS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RCAS_1.14.0.tar.gz && rm -rf RCAS.buildbin-libdir && mkdir RCAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCAS.buildbin-libdir RCAS_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RCAS_1.14.0.zip && rm RCAS_1.14.0.tar.gz RCAS_1.14.0.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
100 1644k 100 1644k 0 0 16.4M 0 --:--:-- --:--:-- --:--:-- 17.4M
install for i386
* installing *source* package 'RCAS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RCAS'
finding HTML links ... done
calculateCoverageProfile html
calculateCoverageProfileFromTxdb html
calculateCoverageProfileList html
calculateCoverageProfileListFromTxdb html
checkSeqDb html
createControlRegions html
createDB html
createOrthologousGeneSetList html
deleteSampleDataFromDB html
discoverFeatureSpecificMotifs html
extractSequences html
findDifferentialMotifs html
findEnrichedFunctions html
generateKmers html
getFeatureBoundaryCoverage html
getFeatureBoundaryCoverageBin html
getFeatureBoundaryCoverageMulti html
getIntervalOverlapMatrix html
getMotifSummaryTable html
getTargetedGenesTable html
getTxdbFeatures html
getTxdbFeaturesFromGRanges html
gff html
importBed html
importBedFiles html
importGtf html
parseMsigdb html
plotFeatureBoundaryCoverage html
printMsigdbDataset html
queryGff html
queryRegions html
retrieveOrthologs html
runGSEA html
runMotifDiscovery html
runMotifRG html
runReport html
runReportMetaAnalysis html
runTopGO html
summarizeDatabaseContent html
summarizeQueryRegions html
summarizeQueryRegionsMulti 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 'RCAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCAS' as RCAS_1.14.0.zip
* DONE (RCAS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RCAS' successfully unpacked and MD5 sums checked
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RCAS.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(RCAS)
Loading required package: plotly
Loading required package: ggplot2
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Loading required package: DT
Loading required package: data.table
>
> test_check("RCAS")
== testthat results ===========================================================
[ OK: 48 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
41.82 3.00 78.48
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RCAS.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(RCAS)
Loading required package: plotly
Loading required package: ggplot2
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Loading required package: DT
Loading required package: data.table
>
> test_check("RCAS")
== testthat results ===========================================================
[ OK: 48 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
41.29 1.84 81.46
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RCAS.Rcheck/examples_i386/RCAS-Ex.timings
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RCAS.Rcheck/examples_x64/RCAS-Ex.timings
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