Bora Uyar
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/RCAS |
| git_branch: RELEASE_3_14 |
| git_last_commit: 1d023c7 |
| git_last_commit_date: 2021-10-26 12:29:09 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:11 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the RCAS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCAS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1541/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RCAS 1.20.0 (landing page) Bora Uyar
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RCAS_1.20.0.tar.gz |
| StartedAt: 2022-04-13 01:17:51 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:37:50 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1199.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCAS.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RCAS_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RCAS.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.20.0'
* 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 LazyData ... 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
getMotifSummaryTable 19.57 0.36 74.04
runMotifDiscovery 18.77 0.38 60.39
getFeatureBoundaryCoverageMulti 16.31 1.05 17.36
calculateCoverageProfileList 14.28 1.49 15.77
calculateCoverageProfile 11.72 0.87 12.59
findDifferentialMotifs 10.72 0.23 33.50
getTargetedGenesTable 9.00 0.25 9.25
summarizeQueryRegions 8.78 0.14 8.92
summarizeQueryRegionsMulti 8.36 0.41 21.57
getTxdbFeaturesFromGRanges 7.88 0.24 8.11
getFeatureBoundaryCoverageBin 4.72 0.31 5.03
createDB 3.63 0.08 27.70
getIntervalOverlapMatrix 1.01 0.09 14.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runMotifDiscovery 20.29 0.58 54.79
getMotifSummaryTable 20.18 0.35 71.80
calculateCoverageProfileList 15.22 0.45 15.67
getFeatureBoundaryCoverageMulti 13.58 0.41 13.98
calculateCoverageProfile 12.18 0.49 12.70
getTxdbFeaturesFromGRanges 9.35 0.17 9.51
getTargetedGenesTable 9.11 0.26 9.38
findDifferentialMotifs 8.52 0.30 32.69
summarizeQueryRegionsMulti 7.83 0.47 22.41
summarizeQueryRegions 8.01 0.20 8.22
plotFeatureBoundaryCoverage 5.29 0.07 5.37
getFeatureBoundaryCoverage 5.03 0.17 5.20
createDB 3.56 0.05 30.26
getIntervalOverlapMatrix 1.00 0.06 14.31
* 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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/RCAS_1.20.0.tar.gz && rm -rf RCAS.buildbin-libdir && mkdir RCAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCAS.buildbin-libdir RCAS_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RCAS_1.20.0.zip && rm RCAS_1.20.0.tar.gz RCAS_1.20.0.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
83 1646k 83 1366k 0 0 1827k 0 --:--:-- --:--:-- --:--:-- 1827k
100 1646k 100 1646k 0 0 1986k 0 --:--:-- --:--:-- --:--:-- 1986k
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
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** 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
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** 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
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
* MD5 sums
packaged installation of 'RCAS' as RCAS_1.20.0.zip
* DONE (RCAS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RCAS' successfully unpacked and MD5 sums checked
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RCAS.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
>
> test_check("RCAS")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
>
> proc.time()
user system elapsed
41.14 3.25 62.28
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RCAS.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
>
> test_check("RCAS")
Error in (function (x) : attempt to apply non-function
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
39.23 1.93 63.48
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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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