Bora Uyar
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/RCAS |
| Branch: RELEASE_3_10 |
| Last Commit: 8b40ab4 |
| Last Changed Date: 2019-10-29 13:09:55 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:27:00 -0400 (Wed, 15 Apr 2020).
| Package 1379/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCAS 1.12.0 Bora Uyar
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RCAS |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RCAS_1.12.0.tar.gz |
| StartedAt: 2020-04-15 05:54:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:18:19 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1452.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCAS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RCAS_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RCAS.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 'RCAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCAS' version '1.12.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'DBI'
All declared Imports should be used.
* 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 or elapsed time > 5s
user system elapsed
getMotifSummaryTable 53.89 0.38 54.28
runMotifRG 43.86 0.17 44.03
calculateCoverageProfile 15.33 0.87 16.20
calculateCoverageProfileList 13.56 1.28 14.86
getFeatureBoundaryCoverageMulti 13.58 0.37 13.95
calculateCoverageProfileListFromTxdb 10.02 0.22 10.23
calculateCoverageProfileFromTxdb 8.05 0.53 8.64
summarizeQueryRegionsMulti 7.82 0.47 21.38
summarizeQueryRegions 7.86 0.23 8.09
getTxdbFeaturesFromGRanges 7.14 0.27 41.53
getTxdbFeatures 7.06 0.23 7.30
getTargetedGenesTable 6.92 0.25 7.19
plotFeatureBoundaryCoverage 4.16 0.23 51.22
createDB 2.25 0.08 28.35
getIntervalOverlapMatrix 1.89 0.05 17.84
runReportMetaAnalysis 1.07 0.39 65.10
createOrthologousGeneSetList 1.07 0.01 11.75
retrieveOrthologs 0.46 0.00 7.83
parseMsigdb 0.00 0.00 33.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runMotifRG 49.19 0.26 49.50
getMotifSummaryTable 48.20 0.49 48.69
getFeatureBoundaryCoverageMulti 15.91 0.37 16.28
calculateCoverageProfileList 11.59 0.36 11.96
calculateCoverageProfile 11.22 0.45 11.68
calculateCoverageProfileListFromTxdb 9.19 0.18 9.37
getTxdbFeatures 8.59 0.18 8.76
summarizeQueryRegionsMulti 8.24 0.40 27.67
getTargetedGenesTable 8.08 0.29 8.33
getTxdbFeaturesFromGRanges 7.78 0.20 7.99
summarizeQueryRegions 6.79 0.28 7.08
calculateCoverageProfileFromTxdb 5.52 0.30 5.81
getFeatureBoundaryCoverage 5.48 0.14 5.62
createDB 2.25 0.03 31.78
getIntervalOverlapMatrix 1.44 0.14 16.58
createOrthologousGeneSetList 0.64 0.04 11.62
retrieveOrthologs 0.48 0.05 7.67
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/RCAS.Rcheck/00check.log'
for details.
RCAS.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RCAS_1.12.0.tar.gz && rm -rf RCAS.buildbin-libdir && mkdir RCAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCAS.buildbin-libdir RCAS_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RCAS_1.12.0.zip && rm RCAS_1.12.0.tar.gz RCAS_1.12.0.zip
###
##############################################################################
##############################################################################
% 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 1692k 100 1692k 0 0 19.2M 0 --:--:-- --:--:-- --:--:-- 20.1M
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
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
converting help for package 'RCAS'
finding HTML links ... done
calculateCoverageProfile html
calculateCoverageProfileFromTxdb html
calculateCoverageProfileList html
calculateCoverageProfileListFromTxdb html
createControlRegions html
createDB html
createOrthologousGeneSetList html
deleteSampleDataFromDB html
discoverFeatureSpecificMotifs html
extractSequences html
geneSets 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
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
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** 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
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'RCAS' as RCAS_1.12.0.zip
* DONE (RCAS)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RCAS' successfully unpacked and MD5 sums checked
|
RCAS.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:data.table':
first, second
The following object is masked from 'package:plotly':
rename
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:plotly':
slice
The following object is masked from 'package:grDevices':
windows
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:plotly':
select
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:graph':
complement
The following object is masked from 'package:base':
strsplit
Loading required package: seqLogo
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:topGO':
depth
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:plotly':
export
Loading required package: BSgenome.Hsapiens.UCSC.hg19
>
> test_check("RCAS")
GGAGAA 1.989701e-06
Skip pattern TTTTCT TTTTTA TTTCTT TTTTTT
Refine GGAGAA 11.9233 : 12.51379 13.89913 12.40968 12.13264 12.74177 TRUE 515 185 506 181
New motif: GGAGAA
== testthat results ===========================================================
[ OK: 81 | SKIPPED: 0 | WARNINGS: 71 | FAILED: 0 ]
>
> proc.time()
user system elapsed
112.60 4.06 131.34
|
RCAS.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:data.table':
first, second
The following object is masked from 'package:plotly':
rename
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:plotly':
slice
The following object is masked from 'package:grDevices':
windows
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:plotly':
select
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:graph':
complement
The following object is masked from 'package:base':
strsplit
Loading required package: seqLogo
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:topGO':
depth
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:plotly':
export
Loading required package: BSgenome.Hsapiens.UCSC.hg19
>
> test_check("RCAS")
GGAGAA 6.87318e-07
Skip pattern TTTTTA
Refine GGAGAA 12.81909 : 13.90938 13.55178 13.09082 13.08209 12.46936 TRUE 515 161 506 156
New motif: GGAGAA
== testthat results ===========================================================
[ OK: 81 | SKIPPED: 0 | WARNINGS: 71 | FAILED: 0 ]
>
> proc.time()
user system elapsed
105.96 1.79 124.93
|
|
RCAS.Rcheck/examples_i386/RCAS-Ex.timings
|
RCAS.Rcheck/examples_x64/RCAS-Ex.timings
|