Taiyun Kim
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/PhosR |
| Branch: RELEASE_3_12 |
| Last Commit: 39a78ff |
| Last Changed Date: 2020-10-27 12:01:31 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:45 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the PhosR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1342/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhosR 1.0.0 (landing page) Taiyun Kim
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: PhosR |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PhosR_1.0.0.tar.gz |
| StartedAt: 2021-05-06 05:32:02 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:43:41 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 698.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhosR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PhosR_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PhosR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PhosR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhosR' version '1.0.0'
* 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 'PhosR' 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
kinaseSubstratePred 38.06 0.00 38.07
Signalomes 37.75 0.08 37.82
siteAnnotate 35.87 0.03 35.90
minmax 29.66 0.02 29.68
kinaseSubstrateHeatmap 29.06 0.02 29.08
kinaseSubstrateScore 22.33 0.00 22.33
matANOVA 17.05 0.02 17.06
kinaseSubstrateProfile 14.28 0.01 14.29
standardise 13.78 0.00 13.78
pathwayRankBasedEnrichment 8.92 0.01 8.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
siteAnnotate 47.78 0.05 47.83
Signalomes 45.30 0.08 45.40
kinaseSubstratePred 41.11 0.04 41.16
minmax 38.88 0.05 38.93
kinaseSubstrateHeatmap 34.05 0.02 34.11
kinaseSubstrateScore 29.32 0.00 29.32
matANOVA 19.42 0.02 19.44
kinaseSubstrateProfile 18.68 0.00 18.68
standardise 14.10 0.02 14.11
pathwayRankBasedEnrichment 8.47 0.01 8.49
* 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
PhosR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PhosR_1.0.0.tar.gz && rm -rf PhosR.buildbin-libdir && mkdir PhosR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhosR.buildbin-libdir PhosR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PhosR_1.0.0.zip && rm PhosR_1.0.0.tar.gz PhosR_1.0.0.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 2118k 100 2118k 0 0 41.4M 0 --:--:-- --:--:-- --:--:-- 42.2M
install for i386
* installing *source* package 'PhosR' ...
** 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 'PhosR'
finding HTML links ... done
KinaseFamily html
Pathways.KEGG html
Pathways.reactome html
PhosphoSite.human html
PhosphoSite.mouse html
PhosphoSite.rat html
RUVphospho html
SPSs html
Signalomes html
createFrequencyMat html
frequencyScoring html
kinaseSubstrateHeatmap html
kinaseSubstratePred html
kinaseSubstrateProfile html
kinaseSubstrateScore html
mIntersect html
matANOVA html
meanAbundance html
medianScaling html
minmax html
motif.human.list html
motif.mouse.list html
motif.rat.list html
pathwayOverrepresent html
pathwayRankBasedEnrichment html
phosCollapse html
phospho.L6.ratio html
phospho.cells.Ins html
phospho.liver.Ins.TC.ratio.RUV html
plotQC html
ptImpute html
scImpute html
selectGrps html
selectOverallPercent html
selectTimes html
siteAnnotate html
standardise html
tImpute 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 'PhosR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PhosR' as PhosR_1.0.0.zip
* DONE (PhosR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'PhosR' successfully unpacked and MD5 sums checked
|
PhosR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(PhosR)
>
> test_check("PhosR")
[1] "idx1: 0"
[1] "idx2: 0"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
>
> proc.time()
user system elapsed
2.59 0.14 2.71
|
PhosR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(PhosR)
>
> test_check("PhosR")
[1] "idx1: 0"
[1] "idx2: 0"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
>
> proc.time()
user system elapsed
2.37 0.20 2.56
|
|
PhosR.Rcheck/examples_i386/PhosR-Ex.timings
|
PhosR.Rcheck/examples_x64/PhosR-Ex.timings
|