Gabriel Odom
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/pathwayPCA |
| Branch: RELEASE_3_11 |
| Last Commit: 4329426 |
| Last Changed Date: 2020-04-27 15:24:49 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:21 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE pathwayPCA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1277/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathwayPCA 1.4.0 Gabriel Odom
| 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: pathwayPCA |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathwayPCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pathwayPCA_1.4.0.tar.gz |
| StartedAt: 2020-10-17 06:46:35 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:52:45 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 370.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.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:pathwayPCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pathwayPCA_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pathwayPCA.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 'pathwayPCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathwayPCA' version '1.4.0'
* 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 'pathwayPCA' 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
SE2Tidy 11.36 0.91 12.26
LoadOntoPCs 0.33 0.34 8.50
AESPCA_pVals 0.42 0.25 17.40
ExtractAESPCs 0.22 0.24 11.99
getPathPCLs 0.21 0.05 10.05
SuperPCA_pVals 0.13 0.05 7.25
getPathpVals 0.15 0.02 8.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SE2Tidy 8.81 0.28 9.10
LoadOntoPCs 0.28 0.33 8.00
AESPCA_pVals 0.37 0.23 7.77
ExtractAESPCs 0.31 0.20 5.65
getPathPCLs 0.22 0.02 10.30
getPathpVals 0.20 0.03 11.53
SuperPCA_pVals 0.09 0.04 7.47
* 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
pathwayPCA.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/pathwayPCA_1.4.0.tar.gz && rm -rf pathwayPCA.buildbin-libdir && mkdir pathwayPCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathwayPCA.buildbin-libdir pathwayPCA_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pathwayPCA_1.4.0.zip && rm pathwayPCA_1.4.0.tar.gz pathwayPCA_1.4.0.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 3415k 100 3415k 0 0 25.9M 0 --:--:-- --:--:-- --:--:-- 27.3M
install for i386
* installing *source* package 'pathwayPCA' ...
** 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 'pathwayPCA'
finding HTML links ... done
AESPCA_pVals html
CheckAssay html
CheckPwyColl html
CheckSampleIDs html
Contains html
ControlFDR html
CreateOmics html
CreateOmicsPathway html
CreatePathwayCollection html
ExtractAESPCs html
GumbelMixpValues html
IntersectOmicsPwyCollct html
JoinPhenoAssay html
LoadOntoPCs html
OmicsCateg-class html
OmicsPathway-class html
OmicsReg-class html
OmicsSurv-class html
OptimGumbelMixParams html
PathwaytValues html
PermTestCateg html
PermTestReg html
PermTestSurv html
SE2Tidy html
SubsetPathwayCollection html
SubsetPathwayData html
SuperPCA_pVals html
TabulatepValues html
TransposeAssay html
ValidOmicsSurv html
WhichPathways html
aespca html
colonSurv_df html
colon_pathwayCollection html
coxTrain_fun html
getPathPCLs html
getPathpVals html
get_set_OmicsPathway html
get_set_OmicsRegCateg html
get_set_OmicsSurv html
glmTrain_fun html
lars.lsa html
mysvd html
normalize html
olsTrain_fun html
pathwayPCA-package html
pathway_tControl html
pathway_tScores html
permuteSamps html
print.pathwayCollection html
read_gmt html
show-OmicsPathway-method html
superpc.st html
superpc.train html
wikipwsHS_Entrez_pathwayCollection html
wikipwsHS_Symbol_pathwayCollection html
write_gmt 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 'pathwayPCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathwayPCA' as pathwayPCA_1.4.0.zip
* DONE (pathwayPCA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pathwayPCA' successfully unpacked and MD5 sums checked
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pathwayPCA.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(pathwayPCA)
>
> test_check("pathwayPCA")
== testthat results ===========================================================
[ OK: 47 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.85 1.81 49.89
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pathwayPCA.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(pathwayPCA)
>
> test_check("pathwayPCA")
== testthat results ===========================================================
[ OK: 47 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.50 1.18 46.67
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pathwayPCA.Rcheck/examples_i386/pathwayPCA-Ex.timings
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pathwayPCA.Rcheck/examples_x64/pathwayPCA-Ex.timings
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