Gabriel Odom
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/pathwayPCA |
| git_branch: master |
| git_last_commit: a11c55e |
| git_last_commit_date: 2022-01-14 19:07:14 -0400 (Fri, 14 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:15 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 pathwayPCA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathwayPCA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1389/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathwayPCA 1.11.1 (landing page) Gabriel Odom
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pathwayPCA |
| Version: 1.11.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pathwayPCA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pathwayPCA_1.11.1.tar.gz |
| StartedAt: 2022-03-17 19:49:24 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:52:37 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 193.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pathwayPCA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pathwayPCA_1.11.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/pathwayPCA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.11.1'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SE2Tidy 9.55 0.48 11.27
AESPCA_pVals 0.39 0.27 9.50
LoadOntoPCs 0.42 0.17 7.66
ExtractAESPCs 0.39 0.17 5.28
SuperPCA_pVals 0.42 0.02 8.36
getPathPCLs 0.31 0.03 12.84
getPathpVals 0.27 0.02 8.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL pathwayPCA
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'pathwayPCA' ...
** using staged installation
** R
** data
** 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
* DONE (pathwayPCA)
Making 'packages.html' ... done
pathwayPCA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(pathwayPCA)
>
> test_check("pathwayPCA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
>
> proc.time()
user system elapsed
9.12 1.25 40.73
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
| name | user | system | elapsed | |
| AESPCA_pVals | 0.39 | 0.27 | 9.50 | |
| CheckAssay | 0 | 0 | 0 | |
| CheckPwyColl | 0 | 0 | 0 | |
| CheckSampleIDs | 0 | 0 | 0 | |
| Contains | 0 | 0 | 0 | |
| ControlFDR | 0 | 0 | 0 | |
| CreateOmics | 0.42 | 0.10 | 0.61 | |
| CreateOmicsPathway | 0.19 | 0.02 | 0.21 | |
| CreatePathwayCollection | 0.00 | 0.02 | 0.01 | |
| ExtractAESPCs | 0.39 | 0.17 | 5.28 | |
| GumbelMixpValues | 0 | 0 | 0 | |
| IntersectOmicsPwyCollct | 0 | 0 | 0 | |
| JoinPhenoAssay | 0 | 0 | 0 | |
| LoadOntoPCs | 0.42 | 0.17 | 7.66 | |
| OptimGumbelMixParams | 0 | 0 | 0 | |
| PathwaytValues | 0 | 0 | 0 | |
| PermTestCateg | 0 | 0 | 0 | |
| PermTestReg | 0 | 0 | 0 | |
| PermTestSurv | 0 | 0 | 0 | |
| SE2Tidy | 9.55 | 0.48 | 11.27 | |
| SubsetPathwayCollection | 0.01 | 0.00 | 0.02 | |
| SubsetPathwayData | 0.42 | 0.05 | 0.50 | |
| SuperPCA_pVals | 0.42 | 0.02 | 8.36 | |
| TabulatepValues | 0.00 | 0.00 | 0.02 | |
| TransposeAssay | 0.05 | 0.03 | 0.14 | |
| WhichPathways | 0.00 | 0.01 | 0.06 | |
| aespca | 0 | 0 | 0 | |
| coxTrain_fun | 0.00 | 0.00 | 0.03 | |
| getPathPCLs | 0.31 | 0.03 | 12.84 | |
| getPathpVals | 0.27 | 0.02 | 8.79 | |
| get_set_OmicsPathway | 0.82 | 0.19 | 1.01 | |
| get_set_OmicsRegCateg | 0.25 | 0.01 | 0.27 | |
| get_set_OmicsSurv | 0.18 | 0.00 | 0.17 | |
| glmTrain_fun | 0 | 0 | 0 | |
| lars.lsa | 0 | 0 | 0 | |
| mysvd | 0 | 0 | 0 | |
| normalize | 0 | 0 | 0 | |
| olsTrain_fun | 0 | 0 | 0 | |
| pathway_tControl | 0 | 0 | 0 | |
| pathway_tScores | 0 | 0 | 0 | |
| permuteSamps | 0 | 0 | 0 | |
| print.pathwayCollection | 0.01 | 0.00 | 0.01 | |
| read_gmt | 0.08 | 0.00 | 0.08 | |
| show-OmicsPathway-method | 0.25 | 0.05 | 0.30 | |
| superpc.st | 0 | 0 | 0 | |
| superpc.train | 0 | 0 | 0 | |
| write_gmt | 0 | 0 | 0 | |