Gabriel Odom
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/pathwayPCA |
| git_branch: RELEASE_3_21 |
| git_last_commit: d745996 |
| git_last_commit_date: 2025-04-15 11:42:25 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 | ||||
| Package 1543/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathwayPCA 1.24.0 (landing page) Gabriel Odom
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the pathwayPCA package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: pathwayPCA |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathwayPCA_1.24.0.tar.gz |
| StartedAt: 2025-04-21 22:33:05 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 22:35:53 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 167.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathwayPCA_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/pathwayPCA.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... 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 code 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 ... NOTE
checkRd: (-1) AESPCA_pVals.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AESPCA_pVals.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AESPCA_pVals.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AESPCA_pVals.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AESPCA_pVals.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AESPCA_pVals.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ControlFDR.Rd:88-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:91-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:94-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:99-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ControlFDR.Rd:49-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ControlFDR.Rd:53-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ControlFDR.Rd:57-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ControlFDR.Rd:61-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOmics.Rd:23-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateOmics.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateOmics.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateOmicsPathway.Rd:42-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateOmicsPathway.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateOmicsPathway.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) JoinPhenoAssay.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JoinPhenoAssay.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) JoinPhenoAssay.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OmicsCateg-class.Rd:19-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsCateg-class.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsCateg-class.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsCateg-class.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsPathway-class.Rd:20-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsPathway-class.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsPathway-class.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsPathway-class.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsReg-class.Rd:19-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsReg-class.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsReg-class.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsReg-class.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsSurv-class.Rd:19-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsSurv-class.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsSurv-class.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OmicsSurv-class.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OptimGumbelMixParams.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OptimGumbelMixParams.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OptimGumbelMixParams.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OptimGumbelMixParams.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OptimGumbelMixParams.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SubsetPathwayCollection.Rd:36: Lost braces
36 | object, then create a new one with the code{\link{CreatePathwayCollection}}
| ^
checkRd: (-1) SuperPCA_pVals.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SuperPCA_pVals.Rd:68-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SuperPCA_pVals.Rd:71-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SuperPCA_pVals.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SuperPCA_pVals.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TabulatepValues.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TabulatepValues.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TabulatepValues.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) TabulatepValues.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aespca.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aespca.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aespca.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aespca.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colon_pathwayCollection.Rd:10-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colon_pathwayCollection.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coxTrain_fun.Rd:22-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxTrain_fun.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxTrain_fun.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxTrain_fun.Rd:29-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathPCLs.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathPCLs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathPCLs.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathPCLs.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathpVals.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathpVals.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathpVals.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathpVals.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPathpVals.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mysvd.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mysvd.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mysvd.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mysvd.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) olsTrain_fun.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) olsTrain_fun.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) olsTrain_fun.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) olsTrain_fun.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pathwayPCA-package.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pathwayPCA-package.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pathwayPCA-package.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pathwayPCA-package.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_gmt.Rd:40-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_gmt.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_gmt.Rd:46-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.st.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.st.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.st.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.st.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.st.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.st.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.st.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.st.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.st.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.train.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.train.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.train.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.train.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superpc.train.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.train.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.train.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superpc.train.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wikipwsHS_Entrez_pathwayCollection.Rd:10-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wikipwsHS_Entrez_pathwayCollection.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wikipwsHS_Entrez_pathwayCollection.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wikipwsHS_Symbol_pathwayCollection.Rd:10-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wikipwsHS_Symbol_pathwayCollection.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wikipwsHS_Symbol_pathwayCollection.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_gmt.Rd:13-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_gmt.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_gmt.Rd:20-25: Lost braces in \itemize; meant \describe ?
* 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 10.736 0.410 11.207
LoadOntoPCs 0.438 0.130 6.606
AESPCA_pVals 0.439 0.121 6.647
getPathPCLs 0.412 0.031 7.455
SuperPCA_pVals 0.298 0.030 6.130
getPathpVals 0.289 0.021 7.518
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/pathwayPCA.Rcheck/00check.log’
for details.
pathwayPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pathwayPCA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘pathwayPCA’ ... ** this is package ‘pathwayPCA’ version ‘1.24.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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)
pathwayPCA.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
15.182 0.852 39.366
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
| name | user | system | elapsed | |
| AESPCA_pVals | 0.439 | 0.121 | 6.647 | |
| CheckAssay | 0 | 0 | 0 | |
| CheckPwyColl | 0.000 | 0.000 | 0.001 | |
| CheckSampleIDs | 0 | 0 | 0 | |
| Contains | 0.000 | 0.000 | 0.001 | |
| ControlFDR | 0.000 | 0.000 | 0.001 | |
| CreateOmics | 0.377 | 0.037 | 0.417 | |
| CreateOmicsPathway | 0.224 | 0.010 | 0.237 | |
| CreatePathwayCollection | 0.006 | 0.001 | 0.007 | |
| ExtractAESPCs | 0.379 | 0.110 | 4.843 | |
| GumbelMixpValues | 0.000 | 0.001 | 0.001 | |
| IntersectOmicsPwyCollct | 0 | 0 | 0 | |
| JoinPhenoAssay | 0 | 0 | 0 | |
| LoadOntoPCs | 0.438 | 0.130 | 6.606 | |
| OptimGumbelMixParams | 0.000 | 0.001 | 0.001 | |
| PathwaytValues | 0.000 | 0.001 | 0.001 | |
| PermTestCateg | 0 | 0 | 0 | |
| PermTestReg | 0.000 | 0.000 | 0.001 | |
| PermTestSurv | 0.000 | 0.000 | 0.001 | |
| SE2Tidy | 10.736 | 0.410 | 11.207 | |
| SubsetPathwayCollection | 0.003 | 0.003 | 0.005 | |
| SubsetPathwayData | 0.307 | 0.079 | 0.387 | |
| SuperPCA_pVals | 0.298 | 0.030 | 6.130 | |
| TabulatepValues | 0.000 | 0.001 | 0.001 | |
| TransposeAssay | 0.056 | 0.032 | 0.088 | |
| WhichPathways | 0.007 | 0.002 | 0.010 | |
| aespca | 0 | 0 | 0 | |
| coxTrain_fun | 0.000 | 0.001 | 0.000 | |
| getPathPCLs | 0.412 | 0.031 | 7.455 | |
| getPathpVals | 0.289 | 0.021 | 7.518 | |
| get_set_OmicsPathway | 0.845 | 0.580 | 1.470 | |
| get_set_OmicsRegCateg | 0.261 | 0.012 | 0.275 | |
| get_set_OmicsSurv | 0.351 | 0.022 | 0.380 | |
| glmTrain_fun | 0.000 | 0.000 | 0.001 | |
| lars.lsa | 0.000 | 0.000 | 0.001 | |
| mysvd | 0.000 | 0.000 | 0.001 | |
| normalize | 0.000 | 0.000 | 0.001 | |
| olsTrain_fun | 0.000 | 0.000 | 0.001 | |
| pathway_tControl | 0.000 | 0.001 | 0.001 | |
| pathway_tScores | 0 | 0 | 0 | |
| permuteSamps | 0 | 0 | 0 | |
| print.pathwayCollection | 0.004 | 0.002 | 0.006 | |
| read_gmt | 0.115 | 0.002 | 0.119 | |
| show-OmicsPathway-method | 0.261 | 0.106 | 0.485 | |
| superpc.st | 0.000 | 0.000 | 0.001 | |
| superpc.train | 0.001 | 0.001 | 0.000 | |
| write_gmt | 0.002 | 0.000 | 0.002 | |