Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1505/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pathwayPCA 1.23.0 (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 22.03 LTS-SP1) / 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-12-23 20:38:57 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:39:55 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 57.6 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/pathwayPCA.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pathwayPCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathwayPCA’ version ‘1.23.0’ * 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 * 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-arm64/Resources/library’ * installing *source* package ‘pathwayPCA’ ... ** 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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 5.528 0.271 14.550
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
name | user | system | elapsed | |
AESPCA_pVals | 0.146 | 0.062 | 2.237 | |
CheckAssay | 0 | 0 | 0 | |
CheckPwyColl | 0 | 0 | 0 | |
CheckSampleIDs | 0 | 0 | 0 | |
Contains | 0 | 0 | 0 | |
ControlFDR | 0 | 0 | 0 | |
CreateOmics | 0.128 | 0.010 | 0.139 | |
CreateOmicsPathway | 0.076 | 0.003 | 0.078 | |
CreatePathwayCollection | 0.003 | 0.001 | 0.003 | |
ExtractAESPCs | 0.126 | 0.047 | 1.486 | |
GumbelMixpValues | 0 | 0 | 0 | |
IntersectOmicsPwyCollct | 0 | 0 | 0 | |
JoinPhenoAssay | 0 | 0 | 0 | |
LoadOntoPCs | 0.153 | 0.067 | 2.272 | |
OptimGumbelMixParams | 0 | 0 | 0 | |
PathwaytValues | 0 | 0 | 0 | |
PermTestCateg | 0 | 0 | 0 | |
PermTestReg | 0.001 | 0.000 | 0.000 | |
PermTestSurv | 0 | 0 | 0 | |
SE2Tidy | 3.781 | 0.102 | 3.884 | |
SubsetPathwayCollection | 0.001 | 0.001 | 0.002 | |
SubsetPathwayData | 0.112 | 0.028 | 0.140 | |
SuperPCA_pVals | 0.383 | 0.010 | 2.438 | |
TabulatepValues | 0 | 0 | 0 | |
TransposeAssay | 0.016 | 0.008 | 0.025 | |
WhichPathways | 0.002 | 0.001 | 0.003 | |
aespca | 0 | 0 | 0 | |
coxTrain_fun | 0.001 | 0.000 | 0.000 | |
getPathPCLs | 0.101 | 0.014 | 2.532 | |
getPathpVals | 0.102 | 0.009 | 2.533 | |
get_set_OmicsPathway | 0.278 | 0.207 | 0.519 | |
get_set_OmicsRegCateg | 0.088 | 0.006 | 0.093 | |
get_set_OmicsSurv | 0.085 | 0.006 | 0.091 | |
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 | 0.002 | 0.000 | 0.002 | |
read_gmt | 0.032 | 0.001 | 0.034 | |
show-OmicsPathway-method | 0.102 | 0.007 | 0.109 | |
superpc.st | 0 | 0 | 0 | |
superpc.train | 0.000 | 0.000 | 0.001 | |
write_gmt | 0.001 | 0.000 | 0.000 | |