############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings pathwayPCA_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/pathwayPCA.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘pathwayPCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathwayPCA’ version ‘1.22.0’ * 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 loading without being on the library search path ... 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 8.674 0.408 9.083 AESPCA_pVals 0.361 0.095 5.318 getPathpVals 0.253 0.027 6.383 getPathPCLs 0.244 0.007 6.889 SuperPCA_pVals 0.235 0.010 5.395 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/pathwayPCA.Rcheck/00check.log’ for details.