############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seq2pathway_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/seq2pathway.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seq2pathway/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seq2pathway’ version ‘1.39.0’ * 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 ... NOTE Found the following hidden files and directories: vignettes/.RData These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘seq2pathway’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ See ‘/home/biocbuild/bbs-3.21-bioc/meat/seq2pathway.Rcheck/00install.out’ for details. * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... WARNING Warning: program compiled against libxml 212 using older 211 'library' or 'require' call not declared from: ‘biomaRt’ 'library' or 'require' call to ‘biomaRt’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 FAIME_EmpiricalP: no visible global function definition for ‘data’ FAIME_EmpiricalP: no visible binding for global variable ‘gencode_coding’ FisherTest_GO_BP_MF_CC: no visible global function definition for ‘data’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_BP_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_MF_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_CC_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_BP_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_MF_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_CC_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_hg_v36’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_hg_v19’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_mm_vM25’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_mm_vM1’ FisherTest_MsigDB: no visible global function definition for ‘data’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_hg_v36’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_hg_v19’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_mm_vM25’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_mm_vM1’ KSrank_EmpiricalP: no visible global function definition for ‘data’ KSrank_EmpiricalP: no visible binding for global variable ‘gencode_coding’ Normalize_F: no visible global function definition for ‘head’ cumulativerank_EmpiricalP: no visible global function definition for ‘data’ cumulativerank_EmpiricalP: no visible binding for global variable ‘gencode_coding’ gene2pathway_test: no visible global function definition for ‘data’ gene2pathway_test: no visible binding for global variable ‘GO_BP_list’ gene2pathway_test: no visible binding for global variable ‘GO_MF_list’ gene2pathway_test: no visible binding for global variable ‘GO_CC_list’ gene2pathway_test: no visible binding for global variable ‘Des_BP_list’ gene2pathway_test: no visible binding for global variable ‘Des_CC_list’ gene2pathway_test: no visible binding for global variable ‘Des_MF_list’ plotTop10: no visible binding for global variable ‘Fisher_odds’ plotTop10: no visible binding for global variable ‘FDR’ plotTop10: no visible global function definition for ‘barplot’ plotTop10: no visible global function definition for ‘lines’ plotTop10: no visible global function definition for ‘text’ plotTop10: no visible global function definition for ‘abline’ rungene2pathway_EmpiricalP: no visible global function definition for ‘txtProgressBar’ rungene2pathway_EmpiricalP: no visible global function definition for ‘setTxtProgressBar’ runseq2gene: no visible global function definition for ‘write.table’ runseq2gene: no visible global function definition for ‘read.table’ runseq2pathway: no visible global function definition for ‘data’ runseq2pathway: no visible binding for global variable ‘GO_BP_list’ runseq2pathway: no visible binding for global variable ‘GO_MF_list’ runseq2pathway: no visible binding for global variable ‘GO_CC_list’ runseq2pathway: no visible binding for global variable ‘Des_BP_list’ runseq2pathway: no visible binding for global variable ‘Des_CC_list’ runseq2pathway: no visible binding for global variable ‘Des_MF_list’ runseq2pathway: no visible global function definition for ‘write.table’ runseq2pathway: no visible global function definition for ‘read.table’ Undefined global functions or variables: Des_BP_list Des_CC_list Des_MF_list FDR Fisher_odds GO_BP_list GO_CC_list GO_GENCODE_df_hg_v19 GO_GENCODE_df_hg_v36 GO_GENCODE_df_mm_vM1 GO_GENCODE_df_mm_vM25 GO_MF_list Msig_GENCODE_df_hg_v19 Msig_GENCODE_df_hg_v36 Msig_GENCODE_df_mm_vM1 Msig_GENCODE_df_mm_vM25 abline barplot data gencode_coding head lines read.table setTxtProgressBar text txtProgressBar write.table Consider adding importFrom("graphics", "abline", "barplot", "lines", "text") importFrom("utils", "data", "head", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) runseq2gene.Rd:22-24: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:25-27: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:28-30: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:31-34: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:35-37: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:41-43: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:44-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:47-49: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:50-52: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:112-114: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:115-117: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:118-120: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:121-123: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:124-127: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:128-131: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:132-134: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:135-137: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:138-140: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2pathway.Rd:26-28: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:29-31: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:32-34: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:35-37: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:38-40: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:44-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:47-49: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:50-52: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:53-55: Lost braces in \enumerate; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... ERROR Running examples in ‘seq2pathway-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: addDescription > ### Title: Retrieve "gene description" attributes for gene symbol. > ### Aliases: addDescription > ### Keywords: methods > > ### ** Examples > > require(biomaRt) Loading required package: biomaRt > data(dat_chip) > gene_description<-addDescription(genome="hg19",genevector=rownames(dat_chip)[1:3]) Error in curl::curl_parse_url(url, baseurl = base_url, decode = FALSE) : Failed to parse URL: Bad scheme Calls: addDescription ... .useMart -> .cleanHostURL -> -> Execution halted * 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 ERROR, 6 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/seq2pathway.Rcheck/00check.log’ for details.