############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seq2pathway_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seq2pathway.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seq2pathway/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seq2pathway’ version ‘1.38.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ See ‘/Users/biocbuild/bbs-3.20-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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING '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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runseq2pathway 11.810 0.123 11.941 runseq2gene 11.624 0.136 11.782 * 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/seq2pathway.Rcheck/00check.log’ for details.