############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:msmsTests.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings msmsTests_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/msmsTests.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘msmsTests/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msmsTests’ version ‘1.40.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘msmsTests’ 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 R 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 ... NOTE Packages in Depends field not imported from: ‘MSnbase’ ‘msmsEDA’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE glm.pois: no visible global function definition for ‘glm’ glm.pois: no visible global function definition for ‘as.formula’ glm.pois: no visible global function definition for ‘poisson’ glm.pois: no visible global function definition for ‘coef’ glm.pois: no visible global function definition for ‘anova’ msms.edgeR: no visible global function definition for ‘exprs’ msms.edgeR: no visible global function definition for ‘pData’ msms.edgeR: no visible global function definition for ‘model.matrix’ msms.edgeR: no visible global function definition for ‘as.formula’ msms.glm.pois: no visible global function definition for ‘exprs’ msms.glm.pois: no visible global function definition for ‘pData’ msms.glm.qlll: no visible global function definition for ‘exprs’ msms.glm.qlll: no visible global function definition for ‘pData’ qp.test: no visible global function definition for ‘glm’ qp.test: no visible global function definition for ‘as.formula’ qp.test: no visible global function definition for ‘quasi’ qp.test: no visible binding for global variable ‘mu’ qp.test: no visible global function definition for ‘coef’ qp.test: no visible global function definition for ‘anova’ res.volcanoplot: no visible global function definition for ‘grid’ res.volcanoplot: no visible global function definition for ‘abline’ res.volcanoplot: no visible global function definition for ‘points’ res.volcanoplot: no visible global function definition for ‘text’ test.results: no visible global function definition for ‘exprs’ test.results: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: abline anova as.formula coef exprs glm grid model.matrix mu p.adjust pData points poisson quasi text Consider adding importFrom("graphics", "abline", "grid", "points", "text") importFrom("stats", "anova", "as.formula", "coef", "glm", "model.matrix", "p.adjust", "poisson", "quasi") to your NAMESPACE file. * checking Rd files ... OK * 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 test.results 5.667 0.073 5.739 res.volcanoplot 5.671 0.064 5.735 msms.glm.qlll 5.577 0.100 5.677 msms.glm.pois 5.504 0.131 5.636 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘msmsTests-Vignette.Rnw’... failed ‘msmsTests-Vignette2.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘msmsTests-Vignette.Rnw’ ... > fp <- sig - tp > tt.nb0 <- data.frame(TP = tp, FP = fp, TN = ny - fp, + FN = nh - tp) > library(xtable) When sourcing ‘msmsTests-Vignette.R’: Error: there is no package called ‘xtable’ Execution halted when running code in ‘msmsTests-Vignette2.Rnw’ ... + tt.ql3, tt.ql33) > rownames(gbl.tt) <- c("subset", "subset filtered", + "global", "global filtered", "blocking", "blocking filtered") > library(xtable) When sourcing ‘msmsTests-Vignette2.R’: Error: there is no package called ‘xtable’ Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘msmsTests-Vignette.Rnw’ using Sweave Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: ProtGenerics Attaching package: ‘ProtGenerics’ The following object is masked from ‘package:stats’: smooth This is MSnbase version 2.28.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: ‘MSnbase’ The following object is masked from ‘package:base’: trimws Loading required package: msmsEDA Error: processing vignette 'msmsTests-Vignette.Rnw' failed with diagnostics: chunk 8 (label = Chunk5.summary) Error in library(xtable) : there is no package called ‘xtable’ --- failed re-building ‘msmsTests-Vignette.Rnw’ --- re-building ‘msmsTests-Vignette2.Rnw’ using Sweave Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: ProtGenerics Attaching package: ‘ProtGenerics’ The following object is masked from ‘package:stats’: smooth This is MSnbase version 2.28.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: ‘MSnbase’ The following object is masked from ‘package:base’: trimws Loading required package: msmsEDA Error: processing vignette 'msmsTests-Vignette2.Rnw' failed with diagnostics: chunk 12 (label = CompChunk) Error in library(xtable) : there is no package called ‘xtable’ --- failed re-building ‘msmsTests-Vignette2.Rnw’ SUMMARY: processing the following files failed: ‘msmsTests-Vignette.Rnw’ ‘msmsTests-Vignette2.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/msmsTests.Rcheck/00check.log’ for details.