############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellHTS2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings cellHTS2_2.64.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cellHTS2.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘cellHTS2/DESCRIPTION’ ... OK * this is package ‘cellHTS2’ version ‘2.64.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'RColorBrewer', 'Biobase', 'genefilter', 'splots', 'vsn', 'hwriter', 'locfit', 'grid' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘cellHTS2’ 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘genefilter’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotPlate: no visible global function definition for ‘dev.cur’ plotPlate: no visible global function definition for ‘plot.new’ Undefined global functions or variables: dev.cur plot.new Consider adding importFrom("grDevices", "dev.cur") importFrom("graphics", "plot.new") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages ‘cellHTS’, ‘prada’ in Rd xrefs * 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 ‘test.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘cellhts2.Rnw’... OK ‘cellhts2Complete.Rnw’... failed ‘twoChannels.Rnw’... OK ‘twoWay.Rnw’... OK WARNING Errors in running code in vignettes: when running code in ‘cellhts2Complete.Rnw’ ... > categs <- cateGOry(genes, unlist(goids, use.names = FALSE)) Loading required namespace: GO.db Failed with error: ‘there is no package called ‘GO.db’’ When sourcing ‘cellhts2Complete.R’: Error: Use 'BiocManager::install("GO.db")' to install the GO.db package recover called non-interactively; frames dumped, use debugger() to view > proc.time() user system elapsed 19.712 0.984 20.618 * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘cellhts2.Rnw’ using Sweave Loading required package: RColorBrewer Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Loading required package: splots Loading required package: vsn Loading required package: hwriter Loading required package: locfit locfit 1.5-9.8 2023-06-11 Loading required package: grid Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. Warning in sprintf("Left: raw, right: normalized", r) : one argument not used by format 'Left: raw, right: normalized' Warning in sprintf("Left: raw, right: normalized", r) : one argument not used by format 'Left: raw, right: normalized' Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. Warning: `qplot()` was deprecated in ggplot2 3.4.0. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Warning: Removed 24 rows containing non-finite values (`stat_bin()`). Warning: Removed 446 rows containing non-finite values (`stat_binhex()`). Warning: Computation failed in `stat_binhex()` Caused by error in `compute_group()`: ! The package "hexbin" is required for `stat_binhex()` Warning: Removed 24 rows containing non-finite values (`stat_qq()`). `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Warning: Removed 24 rows containing non-finite values (`stat_bin()`). Warning: Removed 502 rows containing non-finite values (`stat_binhex()`). Warning: Computation failed in `stat_binhex()` Caused by error in `compute_group()`: ! The package "hexbin" is required for `stat_binhex()` Warning: Removed 24 rows containing non-finite values (`stat_qq()`). --- finished re-building ‘cellhts2.Rnw’ --- re-building ‘cellhts2Complete.Rnw’ using Sweave Loading required package: RColorBrewer Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Loading required package: splots Loading required package: vsn Loading required package: hwriter Loading required package: locfit locfit 1.5-9.8 2023-06-11 Loading required package: grid Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors 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: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Loading required namespace: GO.db Failed with error: ‘there is no package called ‘GO.db’’ Error: processing vignette 'cellhts2Complete.Rnw' failed with diagnostics: chunk 40 (label = cat1) Error in augmentByAncestors(ux) : Use 'BiocManager::install("GO.db")' to install the GO.db package --- failed re-building ‘cellhts2Complete.Rnw’ --- re-building ‘twoChannels.Rnw’ using Sweave Loading required package: RColorBrewer Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Loading required package: splots Loading required package: vsn Loading required package: hwriter Loading required package: locfit locfit 1.5-9.8 2023-06-11 Loading required package: grid Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. --- finished re-building ‘twoChannels.Rnw’ --- re-building ‘twoWay.Rnw’ using Sweave Loading required package: RColorBrewer Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Loading required package: splots Loading required package: vsn Loading required package: hwriter Loading required package: locfit locfit 1.5-9.8 2023-06-11 Loading required package: grid Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. Warning in sprintf("Left: raw, right: normalized", r) : one argument not used by format 'Left: raw, right: normalized' Warning in sprintf("Left: raw, right: normalized", r) : one argument not used by format 'Left: raw, right: normalized' Warning: The R script which produced this cellHTS2 report has not been provided via the 'mainScriptFile' argument. We recommend storing this script for future reference along with the report. --- finished re-building ‘twoWay.Rnw’ SUMMARY: processing the following file failed: ‘cellhts2Complete.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/cellHTS2.Rcheck/00check.log’ for details.