############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:yeastExpData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings yeastExpData_0.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/yeastExpData.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 ‘yeastExpData/DESCRIPTION’ ... OK * this is package ‘yeastExpData’ version ‘0.46.0’ * 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 ‘yeastExpData’ 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 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 Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Data codoc mismatches from documentation object 'gfp': Variables in data frame 'gfp' Code: ER ER_to_Golgi GFP_tagged GFP_visualized Golgi TAP_visualized abundance actin ambiguous bud bud_neck cell_periphery cytoplasm early_Golgi endosome error gene_name late_Golgi lipid_particle localization_summary microtubule missingAbundance mitochondrion nuclear_periphery nucleolus nucleus orfid peroxisome punctate_composite spindle_pole vacuolar_membrane vacuole yORF Docs: GFP_tagged GFP_visualized TAP_visualized abundance error gene_name localization_summary orfid yORF Data codoc mismatches from documentation object 'proteinProperties': Variables in data frame 'proteinProperties' Code: ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER SGDID THR TRP TYR VAL aromaticity cai codonBias cterm fop gravy length molwt nterm pi type yORF Docs: SGDID cai codonBias cterm length molwt nterm pi yORF * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' call not declared from: ‘lattice’ * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... WARNING Warning: large data file saved inefficiently: size ASCII compress ccyclered.rda 364Kb FALSE none Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress ccyclered.rda 364Kb 59Kb xz fcabundance.rda 110Kb 67Kb xz gfp.rda 118Kb 60Kb xz litG.rda 22Kb 8Kb xz proteinProperties.rda 488Kb 312Kb xz y2hG.rda 22Kb 9Kb xz * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘yeastExample.Rnw’... OK OK * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘yeastExample.Rnw’ using Sweave Loading required package: graph 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: Rgraphviz Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘Rgraphviz’ Loading required package: Rgraphviz Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘Rgraphviz’ Error: processing vignette 'yeastExample.Rnw' failed with diagnostics: Running 'texi2dvi' on 'yeastExample.tex' failed. LaTeX errors: !pdfTeX error: pdflatex (file /home/biocbuild/bbs-3.17-data-experiment/meat/yea stExpData.Rcheck/vign_test/yeastExpData/vignettes/yeastExample-subGraphs.pdf): PDF inclusion: required page does not exist <0> ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘yeastExample.Rnw’ SUMMARY: processing the following file failed: ‘yeastExample.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.17-data-experiment/meat/yeastExpData.Rcheck/00check.log’ for details.