############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SMAP.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SMAP_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SMAP.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * 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 ‘SMAP/DESCRIPTION’ ... OK * this is package ‘SMAP’ version ‘1.68.0’ * 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 ‘SMAP’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘SMAP/R/AllClasses.R’: .onLoad calls: require("methods", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. .draw.dist,gaussparam: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘par’ plot,SMAPObservations-missing: no visible global function definition for ‘points’ plot,SMAPObservations-missing: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘box’ plot,SMAPObservations-missing: no visible global function definition for ‘axis’ profilePlot,SMAPProfile: no visible global function definition for ‘par’ profilePlot,SMAPProfile: no visible global function definition for ‘points’ profilePlot,SMAPProfile: no visible global function definition for ‘abline’ profilePlot,SMAPProfile: no visible global function definition for ‘box’ profilePlot,SMAPProfile: no visible global function definition for ‘axis’ profilePlot,SMAPProfiles: no visible global function definition for ‘par’ profilePlot,SMAPProfiles: no visible global function definition for ‘abline’ profilePlot,SMAPProfiles: no visible global function definition for ‘box’ profilePlot,SMAPProfiles: no visible global function definition for ‘axis’ Undefined global functions or variables: abline axis box par points Consider adding importFrom("graphics", "abline", "axis", "box", "par", "points") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed smap 6.019 0.035 6.055 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘SMAP.Rnw’ using Sweave Warning in fun(libname, pkgname) : Package 'SMAP' is deprecated and will be removed from Bioconductor version 3.20 Error: processing vignette 'SMAP.Rnw' failed with diagnostics: cannot open file 'figs/fig-003.pdf' --- failed re-building ‘SMAP.Rnw’ SUMMARY: processing the following file failed: ‘SMAP.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/SMAP.Rcheck/00check.log’ for details.