############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pathview.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pathview_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.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 ‘pathview/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathview’ 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 ‘pathview’ 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 ... WARNING '::' or ':::' import not declared from: ‘BiocManager’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘pathview/R/zzz.R’: .onLoad calls: installed.packages() packageStartupMessage(wordwrap(disclaimer, 80)) Package startup functions should not call ‘installed.packages’. See section ‘Good practice’ in '?.onAttach'. Warning in formals(fun) : argument is not a function Warning in body(fun) : argument is not a function col.key: no visible binding for global variable ‘node.sizes’ cpd2kegg: no visible binding for global variable ‘rn.list’ cpdidmap: no visible binding for global variable ‘cpd.accs’ cpdkegg2name: no visible binding for global variable ‘kegg.met’ cpdname2kegg: no visible binding for global variable ‘cpd.names’ download.kegg: no visible global function definition for ‘download.file’ eg2id: no visible binding for global variable ‘gene.idtype.list’ geneannot.map: no visible binding for global variable ‘bods’ id2eg: no visible binding for global variable ‘gene.idtype.list’ kegg.species.code: no visible binding for global variable ‘korg.1’ pathview: no visible binding for global variable ‘bods’ pathview: no visible binding for global variable ‘gene.idtype.bods’ pathview: no visible binding for global variable ‘rn.list’ sim.mol.data: no visible binding for global variable ‘bods’ sim.mol.data: no visible binding for global variable ‘gene.idtype.bods’ sim.mol.data: no visible binding for global variable ‘cpd.accs’ sim.mol.data: no visible binding for global variable ‘cpd.simtypes’ sim.mol.data: no visible binding for global variable ‘rn.list’ sim.mol.data: no visible binding for global variable ‘ko.ids’ Undefined global functions or variables: bods cpd.accs cpd.names cpd.simtypes download.file gene.idtype.bods gene.idtype.list kegg.met ko.ids korg.1 node.sizes rn.list Consider adding importFrom("utils", "download.file") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) node.color.Rd:71: Escaped LaTeX specials: \# checkRd: (-1) pathview.Rd:204: Escaped LaTeX specials: \# * 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 LazyData ... 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 pathview 16.441 1.027 29.483 sim.mol.data 0.914 0.017 11.008 download.kegg 0.549 0.011 6.992 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘pathview.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘pathview.Rnw’ ... Info: Writing image file eco00640.eco.kegg.png > eco.dat.entrez <- sim.mol.data(mol.type = "gene", + id.type = "entrez", species = "eco", nmol = 3000) Loading required namespace: org.EcK12.eg.db Failed with error: ‘there is no package called ‘org.EcK12.eg.db’’ When sourcing ‘pathview.R’: Error: there is no package called ‘BiocManager’ Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘pathview.Rnw’ using Sweave ############################################################################## Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R. The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG license agreement (details at http://www.kegg.jp/kegg/legal.html). ############################################################################## Info: Downloading xml files for hsa04110, 1/1 pathways.. Info: Downloading png files for hsa04110, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.2layer.png 'select()' returned 1:1 mapping between keys and columns Warning: reconcile groups sharing member nodes! Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.pdf 'select()' returned 1:1 mapping between keys and columns Warning: reconcile groups sharing member nodes! Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.2layer.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.split.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa04110.gse16873.split.expanded.pdf Info: Downloading xml files for hsa00640, 1/1 pathways.. Info: Downloading png files for hsa00640, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.png Warning in .local(from, to, graph) : edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’ 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.match.multi.png Warning in .local(from, to, graph) : edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’ 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.pdf Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi Loading required package: stats4 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: 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 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.sel.genes.sel.cpd.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.sel.genes.cpd.png Note: "CAS Registry Number" has only 4643 unique IDs! Note: "ENSEMBLPROT" has only 21439 unique IDs! 'select()' returned 1:many mapping between keys and columns Note: multiple compounds may map to a input ID, only the first one kept! 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gene.ensprot.cpd.cas.png Note: multiple compounds may map to a input ID, only the first one kept! 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file hsa00640.gene.entrez.cpd.kc.png Info: Downloading xml files for eco00640, 1/1 pathways.. Info: Downloading png files for eco00640, 1/1 pathways.. Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes Info: Writing image file eco00640.eco.kegg.png Loading required namespace: org.EcK12.eg.db Failed with error: ‘there is no package called ‘org.EcK12.eg.db’’ Error: processing vignette 'pathview.Rnw' failed with diagnostics: chunk 34 (label = eco.dat.kegg) Error in loadNamespace(x) : there is no package called ‘BiocManager’ --- failed re-building ‘pathview.Rnw’ SUMMARY: processing the following file failed: ‘pathview.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/00check.log’ for details.