* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EnrichDO.Rcheck’ * using R Under development (unstable) (2024-09-13 r87144) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘EnrichDO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EnrichDO’ version ‘0.99.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Haixiu Yang ’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE File 'LICENSE': # MIT License Copyright (c) 2024 EnrichDO authors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Possibly misspelled words in DESCRIPTION: EnrichDO (15:5) The Title field should be in title case. Current version is: ‘Disease ontology annotation and enrichment analysis’ In title case that is: ‘Disease Ontology Annotation and Enrichment Analysis’ The Description field should not start with the package name, 'This package' or similar. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘EnrichDO’ can be installed ... [17s/17s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... [5s/5s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [20s/20s] NOTE TermStruct: no visible binding for global variable ‘doterms’ TermStruct: no visible binding for global variable ‘.EnrichDOenv’ TermStruct: no visible binding for global variable ‘DOID’ TermStruct: no visible binding for global variable ‘parent.arr’ TermStruct: no visible binding for global variable ‘gene.len’ TermStruct: no visible binding for global variable ‘geneRatio’ TermStruct: no visible binding for global variable ‘p’ Test: no visible binding for global variable ‘dotermgenes’ binomTest: no visible binding for global variable ‘dotermgenes’ computeTermSig: no visible binding for global variable ‘.EnrichDOenv’ computeTermSig : : no visible binding for global variable ‘.EnrichDOenv’ doEnrich: no visible binding for global variable ‘dotermgenes’ doEnrich: no visible binding for global variable ‘.EnrichDOenv’ doEnrich: no visible binding for global variable ‘gene.arr’ doEnrich: no visible binding for global variable ‘cg.arr’ doEnrich: no visible binding for global variable ‘cg.len’ doEnrich: no visible binding for global variable ‘gene.len’ doEnrich: no visible binding for global variable ‘level’ doEnrich: no visible binding for global variable ‘DOID’ doEnrich: no visible binding for global variable ‘p’ drawBarGraph: no visible binding for global variable ‘p’ drawBarGraph: no visible binding for global variable ‘DOID’ drawBarGraph: no visible binding for global variable ‘DOTerm’ drawBarGraph: no visible binding for global variable ‘cg.len’ drawBarGraph: no visible binding for global variable ‘ig.len’ drawBarGraph: no visible global function definition for ‘na.omit’ drawBarGraph: no visible global function definition for ‘reorder’ drawBarGraph: no visible binding for global variable ‘DO’ drawBarGraph: no visible binding for global variable ‘log10p’ drawBarGraph: no visible binding for global variable ‘geneRatio’ drawGraphViz: no visible binding for global variable ‘p’ drawGraphViz: no visible binding for global variable ‘DOID’ drawGraphViz: no visible binding for global variable ‘DOTerm’ drawGraphViz: no visible binding for global variable ‘parent.arr’ drawGraphViz: no visible binding for global variable ‘cg.len’ drawGraphViz: no visible binding for global variable ‘doterms’ drawGraphViz: no visible binding for global variable ‘log10p’ drawGraphViz: no visible global function definition for ‘text’ drawHeatmap: no visible binding for '<<-' assignment to ‘weightMatrix’ drawHeatmap : : no visible binding for '<<-' assignment to ‘weightMatrix’ drawHeatmap : : no visible binding for global variable ‘weightMatrix’ drawHeatmap: no visible binding for global variable ‘weightMatrix’ drawPointGraph: no visible binding for global variable ‘p’ drawPointGraph: no visible binding for global variable ‘DOID’ drawPointGraph: no visible binding for global variable ‘DOTerm’ drawPointGraph: no visible binding for global variable ‘cg.len’ drawPointGraph: no visible binding for global variable ‘gene.len’ drawPointGraph: no visible binding for global variable ‘ig.len’ drawPointGraph: no visible global function definition for ‘na.omit’ drawPointGraph: no visible binding for global variable ‘geneRatio’ drawPointGraph: no visible global function definition for ‘reorder’ drawPointGraph: no visible binding for global variable ‘DO’ drawPointGraph: no visible binding for global variable ‘log10p’ getAncestors: no visible binding for global variable ‘.EnrichDOenv’ getAncestors: no visible global function definition for ‘str’ init: no visible binding for global variable ‘doterms’ init: no visible binding for global variable ‘gene.len’ init: no visible binding for global variable ‘gene.arr’ init: no visible binding for global variable ‘weight.arr’ writeDoTerms: no visible binding for global variable ‘gene.arr’ writeDoTerms: no visible binding for global variable ‘parent.arr’ writeDoTerms: no visible binding for global variable ‘child.arr’ writeDoTerms: no visible binding for global variable ‘DOID’ writeDoTerms: no visible binding for global variable ‘DOTerm’ writeDoTerms: no visible binding for global variable ‘level’ writeDoTerms: no visible binding for global variable ‘genes’ writeDoTerms: no visible binding for global variable ‘parents’ writeDoTerms: no visible binding for global variable ‘children’ writeDoTerms: no visible binding for global variable ‘gene.len’ writeDoTerms: no visible binding for global variable ‘parent.len’ writeDoTerms: no visible binding for global variable ‘child.len’ writeResult: no visible binding for global variable ‘cg.arr’ writeResult: no visible binding for global variable ‘cg.len’ writeResult: no visible binding for global variable ‘ig.len’ writeResult: no visible binding for global variable ‘gene.len’ writeResult: no visible binding for global variable ‘dotermgenes’ writeResult: no visible binding for global variable ‘DOID’ writeResult: no visible binding for global variable ‘DOTerm’ writeResult: no visible binding for global variable ‘p’ writeResult: no visible binding for global variable ‘geneRatio’ writeResult: no visible binding for global variable ‘bgRatio’ writeResult: no visible binding for global variable ‘cg’ show,EnrichResult: no visible binding for global variable ‘cg.len’ show,EnrichResult: no visible binding for global variable ‘gene.len’ show,EnrichResult: no visible binding for global variable ‘p’ Undefined global functions or variables: .EnrichDOenv DO DOID DOTerm bgRatio cg cg.arr cg.len child.arr child.len children dotermgenes doterms gene.arr gene.len geneRatio genes ig.len level log10p na.omit p parent.arr parent.len parents reorder str text weight.arr weightMatrix Consider adding importFrom("graphics", "text") importFrom("stats", "na.omit", "reorder") importFrom("utils", "str") to your NAMESPACE file. Found the following assignments to the global environment: File ‘EnrichDO/R/EnrichDO_algorithm.R’: assign("enrich", enrich, pos = 1) File ‘EnrichDO/R/EnrichDO_visualization.R’: assign("enrich", enrich0, envir = .GlobalEnv) assign("weightMatrix", NULL, pos = 1) * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [112s/112s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed doEnrich 47.391 0.467 47.875 drawPointGraph 11.112 0.036 11.148 drawHeatmap 10.732 0.060 10.792 drawBarGraph 10.642 0.080 10.723 writeResult 10.674 0.016 10.682 drawGraphViz 10.294 0.024 10.320 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [106s/106s] OK Running ‘testthat.R’ [106s/106s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [0s/0s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘EnrichDO.Rmd’ using rmarkdown Error: processing vignette 'EnrichDO.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘EnrichDO.Rmd’ SUMMARY: processing the following file failed: ‘EnrichDO.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 NOTEs