############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R3CPET_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘R3CPET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘R3CPET’ version ‘1.39.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘R3CPET’ can be installed ... WARNING Found the following significant warnings: state.cpp:171:29: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] state.cpp:173:27: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 8.4Mb sub-directories of 1Mb or more: data 3.0Mb example 1.0Mb libs 2.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 Namespace in Imports field not imported from: 'BiocGenerics' All declared Imports should be used. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 .GetClusterInfo: no visible binding for global variable 'TxDb.Hsapiens.UCSC.hg19.knownGene' .GetClusterInfo: no visible global function definition for 'toTable' .GetClusterInfo: no visible binding for global variable 'org.Hs.egUCSCKG' .GetClusterInfo: no visible global function definition for 'select' .GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db' .formatDAVIDResult: no visible global function definition for 'formatGeneReportFull' .formatDAVIDResult: no visible global function definition for 'formatGeneReport' .formatDAVIDResult: no visible global function definition for 'formatList' .formatDAVIDResult: no visible global function definition for 'formatGene2Gene' .formatDAVIDResult: no visible global function definition for 'formatAnnotationReport' .get.NetworksGenes: no visible global function definition for 'annotatePeakInBatch' .plot.sota: no visible global function definition for 'legend' .plot.sota: no visible global function definition for 'lines' EnsemblToHGNC: no visible global function definition for 'useMart' EnsemblToHGNC: no visible global function definition for 'useDataset' EnsemblToHGNC: no visible global function definition for 'getBM' EntrezToHGNC: no visible global function definition for 'useMart' EntrezToHGNC: no visible global function definition for 'useDataset' EntrezToHGNC: no visible global function definition for 'getBM' RunHLDA: no visible binding for global variable '_R3CPET_RunHLDA' createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers: no visible global function definition for 'runApp' plot3CPETRes,ChromMaintainers: no visible global function definition for 'plotCurves' plot3CPETRes,ChromMaintainers: no visible global function definition for 'plotAvgCurves' Undefined global functions or variables: TxDb.Hsapiens.UCSC.hg19.knownGene _R3CPET_RunHLDA annotatePeakInBatch formatAnnotationReport formatGene2Gene formatGeneReport formatGeneReportFull formatList getBM legend lines org.Hs.eg.db org.Hs.egUCSCKG plotAvgCurves plotCurves runApp select toTable useDataset useMart Consider adding importFrom("graphics", "legend", "lines") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) ChiapetExperimentData-class.Rd:109-124: \item in \describe must have non-empty label checkRd: (5) ChiapetExperimentData-class.Rd:125-128: \item in \describe must have non-empty label checkRd: (5) ChiapetExperimentData-class.Rd:129-132: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Biogrid.Rd: igraph ChiapetExperimentData-class.Rd: GRanges, GRanges-class, igraph ChromMaintainers-class.Rd: igraph GenerateNetworks-methods.Rd: igraph HPRD.Rd: igraph cluesOrSota-class.Rd: sota clusterInteractions-methods.Rd: sota createIndexes-methods.Rd: data.table-class getRegionsInNetwork-methods.Rd: GRanges getRegionsIncluster-methods.Rd: GRanges loadPETs-methods.Rd: GRanges-class loadPPI-methods.Rd: igraph loadTFBS-methods.Rd: GRanges-class plotRes-methods.Rd: sota, igraph, pheatmap, cluster visualizeCircos-methods.Rd: GRanges, ggplot visualizeInteractions-methods.Rd: GRanges, ggplot, ggbio Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/R3CPET/libs/R3CPET.so’: Found ‘rand’, possibly from ‘rand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 WARNINGs, 9 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck/00check.log’ for details.