############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CAMERA_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CAMERA.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 ‘CAMERA/DESCRIPTION’ ... OK * this is package ‘CAMERA’ version ‘1.56.0’ * 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: .travis.yml 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 ‘CAMERA’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: mzML 1.7Mb quantiles 3.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘xcms’ 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 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 ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘annotateGrp’ ‘combineHypothese’ ‘fastMatch’ ‘naOmit’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("getEIC", ..., PACKAGE = "xcms") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE File ‘CAMERA/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. annotateGrp: no visible global function definition for ‘na.omit’ annotateGrpMPI2: no visible binding for global variable ‘papply_commondata’ cleanParallel: no visible global function definition for ‘mpi.close.Rslaves’ cleanParallel: no visible global function definition for ‘stopCluster’ compoundQuantiles: no visible global function definition for ‘tail’ createHypothese: no visible global function definition for ‘cutree’ createHypothese: no visible global function definition for ‘hclust’ createHypothese: no visible global function definition for ‘dist’ extractfragments: no visible global function definition for ‘median’ fast_corr: no visible global function definition for ‘pt’ findIsotopesForPS: no visible binding for global variable ‘tableMM48’ findKendrickMasses: no visible global function definition for ‘rainbow’ findKendrickMasses : : no visible global function definition for ‘lines’ findNeutralLoss: no visible global function definition for ‘dist’ findNeutralLossSpecs : : no visible global function definition for ‘dist’ fragments2metfrag : : no visible global function definition for ‘write.table’ fragments2metfusion : : no visible binding for global variable ‘object’ fragments2metfusion : : no visible global function definition for ‘write.table’ getIsotopeCluster : : no visible global function definition for ‘na.omit’ xsAnnotate: no visible global function definition for ‘mpi.comm.size’ xsAnnotate: no visible global function definition for ‘mpi.spawn.Rslaves’ xsAnnotate: no visible global function definition for ‘makeCluster’ xsAnnotate: no visible binding for global variable ‘graphMethod’ findAdducts,xsAnnotate: no visible global function definition for ‘mpi.comm.size’ findAdducts,xsAnnotate: no visible global function definition for ‘xcmsPapply’ findIsotopesWithValidation,xsAnnotate : : no visible global function definition for ‘median’ getReducedPeaklist,xsAnnotate : : : no visible global function definition for ‘median’ getReducedPeaklist,xsAnnotate : : no visible global function definition for ‘prcomp’ getReducedPeaklist,xsAnnotate : : no visible global function definition for ‘na.omit’ groupComplete,xsAnnotate: no visible global function definition for ‘dist’ groupComplete,xsAnnotate: no visible global function definition for ‘cutree’ groupComplete,xsAnnotate: no visible global function definition for ‘hclust’ groupDen,xsAnnotate: no visible global function definition for ‘density’ groupFWHM,xsAnnotate : : no visible global function definition for ‘na.omit’ plotEICs,xsAnnotate: no visible global function definition for ‘rainbow’ plotEICs,xsAnnotate: no visible global function definition for ‘na.omit’ plotPeakEICs,xsAnnotate : : no visible binding for global variable ‘pc’ plotPeakEICs,xsAnnotate: no visible binding for global variable ‘pspec’ plotPeakEICs,xsAnnotate: no visible global function definition for ‘rainbow’ plotPeakEICs,xsAnnotate: no visible global function definition for ‘na.omit’ plotPsSpectrum,xsAnnotate: no visible global function definition for ‘median’ plotPsSpectrum,xsAnnotate: no visible global function definition for ‘na.omit’ Undefined global functions or variables: cutree density dist graphMethod hclust lines makeCluster median mpi.close.Rslaves mpi.comm.size mpi.spawn.Rslaves na.omit object papply_commondata pc prcomp pspec pt rainbow stopCluster tableMM48 tail write.table xcmsPapply Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "lines") importFrom("stats", "cutree", "density", "dist", "hclust", "median", "na.omit", "prcomp", "pt") importFrom("utils", "tail", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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 getIsotopeCluster 22.091 6.216 10.697 groupCorr-methods 19.049 3.204 19.239 calcCaS-methods 10.295 2.132 1.705 annotateDiffreport 9.077 2.052 6.716 getAllPeakEICs-methods 5.557 2.912 4.801 annotate-methods 6.208 0.875 7.024 findIsotopesWithValidation-methods 4.212 2.327 3.161 getReducedPeaklist-methods 3.732 2.037 5.685 * 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 ... ‘CAMERA.Rnw’... OK ‘IsotopeDetectionVignette.Rnw’ using ‘UTF-8’... OK ‘compoundQuantilesVignette.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 8 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/CAMERA.Rcheck/00check.log’ for details.