############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAMERA_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/CAMERA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAMERA/DESCRIPTION’ ... OK * this is package ‘CAMERA’ version ‘1.56.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘Rmpi’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 8.7Mb sub-directories of 1Mb or more: mzML 2.7Mb quantiles 4.9Mb * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getIsotopeCluster 34.134 11.994 25.328 annotateDiffreport 29.696 9.917 17.001 groupCorr-methods 32.477 5.173 42.271 annotate-methods 10.888 2.273 16.668 getAllPeakEICs-methods 9.926 2.775 9.746 findAdducts-methods 7.773 2.473 12.710 getReducedPeaklist-methods 7.661 2.520 12.686 pspec2metfrag 7.613 2.430 12.682 getPeaklist-methods 7.555 2.397 12.653 groupFWHM-methods 6.854 2.498 12.181 groupDen-methods 6.358 2.288 11.255 findIsotopesWithValidation-methods 4.198 2.284 8.132 findIsotopes-methods 3.174 2.064 6.359 findNeutralLossSpecs 3.101 2.087 6.391 calcCaS-methods 3.766 0.345 5.146 findNeutralLoss 0.045 0.036 6.312 getpspectra 0.035 0.028 6.224 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 9 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/CAMERA.Rcheck/00check.log’ for details.