############################################################################## ############################################################################## ### ### 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_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAMERA/DESCRIPTION’ ... OK * this is package ‘CAMERA’ version ‘1.62.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ... WARNING Found the following significant warnings: fastMatch.c:65:81: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck/00install.out’ for details. * 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 8.8Mb 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 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether 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 ... ERROR Running examples in ‘CAMERA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: annotateDiffreport > ### Title: Automatic deconvolution/annotation of LC/ESI-MS data > ### Aliases: annotateDiffreport annotateDiffreport,xsAnnotate-methods > ### Keywords: methods > > ### ** Examples > > #Multiple sample > library(CAMERA) > library(faahKO) > xs.grp <- group(faahko) > xs.fill <- fillPeaks(xs.grp) objc[9118]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[9118]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment Calls: fillPeaks ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add Execution halted objc[9119]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[9119]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: ERROR in /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CAMERA/unitTests/test_annotateDiffreport.R: Error while sourcing /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CAMERA/unitTests/test_annotateDiffreport.R : Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment Test files with failing tests test_annotateDiffreport.R /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CAMERA/unitTests/test_annotateDiffreport.R Error in BiocGenerics:::testPackage("CAMERA") : unit tests failed for package CAMERA In addition: Warning message: In parallel::mccollect(wait = TRUE) : 3 parallel jobs did not deliver results Execution halted * 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: 2 ERRORs, 1 WARNING, 9 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAMERA.Rcheck/00check.log’ for details.