############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMerge.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings flowMerge_2.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/flowMerge.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'flowMerge/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowMerge' version '2.55.0' * checking package namespace information ... OK * checking package dependencies ... INFO Packages which this enhances but not available for checking: 'doMC', 'multicore' Depends: includes the non-default packages: 'graph', 'feature', 'flowClust', 'Rgraphviz', 'foreach', 'snow' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'flowMerge' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... NOTE Packages in Depends field not imported from: 'foreach' 'snow' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE initPFlowMerge: no visible global function definition for 'clusterEvalQ' mergeClusters: no visible global function definition for '%dopar%' mergeClusters: no visible global function definition for 'foreach' mergeClusters: no visible global function definition for '%do%' pFlowClust : : no visible global function definition for 'clusterMap' pFlowClust: no visible global function definition for 'clusterMap' ptree: no visible global function definition for 'subGraph' ptree: no visible global function definition for 'nodes' ptree : : no visible global function definition for 'nodeDataDefaults<-' ptree : : no visible global function definition for 'nodeData<-' ptree : : no visible global function definition for 'subGraph' ptree : : no visible global function definition for 'nodeRenderInfo<-' Undefined global functions or variables: %do% %dopar% clusterEvalQ clusterMap foreach nodeData<- nodeDataDefaults<- nodeRenderInfo<- nodes subGraph * checking Rd files ... WARNING checkRd: (7) NENT.Rd:22: Invalid email address: checkRd: (7) checkForRemoteErrors.Rd:22: Invalid email address: checkRd: (7) fitPiecewiseLinreg.Rd:23: Invalid email address: checkRd: (7) flowMerge-class.Rd:53: Invalid email address: checkRd: (7) flowMerge-package.Rd:29: Invalid email address: checkRd: (7) flowMerge-package.Rd:29: Invalid email address: checkRd: (7) flowMerge-package.Rd:31: Invalid email address: checkRd: (7) flowObj-class.Rd:50: Invalid email address: checkRd: (7) flowObj-class.Rd:50: Invalid email address: checkRd: (7) flowObj.Rd:23: Invalid email address: checkRd: (7) flowObj.Rd:23: Invalid email address: checkRd: (7) initPFlowMerge.Rd:19: Invalid email address: checkRd: (7) merge.Rd:26: Invalid email address: checkRd: (7) mergeClusters.Rd:23: Invalid email address: checkRd: (7) mergeClusters2.Rd:23: Invalid email address: checkRd: (7) pFlowClust.Rd:39: Invalid email address: checkRd: (7) pFlowMerge.Rd:36: Invalid email address: checkRd: (-1) split-methods.Rd:12: Lost braces 12 | \\item{x = "flowMerge", f = "missing"}{ Split a flowMerge object into its component clusters. } | ^ checkRd: (-1) split-methods.Rd:12: Lost braces 12 | \\item{x = "flowMerge", f = "missing"}{ Split a flowMerge object into its component clusters. } | ^ checkRd: (7) updateU.Rd:21: Invalid email address: * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: flowMerge-class.Rd: flowClust-class flowMerge-package.Rd: getData flowObj-class.Rd: flowClust-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in 'vignettes' ... OK * checking examples ... 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: 1 WARNING, 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/flowMerge.Rcheck/00check.log' for details.