############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings flowStats_4.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/flowStats.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘flowStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowStats’ version ‘4.19.0’ * package encoding: UTF-8 * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘flowStats’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’ See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/flowStats.Rcheck/00install.out’ for details. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING Missing or unexported object: ‘flowWorkspace::plotGate’ Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’ Unexported objects imported by ':::' calls: ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’ ‘flowViz:::evalError’ ‘flowViz:::plotType’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .combinePriorsForChildNodes: no visible global function definition for ‘adj’ .combinePriorsForChildNodes: no visible global function definition for ‘nodeData’ .graph_parent: no visible global function definition for ‘ugraph’ .plotGPAprocess: no visible binding for global variable ‘whichS’ .plotGPAprocess: no visible binding for global variable ‘cluster’ .plotWorkFlow: no visible binding for global variable ‘cluster’ .plotWorkFlow: no visible binding for global variable ‘bogus’ .usingSVD: no visible binding for global variable ‘params’ SimulateMixture: no visible global function definition for ‘rbox’ density1d_simple: no visible binding for global variable ‘y’ normQA: no visible binding for global variable ‘group’ normQA: no visible binding for global variable ‘hasPeak’ spillover,flowSet : : no visible global function definition for ‘adist’ Undefined global functions or variables: adist adj bogus cluster group hasPeak nodeData params rbox ugraph whichS y Consider adding importFrom("utils", "adist") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'SimulateMixture.Rd': ‘flowClust’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: SimulateMixture.Rd: flowClust curv1Filter-class.Rd: multipleFilterResult, flowFrame, parameterFilter-class, concreteFilter-class, filter-class, flowSet curv2Filter-class.Rd: multipleFilterResult, flowFrame, parameterFilter-class, concreteFilter-class, filter-class, flowSet norm2Filter-class.Rd: logicalFilterResult, flowFrame, flowSet, parameterFilter-class, concreteFilter-class, filter-class, Subset spillover-flowSet.Rd: compensate, read.FCS, flowSet spillover_match-flowSet.Rd: compensate spillover_ng-flowSet.Rd: compensate 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 ... WARNING Undocumented arguments in Rd file 'ellipse.Rd' ‘cov’ ‘centre’ ‘level’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘GettingStartedWithFlowStats.Rnw’ using Sweave Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’ As part of improvements to flowWorkspace, some behavior of GatingSet objects has changed. For details, please read the section titled "The cytoframe and cytoset classes" in the package vignette: vignette("flowWorkspace-Introduction", "flowWorkspace") Loading required package: ggplot2 Loading required package: ncdfFlow Loading required package: BH Loading required package: scales error #000: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #001: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed error #002: in H5D__chunk_flush_entry(): line 3467 major: Dataset minor: Write failed error #003: in H5F_block_write(): line 161 major: Low-level I/O minor: Write failed error #004: in H5PB_write(): line 1032 major: Page Buffering minor: Write failed error #005: in H5F__accum_write(): line 824 major: Low-level I/O minor: Write failed error #006: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #007: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed error #008: in H5D__chunk_flush_entry(): line 3467 major: Dataset minor: Write failed error #009: in H5F_block_write(): line 161 major: Low-level I/O minor: Write failed error #010: in H5PB_write(): line 1032 major: Page Buffering minor: Write failed error #011: in H5F__accum_write(): line 824 major: Low-level I/O minor: Write failed error #012: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #013: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed error #014: in H5D__chunk_flush_entry(): line 3467 major: Dataset minor: Write failed error #015: in H5F_block_write(): line 161 major: Low-level I/O minor: Write failed error #016: in H5PB_write(): line 1032 major: Page Buffering minor: Write failed error #017: in H5F__accum_write(): line 824 major: Low-level I/O minor: Write failed error #018: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #019: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed error #020: in H5D__chunk_flush_entry(): line 3467 major: Dataset minor: Write failed error #021: in H5F_block_write(): line 161 major: Low-level I/O minor: Write failed error #022: in H5PB_write(): line 1032 major: Page Buffering minor: Write failed error #023: in H5F__accum_write(): line 824 major: Low-level I/O minor: Write failed error #024: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #025: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed error #026: in H5D__chunk_flush_entry(): line 3467 major: Dataset minor: Write failed error #027: in H5F_block_write(): line 161 major: Low-level I/O minor: Write failed error #028: in H5PB_write(): line 1032 major: Page Buffering minor: Write failed error #029: in H5F__accum_write(): line 824 major: Low-level I/O minor: Write failed error #030: in H5FD_write(): line 249 major: Virtual File Layer minor: Write failed error #031: in H5FD__sec2_write(): line 856 major: Low-level I/O minor: Write failed terminate called without an active exception Aborted (core dumped) * checking PDF version of manual ... ERROR Rd conversion errors: Warning in file(outfile, "wt") : cannot open file '/tmp/RtmpxT5EVj/Rd2pdf93d3f53ee4c00/Rd2.tex': No such file or directory Error in file(outfile, "wt") : cannot open the connection * DONE Status: 2 ERRORs, 4 WARNINGs, 1 NOTE See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/flowStats.Rcheck/00check.log’ for details.