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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings flowMatch_1.43.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/flowMatch.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.43.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowMatch’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ClusteredSample: no visible global function definition for ‘cov’
ellipse: no visible global function definition for ‘qchisq’
ellipse: no visible global function definition for ‘lines’
limitcalc: no visible global function definition for ‘qchisq’
plot.cluster.contours: no visible global function definition for ‘par’
plot.cluster.contours: no visible global function definition for
‘plot.new’
plot.cluster.contours: no visible global function definition for
‘mtext’
template.tree,Template: no visible global function definition for
‘as.dendrogram’
Undefined global functions or variables:
as.dendrogram cov lines mtext par plot.new qchisq
Consider adding
importFrom("graphics", "lines", "mtext", "par", "plot.new")
importFrom("stats", "as.dendrogram", "cov", "qchisq")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) ClusteredSample-class.Rd:32: Lost braces
32 | \item{\code{labels } {A vector of integers (from \code{1:num.clusters}) indicating the cluster to which each point is allocated. This is usually obtained from a clustering algorithm.}}
| ^
checkRd: (-1) ClusteredSample-class.Rd:33: Lost braces
33 | \item{\code{centers } {A list of length \code{num.clusters} storing the centers of the clusters. The ith entry of the list \code{centers[[i]]} stores the center of the ith cluster. If not specified, the constructor estimates \code{centers} from \code{sample}.}}
| ^
checkRd: (-1) ClusteredSample-class.Rd:34: Lost braces
34 | \item{\code{covs } {A list of length \code{num.clusters} storing the covariance matrices of the clusters. The ith entry of the list \code{cov[[i]]} stores the covariance matrix of the ith cluster. If not specified, the constructor estimates \code{cov} from \code{sample}.}}
| ^
checkRd: (-1) ClusteredSample-class.Rd:35: Lost braces
35 | \item \code{sample } {A matrix, data frame of observations, or object of class \code{flowFrame}. Rows correspond to observations and columns correspond to variables. It must be passed to the constructor if either \code{centers} or \code{cov} is unspecified; then \code{centers} or \code{cov} is estimated from \code{sample}.}
| ^
checkRd: (-1) ClusteredSample-class.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusteredSample-class.Rd:95: Lost braces
95 | \item{\code{sample: } {A matrix, data.frame or an object of class \code{flowFrame} representing an FC sample.}}
| ^
checkRd: (-1) ClusteredSample-class.Rd:96: Lost braces
96 | \item{\code{ClusteredSample: } { An object of class \code{ClusteredSample} storing the clustering of the sample.}}
| ^
checkRd: (-1) ClusteredSample-class.Rd:97: Lost braces; missing escapes or markup?
97 | \item{\code{... } {Other usual plotting related parameters.}}
| ^
checkRd: (-1) MetaCluster-class.Rd:87: Lost braces
87 | \item{\code{mc } {An object of class \code{MetaCluster} for which the plot function is invoked.}}
| ^
checkRd: (-1) MetaCluster-class.Rd:88: Lost braces; missing escapes or markup?
88 | \item{\code{alpha } { (1-alpha)*100\% quantile of the distribution of the clusters or meta-cluster is plotted.}}
| ^
checkRd: (-1) MetaCluster-class.Rd:89: Lost braces; missing escapes or markup?
89 | \item{\code{plot.mc } { TRUE/FALSE, when TRUE the functions draws contour of the combined meta-cluster and when FALSE the function draws the contours of the individual clusters.}}
| ^
checkRd: (-1) MetaCluster-class.Rd:90: Lost braces; missing escapes or markup?
90 | \item{\code{... } {Other usual plotting related parameters.}}
| ^
checkRd: (-1) Template-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:101: Lost braces in \itemize; meant \describe ?
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS 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
create.template 6.616 0.025 6.644
Template-class 6.483 0.036 6.519
MetaCluster-class 5.454 0.019 5.475
flowMatch-package 5.437 0.009 5.447
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/flowMatch.Rcheck/00check.log’
for details.