##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMatch_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.40.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... 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 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
create.template    16.986  0.304  20.219
Template-class     16.467  0.311  19.521
flowMatch-package  14.289  0.219  16.978
MetaCluster-class  13.918  0.224  15.813
template.tree      13.568  0.169  15.404
ClusterMatch-class  7.773  0.117   8.784
match.clusters      7.643  0.090   8.926
dist.template       6.335  0.081   7.257
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowMatch
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘flowMatch’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BipartiteGraph.cpp -o BipartiteGraph.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o
MinWghtEdgCoverBipartite.cpp:487:10: warning: variable 'delta_cx_cy' set but not used [-Wunused-but-set-variable]
                                        int delta_cx_cy  = 0;
                                            ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c flowMatch.cpp -o flowMatch.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-flowMatch/00new/flowMatch/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowMatch)