Package: flowMatch

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMatch_1.18.1.tar.gz

StartedAt: 2019-04-15 23:58:20 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:00:24 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 124.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowMatch.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMatch_1.18.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowMatch.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.18.1’
* 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
* 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 R 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 ... OK
* 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 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 or elapsed time > 5s
                    user system elapsed
Template-class    10.049  0.315  10.421
create.template   10.049  0.290  10.385
MetaCluster-class  8.182  0.264   8.481
flowMatch-package  8.135  0.251   8.427
template.tree      8.102  0.243   8.387
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowMatch.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowMatch
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowMatch’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c BipartiteGraph.cpp -o BipartiteGraph.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c flowMatch.cpp -o flowMatch.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/3.5/Resources/library/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
* DONE (flowMatch)

name	user	system	elapsed
Cluster-class	0.661	0.058	0.725
ClusterMatch-class	4.701	0.163	4.890
ClusteredSample-class	1.355	0.144	1.505
MetaCluster-class	8.182	0.264	8.481
Template-class	10.049	0.315	10.421
create.template	10.049	0.290	10.385
dist.cluster	0.567	0.023	0.592
dist.matrix	0.867	0.030	0.898
dist.sample	0.961	0.037	0.999
dist.template	3.608	0.116	3.733
flowMatch-package	8.135	0.251	8.427
mahalanobis.dist	0.517	0.019	0.537
match.clusters	4.607	0.154	4.773
symmetric.KL	0.615	0.026	0.643
template.tree	8.102	0.243	8.387