Package: flowPeaks

Version: 1.22.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowPeaks_1.22.0.tar.gz

StartedAt: 2018-04-11 23:30:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:31:21 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 28.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowPeaks.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowPeaks_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/flowPeaks.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPeaks/DESCRIPTION’ ... OK
* this is package ‘flowPeaks’ version ‘1.22.0’
* 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 ‘flowPeaks’ 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 ... NOTE
Call with DUP:
   .C("Rpack_kmeans", as.double(t(data.matrix(x))), as.integer(n), 
       as.integer(p), as.integer(K), cluster = integer(n), m = double(K * 
           p), nc = integer(K), S = double(K * p * p), Nb = integer(K * 
           K), twss = double(1), as.double(stime), DUP = FALSE, 
       PACKAGE = "flowPeaks")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
getS0K : <anonymous>: no visible global function definition for
  ‘nclass.FD’
getS0K: no visible global function definition for ‘median’
plot.flowPeaks: no visible global function definition for ‘hist’
plot.flowPeaks: no visible global function definition for ‘points’
plot.flowPeaks: no visible global function definition for ‘plot’
plot.flowPeaks: no visible global function definition for ‘text’
plot.flowPeaks: no visible global function definition for ‘par’
plot.flowPeaks: no visible global function definition for ‘segments’
traditional.kmeans: no visible global function definition for ‘kmeans’
traditional.kmeans: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist kmeans median nclass.FD par plot points segments text var
Consider adding
  importFrom("grDevices", "nclass.FD")
  importFrom("graphics", "hist", "par", "plot", "points", "segments",
             "text")
  importFrom("stats", "kmeans", "median", "var")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/flowPeaks.Rcheck/00check.log’
for details.

* installing *source* package ‘flowPeaks’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c Rpack.cpp -o Rpack.o
Rpack.cpp: In function ‘void Rpack_relevel(int*, int*, int*, int*, int*, int*)’:
Rpack.cpp:141:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if(levels.size()<(i+1)){
                  ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c Rregistrate.cpp -o Rregistrate.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
VoronoiDiagramGenerator.cpp: In member function ‘void VoronoiDiagramGenerator::out_site(Site*)’:
VoronoiDiagramGenerator.cpp:803:6: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘˜’ [-Wparentheses]
  if(!triangulate & plot & !debug)
      ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c flowPeaks.cpp -o flowPeaks.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c func_collect.cpp -o func_collect.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c func_collect_supp.cpp -o func_collect_supp.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c gvector_gmatrix.cpp -o gvector_gmatrix.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c kd_tree.cpp -o kd_tree.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags`  -fpic  -g -O2  -Wall -c kmns.cpp -o kmns.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o flowPeaks.so Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/flowPeaks.Rcheck/flowPeaks/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowPeaks)

name	user	system	elapsed
flowPeaks	3.096	0.048	3.191