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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings flowPeaks_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/flowPeaks.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘flowPeaks/DESCRIPTION’ ... OK
* this is package ‘flowPeaks’ version ‘1.45.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ‘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 points segments text var
Consider adding
  importFrom("grDevices", "nclass.FD")
  importFrom("graphics", "hist", "par", "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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/flowPeaks/libs/flowPeaks.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
flowPeaks 2.635  0.067   5.421
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘flowPeaks-guide.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/flowPeaks.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flowPeaks
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘flowPeaks’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-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:141:25: warning: comparison of integer expressions of different signedness: ‘std::map<int, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  141 |         if(levels.size()<(i+1)){
      |            ~~~~~~~~~~~~~^~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c Rregistrate.cpp -o Rregistrate.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-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:803:12: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
  803 |         if(!triangulate & plot & !debug)
      |            ^~~~~~~~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c flowPeaks.cpp -o flowPeaks.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c func_collect.cpp -o func_collect.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-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++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c gvector_gmatrix.cpp -o gvector_gmatrix.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c kd_tree.cpp -o kd_tree.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags`  -fPIC  -g -O2  -Wall  -c kmns.cpp -o kmns.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-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/aarch64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowPeaks/00new/flowPeaks/libs
** R
** data
** inst
** 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 (flowPeaks)