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CHECK report for flowPeaks on celaya2

This page was generated on 2019-10-16 12:50:12 -0400 (Wed, 16 Oct 2019).

Package 572/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPeaks 1.30.0
Yongchao Ge
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/flowPeaks
Branch: RELEASE_3_9
Last Commit: 2f5c540
Last Changed Date: 2019-05-02 11:53:36 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowPeaks
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPeaks_1.30.0.tar.gz
StartedAt: 2019-10-16 02:52:33 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:53:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPeaks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPeaks_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowPeaks.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPeaks/DESCRIPTION’ ... OK
* this is package ‘flowPeaks’ version ‘1.30.0’
* 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 : : 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowPeaks/libs/flowPeaks.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_printf’, possibly from ‘printf’ (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. 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 sizes of PDF files under ‘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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowPeaks.Rcheck/00check.log’
for details.



Installation output

flowPeaks.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowPeaks
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowPeaks’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c Rpack.cpp -o Rpack.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c Rregistrate.cpp -o Rregistrate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
VoronoiDiagramGenerator.cpp:803:5: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
        if(!triangulate & plot & !debug)
           ^            ~
VoronoiDiagramGenerator.cpp:803:5: note: add parentheses after the '!' to evaluate the bitwise operator first
        if(!triangulate & plot & !debug)
           ^
            (                 )
VoronoiDiagramGenerator.cpp:803:5: note: add parentheses around left hand side expression to silence this warning
        if(!triangulate & plot & !debug)
           ^
           (           )
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c flowPeaks.cpp -o flowPeaks.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c func_collect.cpp -o func_collect.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c func_collect_supp.cpp -o func_collect_supp.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c gvector_gmatrix.cpp -o gvector_gmatrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c kd_tree.cpp -o kd_tree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `gsl-config --cflags`  -fPIC  -Wall -g -O2  -c kmns.cpp -o kmns.o
clang++ -std=gnu++11 -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 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/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output


Example timings

flowPeaks.Rcheck/flowPeaks-Ex.timings

nameusersystemelapsed
flowPeaks3.2550.2733.611