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CHECK report for DNABarcodes on merida2

This page was generated on 2018-10-17 08:55:21 -0400 (Wed, 17 Oct 2018).

Package 401/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNABarcodes 1.10.0
Tilo Buschmann
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/DNABarcodes
Branch: RELEASE_3_7
Last Commit: 9f40368
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DNABarcodes
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNABarcodes_1.10.0.tar.gz
StartedAt: 2018-10-16 21:01:23 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:02:22 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 59.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DNABarcodes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNABarcodes_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DNABarcodes.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodes’ version ‘1.10.0’
* 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 ‘DNABarcodes’ 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
analyse.barcodes : <anonymous>: no visible global function definition
  for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
create.dnabarcodes 9.079  0.927   1.606
* 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-3.7-bioc/meat/DNABarcodes.Rcheck/00check.log’
for details.



Installation output

DNABarcodes.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DNABarcodes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DNABarcodes’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c analyse_barcodes.cpp -o analyse_barcodes.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c barcode_set_distances.cpp -o barcode_set_distances.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c cachedistance.cpp -o cachedistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c chromosome.cpp -o chromosome.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c code_falsification.cpp -o code_falsification.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c conway.cpp -o conway.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_distance_func.cpp -o create_distance_func.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from create_dnabarcodes.cpp:26:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/graph/adjacency_list.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_set.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_set.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_pool.cpp -o create_pool.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c demultiplex.cpp -o demultiplex.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c distance_for_R.cpp -o distance_for_R.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c genericchromosome.cpp -o genericchromosome.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c greedyevolution.cpp -o greedyevolution.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c hammingdistance.cpp -o hammingdistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c helpers.cpp -o helpers.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c levenshteindistance.cpp -o levenshteindistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from maxclique_pattabiraman_heuristic.cpp:6:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/graph/adjacency_list.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_set.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_set.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c phaseshiftdist.cpp -o phaseshiftdist.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequence.cpp -o sequence.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequencepool.cpp -o sequencepool.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 DNABarcodes.so DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/DNABarcodes/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
* DONE (DNABarcodes)

Tests output


Example timings

DNABarcodes.Rcheck/DNABarcodes-Ex.timings

nameusersystemelapsed
DNABarcodes-package1.7620.1500.455
analyse.barcodes0.4360.0090.040
barcode.set.distances0.8170.0140.073
create.dnabarcodes9.0790.9271.606
create.pool0.2590.2580.073
demultiplex2.6320.5922.787
distance0.0010.0000.001