Tilo Buschmann
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DNABarcodes |
| Branch: RELEASE_3_8 |
| Last Commit: fc16fa4 |
| Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:35 -0400 (Tue, 16 Apr 2019).
| Package 425/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DNABarcodes 1.12.0 Tilo Buschmann
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DNABarcodes |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DNABarcodes_1.12.0.tar.gz |
| StartedAt: 2019-04-15 23:33:56 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:34:43 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 47.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNABarcodes.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DNABarcodes_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DNABarcodes.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
libs 6.6Mb
* 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 17.228 0.16 3.474
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/DNABarcodes.Rcheck/00check.log’
for details.
DNABarcodes.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DNABarcodes
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DNABarcodes’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DNABarcodes_init.c -o DNABarcodes_init.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c analyse_barcodes.cpp -o analyse_barcodes.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c barcode_set_distances.cpp -o barcode_set_distances.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c cachedistance.cpp -o cachedistance.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c chromosome.cpp -o chromosome.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from chromosome.h:8,
from chromosome.cpp:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c code_falsification.cpp -o code_falsification.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from chromosome.h:8,
from code_falsification.cpp:11:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c conway.cpp -o conway.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_distance_func.cpp -o create_distance_func.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
from create_dnabarcodes.cpp:11:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c create_pool.cpp -o create_pool.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c demultiplex.cpp -o demultiplex.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c distance_for_R.cpp -o distance_for_R.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c genericchromosome.cpp -o genericchromosome.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c greedyevolution.cpp -o greedyevolution.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c hammingdistance.cpp -o hammingdistance.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c helpers.cpp -o helpers.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c levenshteindistance.cpp -o levenshteindistance.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c phaseshiftdist.cpp -o phaseshiftdist.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequence.cpp -o sequence.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sequencepool.cpp -o sequencepool.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/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 -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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)
DNABarcodes.Rcheck/DNABarcodes-Ex.timings
| name | user | system | elapsed | |
| DNABarcodes-package | 4.948 | 0.052 | 0.998 | |
| analyse.barcodes | 0.012 | 0.008 | 0.022 | |
| barcode.set.distances | 0.020 | 0.024 | 0.056 | |
| create.dnabarcodes | 17.228 | 0.160 | 3.474 | |
| create.pool | 0.012 | 0.056 | 0.098 | |
| demultiplex | 1.664 | 0.040 | 1.708 | |
| distance | 0 | 0 | 0 | |