Kieran O'Neill
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: RELEASE_3_8 |
| Last Commit: 750bd27 |
| Last Changed Date: 2019-01-04 13:26:34 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:18 -0400 (Tue, 16 Apr 2019).
| Package 322/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.10.1 Kieran O'Neill
| 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: contiBAIT |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.10.1.tar.gz |
| StartedAt: 2019-04-15 23:12:33 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:18:02 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 329.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: contiBAIT.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/contiBAIT.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.10.1’
* 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 ‘contiBAIT’ 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
ideogramPlot.func: no visible binding for global variable ‘w’
ideogramPlot.func: no visible binding for global variable ‘w2’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
orderContigsGreedy: no visible global function definition for
‘makeCluster’
orderContigsGreedy: no visible global function definition for
‘clusterCall’
orderContigsGreedy: no visible global function definition for
‘stopCluster’
strandSeqFreqTable: no visible global function definition for
‘queryHits’
strandSeqFreqTable: no visible global function definition for
‘subjectHits’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w2’
Undefined global functions or variables:
clusterCall makeCluster queryHits stopCluster subjectHits w w2
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
contiBAIT 5.456 0.113 5.644
* 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-3.8-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.
contiBAIT.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL contiBAIT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘contiBAIT’ ...
** 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 -fPIC -Wall -g -O2 -c buildLinkageGroups.cpp -o buildLinkageGroups.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 -fPIC -Wall -g -O2 -c computeSim.cpp -o computeSim.o
In file included from computeSim.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:47:
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 -fPIC -Wall -g -O2 -c orderContigsGreedy.cpp -o orderContigsGreedy.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 contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/contiBAIT/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 (contiBAIT)
contiBAIT.Rcheck/contiBAIT-Ex.timings
| name | user | system | elapsed | |
| BAIT | 0.000 | 0.001 | 0.000 | |
| ContigOrdering | 0.002 | 0.000 | 0.002 | |
| LibraryGroupList | 0.011 | 0.000 | 0.012 | |
| LinkageGroupList | 0.001 | 0.000 | 0.001 | |
| StrandFreqMatrix | 0.029 | 0.009 | 0.038 | |
| StrandReadMatrix | 0.015 | 0.003 | 0.018 | |
| StrandStateMatrix | 0.002 | 0.000 | 0.003 | |
| barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.501 | 0.058 | 0.562 | |
| clusterContigs-StrandStateMatrix-method | 0.031 | 0.006 | 0.037 | |
| contiBAIT | 5.456 | 0.113 | 5.644 | |
| findSimilarLibraries | 0.365 | 0.027 | 0.395 | |
| ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 2.438 | 0.032 | 2.485 | |
| makeBoxPlot | 0.034 | 0.005 | 0.038 | |
| makeChrTable | 0.807 | 0.004 | 0.816 | |
| orderAllLinkageGroups | 1.457 | 0.026 | 1.496 | |
| plotContigOrder | 0.397 | 0.010 | 0.414 | |
| plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.159 | 0.005 | 0.169 | |
| plotWCdistribution-StrandFreqMatrix-method | 0.082 | 0.002 | 0.085 | |
| preprocessStrandTable-StrandFreqMatrix-method | 0.257 | 0.003 | 0.262 | |
| reorientAndMergeLGs | 0.116 | 0.003 | 0.119 | |
| strandSeqFreqTable | 4.236 | 0.031 | 4.306 | |
| thoroughBed | 0.025 | 0.002 | 0.027 | |
| writeBed | 0 | 0 | 0 | |