Package: contiBAIT

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings contiBAIT_1.6.0.tar.gz

StartedAt: 2018-04-12 02:10:45 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:15:49 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 304.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: contiBAIT.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings contiBAIT_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 ‘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 loading without being on the library search path ... 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
clusterContigs.func : runOnce: no visible global function definition
  for ‘runif’
locateMisorients.func: no visible global function definition for
  ‘unstrand’
makeBoxPlot.func: no visible global function definition for ‘boxplot’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
mergeFlankedLGs.func: no visible binding for global variable ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘tail’
plotContigOrder.func: no visible global function definition for ‘lm’
plotLGDistances.func: no visible global function definition for
  ‘legend’
plotWCdistribution.func : <anonymous>: no visible global function
  definition for ‘hist’
plotWCdistribution.func: no visible global function definition for
  ‘rbinom’
plotWCdistribution.func: no visible global function definition for
  ‘boxplot’
plotWCdistribution.func: no visible global function definition for
  ‘lines’
plotWCdistribution.func: no visible global function definition for
  ‘text’
clusterContigs,StrandStateMatrix : runOnce: no visible global function
  definition for ‘runif’
locateMisorients,GRanges: no visible global function definition for
  ‘unstrand’
makeBoxPlot,ChrTable-LinkageGroupList: no visible global function
  definition for ‘boxplot’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix: no visible binding
  for global variable ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘tail’
plotContigOrder,ContigOrdering: no visible global function definition
  for ‘lm’
plotLGDistances,LinkageGroupList-StrandStateMatrix: no visible global
  function definition for ‘legend’
plotWCdistribution,StrandFreqMatrix : <anonymous>: no visible global
  function definition for ‘hist’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘rbinom’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘boxplot’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘lines’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘text’
show,ContigOrdering: no visible global function definition for ‘head’
show,ContigOrdering: no visible global function definition for ‘tail’
show,LibraryGroupList: no visible global function definition for ‘head’
show,LibraryGroupList: no visible global function definition for ‘tail’
show,LinkageGroupList: no visible global function definition for ‘head’
show,LinkageGroupList: no visible global function definition for ‘tail’
show,StrandStateList: no visible global function definition for ‘head’
show,StrandStateList: no visible global function definition for ‘tail’
Undefined global functions or variables:
  boxplot head hist legend lines lm queryHits rbinom runif subjectHits
  tail text unstrand
Consider adding
  importFrom("graphics", "boxplot", "hist", "legend", "lines", "text")
  importFrom("stats", "lm", "rbinom", "runif")
  importFrom("utils", "head", "tail")
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'switch' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
            user system elapsed
contiBAIT 10.199  0.145  10.644
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘contiBAIT’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
In file included from orderContigsGreedy.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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++ -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 computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck/contiBAIT/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (contiBAIT)

name	user	system	elapsed
BAIT	0.000	0.000	0.001
ContigOrdering	0.002	0.000	0.002
LibraryGroupList	0.007	0.000	0.007
LinkageGroupList	0.002	0.000	0.001
OrientationFrame	0.008	0.000	0.008
StrandFreqMatrix	0.035	0.005	0.040
StrandReadMatrix	0.011	0.001	0.013
StrandStateMatrix	0.002	0.000	0.002
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method	1.247	0.009	1.275
clusterContigs-StrandStateMatrix-method	1.635	0.006	1.661
contiBAIT	10.199	0.145	10.644
findSimilarLibraries	2.774	0.042	2.869
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method	3.987	0.034	4.119
makeBoxPlot	0.034	0.003	0.039
makeChrTable	1.214	0.006	1.299
orderAllLinkageGroups	1.033	0.021	1.155
plotContigOrder	0.858	0.008	0.882
plotLGDistances-LinkageGroupList-StrandStateMatrix-method	1.042	0.008	1.075
plotWCdistribution-StrandFreqMatrix-method	0.072	0.003	0.076
preprocessStrandTable-StrandFreqMatrix-method	0.191	0.002	0.194
reorientAndMergeLGs	1.253	0.006	1.269
strandSeqFreqTable	3.268	0.031	3.328
thoroughBed	0.032	0.002	0.033
writeBed	0.000	0.000	0.001