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CHECK report for Rtreemix on merida2

This page was generated on 2019-04-09 13:24:04 -0400 (Tue, 09 Apr 2019).

Package 1409/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.45.0
Jasmina Bogojeska
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Rtreemix
Branch: master
Last Commit: d919d44
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: Rtreemix
Version: 1.45.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rtreemix_1.45.0.tar.gz
StartedAt: 2019-04-09 03:30:18 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:31:51 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 93.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Rtreemix.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rtreemix_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rtreemix.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rtreemix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rtreemix’ version ‘1.45.0’
* 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 ‘Rtreemix’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
.plott1: no visible binding for global variable ‘drawAgNode’
.plott1: no visible global function definition for ‘plot.new’
.plott1: no visible global function definition for ‘par’
.plott1: no visible global function definition for ‘upRight’
.plott1: no visible global function definition for ‘boundBox’
.plott1: no visible global function definition for ‘plot.window’
.plott1: no visible global function definition for ‘getX’
.plott1: no visible global function definition for ‘getY’
.plott1: no visible global function definition for ‘box’
.plott1: no visible global function definition for ‘xy.coords’
.plott1: no visible global function definition for ‘getDefaultAttrs’
.plott1: no visible global function definition for ‘plot.xy’
.plott1: no visible global function definition for ‘title’
.plott1: no visible global function definition for ‘AgNode’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeRW’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeLW’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeHeight’
.plott1 : <anonymous>: no visible global function definition for
  ‘labelText’
.plott1 : <anonymous>: no visible global function definition for
  ‘txtLabel’
.plott1 : <anonymous>: no visible global function definition for
  ‘strwidth’
.plott1 : <anonymous>: no visible global function definition for
  ‘strheight’
.plott1 : <anonymous>: no visible global function definition for
  ‘labelFontsize’
.plott1: no visible global function definition for ‘AgEdge’
.plott1: no visible binding for global variable ‘lines’
.plott2: no visible global function definition for ‘getDefaultAttrs’
.plott2: no visible global function definition for ‘removedEdges’
.plott2: no visible global function definition for ‘agopen’
plot,RtreemixModel-missing: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  AgEdge AgNode agopen boundBox box drawAgNode getDefaultAttrs
  getNodeHeight getNodeLW getNodeRW getX getY labelFontsize labelText
  lines par plot.new plot.window plot.xy removedEdges strheight
  strwidth title txtLabel upRight xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("graphics", "box", "lines", "par", "plot.new",
             "plot.window", "plot.xy", "strheight", "strwidth", "title")
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/Rtreemix/libs/Rtreemix.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (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/Rtreemix.Rcheck/00check.log’
for details.



Installation output

Rtreemix.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rtreemix
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Rtreemix’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtreemix.cc -o Rtreemix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtreemix_patch.cc -o Rtreemix_patch.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c WrapGraph.cc -o WrapGraph.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cfunctions.cc -o cfunctions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c kmeans.cc -o kmeans.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c max_weight_branch.cc -o max_weight_branch.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mtree.cc -o mtree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mtreemix.cc -o mtreemix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c replaceleda.cc -o replaceleda.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 Rtreemix.so Rtreemix.o Rtreemix_patch.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rtreemix/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 (Rtreemix)

Tests output


Example timings

Rtreemix.Rcheck/Rtreemix-Ex.timings

nameusersystemelapsed
L1.dist0.0010.0000.001
L2.norm0.0010.0000.001
Pval.dist0.0010.0010.001
RtreemixData-class0.1690.0250.196
RtreemixGPS-class0.0000.0010.001
RtreemixModel-class1.2490.0701.334
RtreemixSim-class0.0230.0070.030
RtreemixStats-class0.0620.0200.083
bootstrap-methods000
comp.models0.0240.0000.024
comp.trees0.0130.0000.013
confIntGPS-methods0.0000.0000.001
distribution-methods0.0740.0130.087
fit-methods2.9230.0162.962
generate-methods0.0040.0000.004
get.tree.levels0.0020.0000.003
gps-methods0.0010.0000.000
hiv.data0.0060.0040.010
kullback.leibler0.0000.0000.001
likelihoods-methods0.0380.0040.042
sim-methods0.0440.0040.048
stability.sim0.0000.0000.001