Package: Rtreemix

Version: 1.49.0

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_1.49.0.tar.gz

StartedAt: 2020-01-16 08:29:56 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:32:09 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 132.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rtreemix.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:Rtreemix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rtreemix_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rtreemix.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.49.0’
* 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 use of PKG_*FLAGS in Makefiles ... NOTE
   PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.

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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/4.0/Resources/library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/00LOCK-Rtreemix/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rtreemix)

name	user	system	elapsed
L1.dist	0.002	0.000	0.003
L2.norm	0.001	0.001	0.001
Pval.dist	0.002	0.001	0.002
RtreemixData-class	0.284	0.043	0.345
RtreemixGPS-class	0.001	0.001	0.001
RtreemixModel-class	1.577	0.111	1.693
RtreemixSim-class	0.033	0.014	0.047
RtreemixStats-class	0.061	0.027	0.089
bootstrap-methods	0.000	0.000	0.001
comp.models	0.021	0.001	0.021
comp.trees	0.013	0.001	0.013
confIntGPS-methods	0.001	0.000	0.001
distribution-methods	0.110	0.032	0.142
fit-methods	0.608	0.007	0.616
generate-methods	0.003	0.001	0.003
get.tree.levels	0.002	0.000	0.002
gps-methods	0.001	0.000	0.001
hiv.data	0.007	0.006	0.012
kullback.leibler	0.000	0.000	0.001
likelihoods-methods	0.042	0.008	0.049
sim-methods	0.049	0.008	0.056
stability.sim	0.000	0.000	0.001