Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for Rtreemix on perceval

This page was generated on 2015-04-10 09:53:46 -0700 (Fri, 10 Apr 2015).

Package 787/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.28.0
Jasmina Bogojeska
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rtreemix
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Rtreemix
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rtreemix_1.28.0.tar.gz
StartedAt: 2015-04-10 06:05:07 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:07:19 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 131.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rtreemix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rtreemix_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rtreemix.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.28.0’
* 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 ... [40s/45s] 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
.plott1: no visible binding for global variable ‘drawAgNode’
.plott1: no visible global function definition for ‘upRight’
.plott1: no visible global function definition for ‘boundBox’
.plott1: no visible global function definition for ‘getX’
.plott1: no visible global function definition for ‘getY’
.plott1: no visible global function definition for ‘getDefaultAttrs’
.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
  ‘labelFontsize’
.plott1: no visible global function definition for ‘AgEdge’
.plott2: no visible global function definition for ‘getDefaultAttrs’
.plott2: no visible global function definition for ‘removedEdges’
.plott2: no visible global function definition for ‘agopen’
* 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
File ‘Rtreemix/libs/Rtreemix.so’:
  Found ‘__ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘Rtreemix.o’, ‘cfunctions.o’, ‘kmeans.o’,
      ‘max_weight_branch.o’, ‘mtree.o’, ‘mtreemix.o’, ‘replaceleda.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘cfunctions.o’, ‘mtree.o’, ‘mtreemix.o’, ‘replaceleda.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘Rtreemix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.

Rtreemix.Rcheck/00install.out:

* installing *source* package ‘Rtreemix’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rtreemix.cc -o Rtreemix.o
Rtreemix.cc: In function ‘SEXPREC* R_fit(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Rtreemix.cc:596: warning: value computed is not used
Rtreemix.cc: In function ‘SEXPREC* R_fit1(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Rtreemix.cc:938: warning: value computed is not used
Rtreemix.cc: In function ‘SEXPREC* R_fit0(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Rtreemix.cc:1281: warning: value computed is not used
Rtreemix.cc: In function ‘SEXPREC* R_bootstrap(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Rtreemix.cc:1728: warning: value computed is not used
Rtreemix.cc: In function ‘SEXPREC* R_random(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
Rtreemix.cc:2629: warning: value computed is not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rtreemix_patch.cc -o Rtreemix_patch.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c WrapGraph.cc -o WrapGraph.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cfunctions.cc -o cfunctions.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c kmeans.cc -o kmeans.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c max_weight_branch.cc -o max_weight_branch.o
max_weight_branch.cc: In function ‘void DOT(replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, char*)’:
max_weight_branch.cc:97: warning: value computed is not used
max_weight_branch.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > max_weight_subgraph_indeg_le_1(replaceleda::graph&)’:
max_weight_branch.cc:142: warning: value computed is not used
max_weight_branch.cc: In function ‘void contract_all_cycles(replaceleda::graph&, int, replaceleda::array<replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > >, replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&)’:
max_weight_branch.cc:341: warning: value computed is not used
max_weight_branch.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > MAX_WEIGHT_BRANCHING(replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >&, replaceleda::edge_array<double>&)’:
max_weight_branch.cc:432: warning: value computed is not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mtree.cc -o mtree.o
mtree.cc: In function ‘void mgraph_init(replaceleda::array<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >&, replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >&, replaceleda::edge_array<double>&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&)’:
mtree.cc:185: warning: value computed is not used
mtree.cc:186: warning: value computed is not used
mtree.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > mtree_bfs(replaceleda::graph&, replaceleda::node&)’:
mtree.cc:272: warning: value computed is not used
mtree.cc: In function ‘double mtree_like(replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&)’:
mtree.cc:321: warning: value computed is not used
mtree.cc: In function ‘replaceleda::integer_vector mtree_draw(int, replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, int>&)’:
mtree.cc:444: warning: value computed is not used
mtree.cc: In function ‘void mtree_directed(replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, double, double)’:
mtree.cc:784: warning: value computed is not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mtreemix.cc -o mtreemix.o
mtreemix.cc: In function ‘double mtree_state(replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, int>&, replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&)’:
mtreemix.cc:1035: warning: value computed is not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c replaceleda.cc -o replaceleda.o
replaceleda.cc: In function ‘bool replaceleda::Is_Acyclic(replaceleda::graph&, replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> >&)’:
replaceleda.cc:81: warning: value computed is not used
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)’:
replaceleda.cc:128: warning: value computed is not used
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&, replaceleda::graph&)’:
replaceleda.cc:149: warning: value computed is not used
replaceleda.cc: In function ‘std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)’:
replaceleda.cc:352: warning: value computed is not used
replaceleda.cc: In function ‘void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)’:
replaceleda.cc:373: warning: value computed is not used
llvm-g++-4.2 -arch x86_64 -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 -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 /Users/biocbuild/bbs-3.0-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘Rtreemix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rtreemix)

Rtreemix.Rcheck/Rtreemix-Ex.timings:

nameusersystemelapsed
L1.dist0.0020.0000.003
L2.norm0.0010.0000.001
Pval.dist0.0030.0010.004
RtreemixData-class0.0490.0050.054
RtreemixGPS-class0.0010.0000.002
RtreemixModel-class1.5740.0631.650
RtreemixSim-class0.0280.0060.034
RtreemixStats-class0.0690.0200.090
bootstrap-methods0.0010.0000.001
comp.models0.0300.0010.031
comp.trees0.0190.0000.019
confIntGPS-methods0.0010.0000.001
distribution-methods0.0510.0140.064
fit-methods0.5110.0040.514
generate-methods0.0060.0010.006
get.tree.levels0.0040.0000.004
gps-methods0.0020.0010.002
hiv.data0.0060.0040.010
kullback.leibler0.0010.0000.001
likelihoods-methods0.0420.0040.046
sim-methods0.0210.0050.027
stability.sim0.0010.0000.000