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Package 525/609HostnameOS / ArchBUILDCHECKBUILD BIN
Rtreemix 1.20.0
Jasmina Bogojeska
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Rtreemix
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: Rtreemix
Version: 1.20.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.20.0.tar.gz
StartedAt: 2013-03-25 04:43:53 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:45:52 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 118.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rtreemix.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rtreemix.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.20.0’
* 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 whether package ‘Rtreemix’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rtreemix.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 ... OK
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rtreemix.Rcheck/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 ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘cfunctions.o’, ‘kmeans.o’, ‘mtree.o’, ‘mtreemix.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.

Rtreemix.Rcheck/00install.out:

* installing *source* package ‘Rtreemix’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rtreemix.cc -o Rtreemix.o
In file included from Rtreemix.cc:31:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
Rtreemix.cc: In function ‘SEXPREC* R_fit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Rtreemix.cc:596:7: warning: value computed is not used [-Wunused-value]
Rtreemix.cc: In function ‘SEXPREC* R_fit1(SEXP, SEXP, SEXP, SEXP)’:
Rtreemix.cc:938:7: warning: value computed is not used [-Wunused-value]
Rtreemix.cc: In function ‘SEXPREC* R_fit0(SEXP, SEXP, SEXP, SEXP)’:
Rtreemix.cc:1281:7: warning: value computed is not used [-Wunused-value]
Rtreemix.cc: In function ‘SEXPREC* R_bootstrap(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Rtreemix.cc:1728:7: warning: value computed is not used [-Wunused-value]
Rtreemix.cc: In function ‘SEXPREC* R_random(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Rtreemix.cc:2629:7: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cfunctions.cc -o cfunctions.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c kmeans.cc -o kmeans.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -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> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, char*)’:
max_weight_branch.cc:97:3: warning: value computed is not used [-Wunused-value]
max_weight_branch.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > max_weight_subgraph_indeg_le_1(replaceleda::graph&)’:
max_weight_branch.cc:142:3: warning: value computed is not used [-Wunused-value]
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:341:3: warning: value computed is not used [-Wunused-value]
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> >&, replaceleda::edge_array<double>&)’:
max_weight_branch.cc:432:3: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mtree.cc -o mtree.o
mtree.cc: In function ‘void mgraph_init(replaceleda::array<std::basic_string<char> >&, replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::basic_string<char> >&, replaceleda::edge_array<double>&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&)’:
mtree.cc:181:3: warning: value computed is not used [-Wunused-value]
mtree.cc:182:5: warning: value computed is not used [-Wunused-value]
mtree.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > mtree_bfs(replaceleda::graph&, replaceleda::node&)’:
mtree.cc:268:3: warning: value computed is not used [-Wunused-value]
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:317:3: warning: value computed is not used [-Wunused-value]
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:440:3: warning: value computed is not used [-Wunused-value]
mtree.cc: In function ‘void mtree_directed(replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, double, double)’:
mtree.cc:780:3: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -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:1031:3: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -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:78:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)’:
replaceleda.cc:125:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&, replaceleda::graph&)’:
replaceleda.cc:146:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)’:
replaceleda.cc:349:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)’:
replaceleda.cc:370:5: warning: value computed is not used [-Wunused-value]
g++ -shared -L/usr/local/lib64 -o Rtreemix.so Rtreemix.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o -lm -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘plot’ when loading ‘graphics’
Creating a generic function for ‘print’ from package ‘base’ in package ‘Rtreemix’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rtreemix.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘plot’ when loading ‘graphics’

* DONE (Rtreemix)

Rtreemix.Rcheck/Rtreemix-Ex.timings:

nameusersystemelapsed
L1.dist0.0040.0000.100
L2.norm0.0040.0000.000
Pval.dist0.0000.0000.002
RtreemixData-class0.0240.0080.056
RtreemixGPS-class000
RtreemixModel-class0.9680.0241.514
RtreemixSim-class0.0280.0040.068
RtreemixStats-class0.0560.0120.070
bootstrap-methods000
comp.models0.0440.0000.046
comp.trees0.0320.0000.031
confIntGPS-methods0.0000.0000.001
distribution-methods0.0400.0040.053
fit-methods0.2560.0040.279
generate-methods0.0040.0000.015
get.tree.levels0.0040.0000.004
gps-methods000
hiv.data0.0040.0040.009
kullback.leibler0.0000.0000.001
likelihoods-methods0.0360.0000.050
sim-methods0.0240.0000.030
stability.sim000