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BioC 2.14: CHECK report for Rtreemix on zin2

This page was generated on 2014-10-08 08:48:19 -0700 (Wed, 08 Oct 2014).

Package 697/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.26.0
Jasmina Bogojeska
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rtreemix
Last Changed Rev: 89916 / Revision: 95116
Last Changed Date: 2014-05-05 05:47:36 -0700 (Mon, 05 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: Rtreemix
Version: 1.26.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.26.0.tar.gz
StartedAt: 2014-10-08 02:37:49 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:39:07 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 77.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Rtreemix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Rtreemix.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.26.0’
* 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 ... [36s/37s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
* 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 ... 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.14-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’

Compiled code should not call entry points 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.

Rtreemix.Rcheck/00install.out:

* installing *source* package ‘Rtreemix’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rtreemix.cc -o Rtreemix.o
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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rtreemix_patch.cc -o Rtreemix_patch.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cfunctions.cc -o cfunctions.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c kmeans.cc -o kmeans.o
g++ -I/home/biocbuild/bbs-2.14-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-2.14-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:185:3: warning: value computed is not used [-Wunused-value]
mtree.cc:186:5: 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:272:3: 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:321:3: 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:444:3: 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:784:3: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.14-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:1035:3: warning: value computed is not used [-Wunused-value]
g++ -I/home/biocbuild/bbs-2.14-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:81:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)’:
replaceleda.cc:128:5: 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:149:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)’:
replaceleda.cc:352:5: warning: value computed is not used [-Wunused-value]
replaceleda.cc: In function ‘void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)’:
replaceleda.cc:373:5: warning: value computed is not used [-Wunused-value]
g++ -shared -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 -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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.dist0.0000.0000.002
L2.norm0.0000.0000.001
Pval.dist0.0040.0000.002
RtreemixData-class0.0240.0000.023
RtreemixGPS-class0.0000.0000.002
RtreemixModel-class0.8320.0200.854
RtreemixSim-class0.0240.0040.029
RtreemixStats-class0.0440.0120.056
bootstrap-methods0.0000.0000.001
comp.models0.0400.0000.039
comp.trees0.0280.0000.025
confIntGPS-methods0.0000.0000.001
distribution-methods0.0360.0000.040
fit-methods0.8360.0120.854
generate-methods0.0040.0000.006
get.tree.levels0.0000.0000.004
gps-methods0.0000.0000.001
hiv.data0.0080.0000.006
kullback.leibler0.0000.0000.001
likelihoods-methods0.0280.0000.025
sim-methods0.0160.0040.019
stability.sim000