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 

Package 218/264HostnameOS / ArchBUILDCHECKBUILD BIN
Rtreemix 1.0.0
Jasmina Bogojeska
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix
Last Changed Rev: 30733 / Revision: 30951
Last Changed Date: 2008-03-28 08:38:30 -0700 (Fri, 28 Mar 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  ERROR 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK [ ERROR ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  ERROR  OK 
Package: Rtreemix
Version: 1.0.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check Rtreemix_1.0.0.tar.gz
StartedAt: 2008-04-09 10:30:27 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 10:33:46 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 198.2 seconds
RetCode: 1
Status: ERROR
CheckDir: Rtreemix.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/Rtreemix.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'Rtreemix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rtreemix' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rtreemix' can be installed ... OK
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... 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 ... OK
* creating Rtreemix-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Rtreemix-manual.tex ... OK
* checking Rtreemix-manual.tex using pdflatex ... ERROR
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:

! Missing $ inserted.
<inserted text> 
                $
l.318 is in this case 2^
                        20. This demands too much memory.
--
! LaTeX Error: Command \end{list} invalid in math mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! Missing $ inserted.
<inserted text> 
                $
l.321 \end{Note}
                
--
! Missing $ inserted.
<inserted text> 
                $
l.1644 is in this case 2^
                         20. This demands too much memory.
--
! LaTeX Error: Command \end{list} invalid in math mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--
! Missing $ inserted.
<inserted text> 
                $
l.1647 \end{Note}

Rtreemix.Rcheck/00install.out:

* Installing *source* package 'Rtreemix' ...
** libs
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c cfunctions.cc -o cfunctions.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c kmeans.cc -o kmeans.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -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, 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
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -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, 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:181: warning: value computed is not used
mtree.cc:182: warning: value computed is not used
mtree.cc: In function 'replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > mtree_bfs(replaceleda::graph&, replaceleda::node&)':
mtree.cc:268: 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:317: 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:440: 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:780: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -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: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -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: warning: value computed is not used
replaceleda.cc: In function 'void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)':
replaceleda.cc:125: 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:146: warning: value computed is not used
replaceleda.cc: In function 'std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)':
replaceleda.cc:349: warning: value computed is not used
replaceleda.cc: In function 'void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)':
replaceleda.cc:370: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -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:591: warning: value computed is not used
Rtreemix.cc: In function 'SEXPREC* R_fit1(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
Rtreemix.cc:929: warning: value computed is not used
Rtreemix.cc: In function 'SEXPREC* R_fit0(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
Rtreemix.cc:1267: 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:1709: warning: value computed is not used
Rtreemix.cc: In function 'SEXPREC* R_random(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
Rtreemix.cc:2605: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -shared -L/usr/local/lib -o Rtreemix.so cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o Rtreemix.o WrapGraph.o -lm  -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Creating a new generic function for "print" in "Rtreemix"
** help
 >>> Building/Updating help pages for package 'Rtreemix'
     Formats: text html latex example 
  L1.dist                           text    html    latex   example
  L2.norm                           text    html    latex   example
  Pval.dist                         text    html    latex   example
  RtreemixData-class                text    html    latex   example
  RtreemixGPS-class                 text    html    latex   example
  RtreemixModel-class               text    html    latex   example
  RtreemixSim-class                 text    html    latex   example
  RtreemixStats-class               text    html    latex   example
  bootstrap-methods                 text    html    latex   example
  comp.models                       text    html    latex   example
  comp.trees                        text    html    latex   example
  confIntGPS-methods                text    html    latex   example
  distribution-methods              text    html    latex   example
  fit-methods                       text    html    latex   example
  generate-methods                  text    html    latex   example
  get.tree.levels                   text    html    latex   example
  gps-methods                       text    html    latex   example
  hiv.data                          text    html    latex   example
  kullback.leibler                  text    html    latex   example
  likelihoods-methods               text    html    latex   example
  plot-methods                      text    html    latex   example
  sim-methods                       text    html    latex   example
  stability.sim                     text    html    latex   example
** building package indices ...
* DONE (Rtreemix)