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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: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check Rtreemix_1.0.0.tar.gz
StartedAt: 2008-04-09 07:25:48 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 07:27:56 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 127.5 seconds
RetCode: 1
Status: ERROR
CheckDir: Rtreemix.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/Rtreemix.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* 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 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.257 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.260 \end{Note}
                
--
! Missing $ inserted.
<inserted text> 
                $
l.632 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.635 \end{Note}

Rtreemix.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/Rtreemix.Rcheck


---------- Making package Rtreemix ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making Rtreemix.d from Rtreemix.cc
making WrapGraph.d from WrapGraph.cc
making cfunctions.d from cfunctions.cc
making kmeans.d from kmeans.cc
making max_weight_branch.d from max_weight_branch.cc
making mtree.d from mtree.cc
making mtreemix.d from mtreemix.cc
making replaceleda.d from replaceleda.cc
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -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++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c WrapGraph.cc -o WrapGraph.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c cfunctions.cc -o cfunctions.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c kmeans.cc -o kmeans.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -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++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -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++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -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++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -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
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i Rtreemix_res.rc -o Rtreemix_res.o
g++   -shared -s  -o Rtreemix.dll Rtreemix.def Rtreemix.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o Rtreemix_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin -lm    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package Rtreemix 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"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'Rtreemix'
     Formats: text html latex example chm 
  L1.dist                           text    html    latex   example chm
  L2.norm                           text    html    latex   example chm
  Pval.dist                         text    html    latex   example chm
  RtreemixData-class                text    html    latex   example chm
  RtreemixGPS-class                 text    html    latex   example chm
  RtreemixModel-class               text    html    latex   example chm
  RtreemixSim-class                 text    html    latex   example chm
  RtreemixStats-class               text    html    latex   example chm
  bootstrap-methods                 text    html    latex   example chm
  comp.models                       text    html    latex   example chm
  comp.trees                        text    html    latex   example chm
  confIntGPS-methods                text    html    latex   example chm
  distribution-methods              text    html    latex   example chm
  fit-methods                       text    html    latex   example chm
  generate-methods                  text    html    latex   example chm
  get.tree.levels                   text    html    latex   example chm
  gps-methods                       text    html    latex   example chm
  hiv.data                          text    html    latex   example chm
  kullback.leibler                  text    html    latex   example chm
  likelihoods-methods               text    html    latex   example chm
  plot-methods                      text    html    latex   example chm
  sim-methods                       text    html    latex   example chm
  stability.sim                     text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.2-bioc\meat\Rtreemix.Rcheck\00_pkg_src\Rtreemix\chm\Rtreemix.chm


Compile time: 0 minutes, 0 seconds
24	Topics
260	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.2-bioc\meat\Rtreemix.Rcheck\00_pkg_src\Rtreemix\chm\Rtreemix.chm, 61,153 bytes
Compression decreased file by 97,545 bytes.
  adding MD5 sums

* DONE (Rtreemix)