Rtreemix 1.0.0
Jasmina Bogojeska
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix | | Last Changed Rev: 28790 / Revision: 29143 | | Last Changed Date: 2007-11-16 13:25:16 -0800 (Fri, 16 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | [ ERROR ] | skipped | skipped |
| lemming | Windows Server 2003 (32-bit) / x64 | ERROR | skipped | skipped |
* checking for file 'Rtreemix/DESCRIPTION' ... OK
* preparing 'Rtreemix':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst502457345
---------- 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++-sjlj -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++-sjlj -Ie:/biocbld/bbs-2.2-bioc/R/include -O2 -Wall -c WrapGraph.cc -o WrapGraph.o
g++-sjlj -Ie:/biocbld/bbs-2.2-bioc/R/include -O2 -Wall -c cfunctions.cc -o cfunctions.o
g++-sjlj -Ie:/biocbld/bbs-2.2-bioc/R/include -O2 -Wall -c kmeans.cc -o kmeans.o
g++-sjlj -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++-sjlj -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++-sjlj -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++-sjlj -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-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i Rtreemix_res.rc -o Rtreemix_res.o
g++-sjlj -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\chm\Rtreemix.chm
Compile time: 0 minutes, 1 second
24 Topics
260 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\Rtreemix\chm\Rtreemix.chm, 60,627 bytes
Compression decreased file by 97,289 bytes.
adding MD5 sums
* DONE (Rtreemix)
* creating vignettes ... ERROR
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: Rgraphviz
Error: processing vignette 'Rtreemix.Rnw' failed with diagnostics:
chunk 8
Error in .local(x, ...) : package Rgraphviz is required
In addition: Warning messages:
1: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object.
2: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object.
3: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object.
4: The edgemode slot is deprecated. Use 'updateGraph' to update this graph object.
5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'Rgraphviz'
Execution halted