Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-03-28 11:37:01 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1818/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.65.0  (landing page)
Jasmina Bogojeska
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/Rtreemix
git_branch: devel
git_last_commit: a86dc9f
git_last_commit_date: 2023-10-24 09:39:10 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for Rtreemix on nebbiolo1


To the developers/maintainers of the Rtreemix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rtreemix.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rtreemix
Version: 1.65.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Rtreemix_1.65.0.tar.gz
StartedAt: 2024-03-28 02:17:30 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:18:25 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rtreemix.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Rtreemix_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Rtreemix.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Rtreemix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rtreemix’ version ‘1.65.0’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
.plott1: no visible binding for global variable ‘drawAgNode’
.plott1: no visible global function definition for ‘plot.new’
.plott1: no visible global function definition for ‘par’
.plott1: no visible global function definition for ‘upRight’
.plott1: no visible global function definition for ‘boundBox’
.plott1: no visible global function definition for ‘plot.window’
.plott1: no visible global function definition for ‘getX’
.plott1: no visible global function definition for ‘getY’
.plott1: no visible global function definition for ‘box’
.plott1: no visible global function definition for ‘xy.coords’
.plott1: no visible global function definition for ‘getDefaultAttrs’
.plott1: no visible global function definition for ‘plot.xy’
.plott1: no visible global function definition for ‘title’
.plott1: no visible global function definition for ‘AgNode’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeRW’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeLW’
.plott1 : <anonymous>: no visible global function definition for
  ‘getNodeHeight’
.plott1 : <anonymous>: no visible global function definition for
  ‘labelText’
.plott1 : <anonymous>: no visible global function definition for
  ‘txtLabel’
.plott1 : <anonymous>: no visible global function definition for
  ‘strwidth’
.plott1 : <anonymous>: no visible global function definition for
  ‘strheight’
.plott1 : <anonymous>: no visible global function definition for
  ‘labelFontsize’
.plott1: no visible global function definition for ‘AgEdge’
.plott1: no visible binding for global variable ‘lines’
.plott2: no visible global function definition for ‘getDefaultAttrs’
.plott2: no visible global function definition for ‘removedEdges’
.plott2: no visible global function definition for ‘agopen’
plot,RtreemixModel-missing: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  AgEdge AgNode agopen boundBox box drawAgNode getDefaultAttrs
  getNodeHeight getNodeLW getNodeRW getX getY labelFontsize labelText
  lines par plot.new plot.window plot.xy removedEdges strheight
  strwidth title txtLabel upRight xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("graphics", "box", "lines", "par", "plot.new",
             "plot.window", "plot.xy", "strheight", "strwidth", "title")
to your NAMESPACE file.
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
   PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/Rtreemix/libs/Rtreemix.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.


Installation output

Rtreemix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Rtreemix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c Rtreemix.cc -o Rtreemix.o
In file included from include/replaceleda.hh:7,
                 from include/max_weight_branch.h:25,
                 from include/mtree.h:14,
                 from include/mtreemix.h:14,
                 from Rtreemix.cc:3:
Rtreemix.cc: In function ‘SEXPREC* R_fit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:596:7: note: in expansion of macro ‘forall_nodes’
  596 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function ‘SEXPREC* R_fit1(SEXP, SEXP, SEXP, SEXP)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:938:7: note: in expansion of macro ‘forall_nodes’
  938 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function ‘SEXPREC* R_fit0(SEXP, SEXP, SEXP, SEXP)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1281:7: note: in expansion of macro ‘forall_nodes’
 1281 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function ‘SEXPREC* R_bootstrap(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1728:7: note: in expansion of macro ‘forall_nodes’
 1728 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function ‘SEXPREC* R_random(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:2629:7: note: in expansion of macro ‘forall_nodes’
 2629 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c Rtreemix_patch.cc -o Rtreemix_patch.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c WrapGraph.cc -o WrapGraph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c cfunctions.cc -o cfunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c kmeans.cc -o kmeans.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c max_weight_branch.cc -o max_weight_branch.o
In file included from include/replaceleda.hh:7,
                 from include/max_weight_branch.h:25,
                 from max_weight_branch.cc:11:
max_weight_branch.cc: In function ‘void DOT(replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, char*)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
max_weight_branch.cc:97:3: note: in expansion of macro ‘forall_nodes’
   97 |   forall_nodes(v, G)
      |   ^~~~~~~~~~~~
max_weight_branch.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > max_weight_subgraph_indeg_le_1(replaceleda::graph&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
max_weight_branch.cc:142:3: note: in expansion of macro ‘forall_nodes’
  142 |   forall_nodes(v, G)  // choose heaviest inedge
      |   ^~~~~~~~~~~~
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> >&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
max_weight_branch.cc:341:3: note: in expansion of macro ‘forall_nodes’
  341 |   forall_nodes(v, G)
      |   ^~~~~~~~~~~~
max_weight_branch.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > MAX_WEIGHT_BRANCHING(replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::edge_array<double>&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
max_weight_branch.cc:432:3: note: in expansion of macro ‘forall_nodes’
  432 |   forall_nodes(v, G[0])  // node labels
      |   ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c mtree.cc -o mtree.o
In file included from include/replaceleda.hh:7,
                 from include/max_weight_branch.h:25,
                 from include/mtree.h:14,
                 from mtree.cc:12:
mtree.cc: In function ‘void mgraph_init(replaceleda::array<std::__cxx11::basic_string<char> >&, replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::edge_array<double>&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:185:3: note: in expansion of macro ‘forall_nodes’
  185 |   forall_nodes(v, G)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:186:5: note: in expansion of macro ‘forall_nodes’
  186 |     forall_nodes(w, G)
      |     ^~~~~~~~~~~~
mtree.cc: In function ‘replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > mtree_bfs(replaceleda::graph&, replaceleda::node&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:272:3: note: in expansion of macro ‘forall_nodes’
  272 |   forall_nodes(w, G)
      |   ^~~~~~~~~~~~
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>&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:321:3: note: in expansion of macro ‘forall_nodes’
  321 |   forall_nodes(w, G)
      |   ^~~~~~~~~~~~
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>&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:444:3: note: in expansion of macro ‘forall_nodes’
  444 |   forall_nodes(w, G)
      |   ^~~~~~~~~~~~
mtree.cc: In function ‘void mtree_directed(replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, double, double)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtree.cc:784:3: note: in expansion of macro ‘forall_nodes’
  784 |   forall_nodes(w, G)
      |   ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c mtreemix.cc -o mtreemix.o
In file included from include/replaceleda.hh:7,
                 from include/max_weight_branch.h:25,
                 from include/mtree.h:14,
                 from mtreemix.cc:11:
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>&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mtreemix.cc:1035:3: note: in expansion of macro ‘forall_nodes’
 1035 |   forall_nodes(w, G)
      |   ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c replaceleda.cc -o replaceleda.o
In file included from include/replaceleda.hh:7,
                 from replaceleda.cc:2:
replaceleda.cc: In function ‘bool replaceleda::Is_Acyclic(replaceleda::graph&, replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> >&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
replaceleda.cc:81:5: note: in expansion of macro ‘forall_nodes’
   81 |     forall_nodes(v,G)
      |     ^~~~~~~~~~~~
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
replaceleda.cc:128:5: note: in expansion of macro ‘forall_nodes’
  128 |     forall_nodes(v, g_source){
      |     ^~~~~~~~~~~~
replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&, replaceleda::graph&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
replaceleda.cc:149:5: note: in expansion of macro ‘forall_nodes’
  149 |     forall_nodes(v, g_source){
      |     ^~~~~~~~~~~~
replaceleda.cc: In function ‘std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
replaceleda.cc:352:5: note: in expansion of macro ‘forall_nodes’
  352 |     forall_nodes(v, g){
      |     ^~~~~~~~~~~~
replaceleda.cc: In function ‘void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)’:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
replaceleda.cc:373:5: note: in expansion of macro ‘forall_nodes’
  373 |     forall_nodes(v, g){
      |     ^~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-Rtreemix/00new/Rtreemix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rtreemix)

Tests output


Example timings

Rtreemix.Rcheck/Rtreemix-Ex.timings

nameusersystemelapsed
L1.dist0.0000.0020.002
L2.norm0.0010.0000.000
Pval.dist0.0010.0000.001
RtreemixData-class0.2700.0040.275
RtreemixGPS-class0.0010.0000.000
RtreemixModel-class0.6370.0900.726
RtreemixSim-class0.0150.0080.023
RtreemixStats-class0.0380.0160.053
bootstrap-methods000
comp.models0.0210.0200.040
comp.trees0.0070.0040.010
confIntGPS-methods0.0010.0000.000
distribution-methods0.0390.0240.063
fit-methods0.2320.0040.237
generate-methods0.0020.0000.003
get.tree.levels0.0020.0000.001
gps-methods0.0010.0000.000
hiv.data0.0040.0040.008
kullback.leibler0.0000.0000.001
likelihoods-methods0.0160.0040.020
sim-methods0.0310.0110.043
stability.sim000