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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1821/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.68.0  (landing page)
Jasmina Bogojeska
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/Rtreemix
git_branch: RELEASE_3_20
git_last_commit: 37417f2
git_last_commit_date: 2024-10-29 09:28:26 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for Rtreemix on nebbiolo2

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: 1.68.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rtreemix_1.68.0.tar.gz
StartedAt: 2024-12-20 05:00:41 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:01:33 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rtreemix.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rtreemix_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rtreemix.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rtreemix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rtreemix’ version ‘1.68.0’
* 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 ... WARNING
Found the following significant warnings:
  include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/Rtreemix.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
* 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-3.20-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: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.


Installation output

Rtreemix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rtreemix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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-3.20-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:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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-3.20-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)
      |   ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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-3.20-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(graph&, list<RefCountPtr<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)
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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(graph&, 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){
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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(GRAPH<RefCountPtr<Node>, RefCountPtr<Edge> >&, 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){
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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&, 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){
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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(graph&, 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){
      |     ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   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-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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.dist0.0020.0000.001
L2.norm000
Pval.dist0.0010.0000.000
RtreemixData-class0.0820.0100.093
RtreemixGPS-class000
RtreemixModel-class0.5640.0730.636
RtreemixSim-class0.0100.0010.012
RtreemixStats-class0.0180.0070.025
bootstrap-methods000
comp.models0.0120.0010.012
comp.trees0.0060.0010.008
confIntGPS-methods000
distribution-methods0.0340.0020.035
fit-methods0.1620.0010.163
generate-methods0.0020.0000.002
get.tree.levels0.0010.0000.001
gps-methods000
hiv.data0.0020.0010.003
kullback.leibler0.0000.0000.001
likelihoods-methods0.0110.0010.013
sim-methods0.0290.0020.031
stability.sim000