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This page was generated on 2021-07-21 15:05:09 -0400 (Wed, 21 Jul 2021).

CHECK results for Rtreemix on nebbiolo1

To the developers/maintainers of the Rtreemix package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1651/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.54.0  (landing page)
Jasmina Bogojeska
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/Rtreemix
Branch: RELEASE_3_13
Last Commit: 5821181
Last Changed Date: 2021-05-19 11:39:55 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rtreemix
Version: 1.54.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rtreemix_1.54.0.tar.gz
StartedAt: 2021-07-20 11:26:13 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 11:27:17 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 64.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Rtreemix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rtreemix.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rtreemix_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Rtreemix.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rtreemix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rtreemix’ version ‘1.54.0’
* 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
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
* 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 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 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 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.13-bioc/R/library/Rtreemix/libs/Rtreemix.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (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. 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.



Installation output

Rtreemix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rtreemix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rtreemix_patch.cc -o Rtreemix_patch.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cfunctions.cc -o cfunctions.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c kmeans.cc -o kmeans.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-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++14 -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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.dist0.0020.0000.002
L2.norm000
Pval.dist0.0010.0000.001
RtreemixData-class0.0950.0040.100
RtreemixGPS-class0.0000.0000.001
RtreemixModel-class0.9430.0631.007
RtreemixSim-class0.0150.0120.026
RtreemixStats-class0.0210.0350.055
bootstrap-methods000
comp.models0.0120.0000.013
comp.trees0.0080.0000.007
confIntGPS-methods0.0000.0000.001
distribution-methods0.0250.0310.056
fit-methods0.6080.0190.626
generate-methods0.0010.0010.003
get.tree.levels0.0010.0000.002
gps-methods000
hiv.data0.0050.0040.008
kullback.leibler000
likelihoods-methods0.0100.0100.019
sim-methods0.0320.0110.044
stability.sim0.0000.0000.001