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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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Package 1421/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.40.0  (landing page)
Ahmed Mohamed
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/NetPathMiner
git_branch: RELEASE_3_19
git_last_commit: a1d4b92
git_last_commit_date: 2024-04-30 10:36:27 -0400 (Tue, 30 Apr 2024)
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


CHECK results for NetPathMiner on nebbiolo1

To the developers/maintainers of the NetPathMiner package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetPathMiner.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: NetPathMiner
Version: 1.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NetPathMiner_1.40.0.tar.gz
StartedAt: 2024-06-13 01:33:33 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 01:34:33 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NetPathMiner.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NetPathMiner_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/NetPathMiner.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.40.0’
* package encoding: UTF-8
* 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 ‘NetPathMiner’ can be installed ... WARNING
Found the following significant warnings:
  sbml_interface.cpp:44:47: warning: format not a string literal and no format arguments [-Wformat-security]
  sbml_interface.cpp:48:31: warning: format not a string literal and no format arguments [-Wformat-security]
  sbml_interface.cpp:369:39: warning: format not a string literal and no format arguments [-Wformat-security]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/NetPathMiner.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha: no visible global function definition for ‘col2rgb’
alpha: no visible global function definition for ‘rgb’
assignEdgeWeights : wt.func: no visible global function definition for
  ‘median’
assignEdgeWeights: no visible global function definition for
  ‘complete.cases’
assignEdgeWeights: no visible global function definition for ‘na.omit’
assignEdgeWeights : <anonymous>: no visible global function definition
  for ‘na.omit’
bpGetAnnFromXRef: no visible global function definition for ‘na.omit’
bpGetReferences: no visible global function definition for ‘setNames’
bpMetabolicL2: no visible global function definition for ‘setNames’
bpMetabolicL3: no visible global function definition for ‘setNames’
bpSignalingL3: no visible global function definition for ‘na.omit’
bpSplitComplex: no visible global function definition for ‘na.omit’
colorVertexByAttr: no visible global function definition for ‘palette’
colorVertexByAttr: no visible global function definition for
  ‘colorRampPalette’
drawLegend: no visible global function definition for ‘par’
drawLegend: no visible global function definition for ‘plot.new’
drawLegend: no visible global function definition for ‘strwidth’
drawLegend: no visible global function definition for ‘legend’
fetchAttribute: no visible global function definition for ‘na.omit’
fetchAttribute: no visible global function definition for ‘URLencode’
fetchAttribute: no visible global function definition for ‘setNames’
fetchAttribute : <anonymous>: no visible global function definition for
  ‘read.table’
getGeneSetNetworks: no visible global function definition for
  ‘setClass’
getGeneSetNetworks: no visible global function definition for
  ‘representation’
getPaths : <anonymous>: no visible global function definition for
  ‘head’
getPaths: no visible global function definition for ‘.to’
getPaths: no visible global function definition for ‘.from’
getPaths: no visible global function definition for ‘tail’
graph.sizes: no visible global function definition for ‘par’
makeReactionNetwork: no visible global function definition for
  ‘complete.cases’
pathClassifier: no visible binding for global variable ‘sd’
pathClassifier: no visible global function definition for ‘aggregate’
pathCluster: no visible binding for global variable ‘sd’
pathCluster: no visible global function definition for ‘aggregate’
plotAllNetworks: no visible global function definition for ‘palette’
plotAllNetworks: no visible global function definition for ‘par’
plotAllNetworks: no visible global function definition for
  ‘colorRampPalette’
plotClassifierROC: no visible global function definition for ‘palette’
plotClassifierROC: no visible global function definition for ‘layout’
plotClassifierROC: no visible global function definition for ‘na.omit’
plotClusterMatrix: no visible global function definition for ‘rainbow’
plotClusterMatrix: no visible global function definition for ‘image’
plotClusterMatrix: no visible global function definition for ‘axis’
plotClusterProbs: no visible global function definition for ‘rainbow’
plotClusterProbs: no visible global function definition for ‘matplot’
plotClusters: no visible global function definition for ‘rainbow’
plotClusters: no visible global function definition for ‘strwidth’
plotClusters: no visible global function definition for ‘layout’
plotClusters: no visible global function definition for ‘par’
plotClusters: no visible global function definition for ‘legend’
plotCytoscapeGML : col2hex: no visible global function definition for
  ‘rgb’
plotCytoscapeGML : col2hex: no visible global function definition for
  ‘col2rgb’
plotCytoscapeGML: no visible global function definition for
  ‘packageVersion’
plotNetwork: no visible global function definition for ‘palette’
plotNetwork: no visible global function definition for ‘par’
plotNetwork_internal: no visible global function definition for
  ‘palette’
plotNetwork_internal: no visible global function definition for
  ‘setNames’
plotPathClassifier: no visible global function definition for ‘palette’
plotPathClassifier: no visible global function definition for ‘par’
plotPathClassifier: no visible global function definition for ‘layout’
plotPathClassifier: no visible global function definition for ‘barplot’
plotPathClassifier: no visible global function definition for ‘abline’
plotPathClassifier: no visible global function definition for ‘points’
plotPathClassifier: no visible global function definition for ‘axis’
plotPathClassifier: no visible global function definition for ‘image’
plotPathClassifier: no visible global function definition for
  ‘cm.colors’
plotPathClassifier: no visible global function definition for ‘mtext’
plotPathClassifier: no visible global function definition for ‘lines’
plotPathCluster: no visible global function definition for ‘par’
plotPathCluster: no visible global function definition for ‘layout’
plotPathCluster: no visible global function definition for ‘barplot’
plotPathCluster: no visible global function definition for ‘abline’
plotPathCluster: no visible global function definition for ‘axis’
plotPathCluster: no visible global function definition for ‘image’
plotPathCluster: no visible global function definition for ‘cm.colors’
plotPathCluster: no visible global function definition for ‘mtext’
plotPathROC: no visible global function definition for ‘palette’
plotPathROC: no visible global function definition for ‘lines’
plotPathROC: no visible global function definition for ‘axis’
plotPathROC: no visible global function definition for ‘mtext’
plotPathROC: no visible global function definition for ‘legend’
plotPaths: no visible global function definition for ‘palette’
plotPaths: no visible global function definition for ‘par’
process.color: no visible global function definition for
  ‘colorRampPalette’
process.color: no visible global function definition for ‘setNames’
process.layout: no visible global function definition for ‘par’
processNetwork : <anonymous>: no visible global function definition for
  ‘ecdf’
reindexNetwork: no visible binding for global variable ‘head’
stdAttrNames : <anonymous>: no visible global function definition for
  ‘head’
stdAttrNames : <anonymous>: no visible global function definition for
  ‘setNames’
vertexDeleteReconnect: no visible global function definition for ‘.nei’
Undefined global functions or variables:
  .from .nei .to URLencode abline aggregate axis barplot cm.colors
  col2rgb colorRampPalette complete.cases ecdf head image layout legend
  lines matplot median mtext na.omit packageVersion palette par
  plot.new points rainbow read.table representation rgb sd setClass
  setNames strwidth tail
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "colorRampPalette",
             "palette", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "image", "layout",
             "legend", "lines", "matplot", "mtext", "par", "plot.new",
             "points", "strwidth")
  importFrom("methods", "representation", "setClass")
  importFrom("stats", "aggregate", "complete.cases", "ecdf", "median",
             "na.omit", "sd", "setNames")
  importFrom("utils", "URLencode", "head", "packageVersion",
             "read.table", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) plotClassifierROC.Rd:14: Lost braces
    14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs})
       |     ^
checkRd: (-1) plotClassifierROC.Rd:14-17: Lost braces
    14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs})
       |          ^
checkRd: (-1) plotClassifierROC.Rd:18: Lost braces
    18 | item{Bottom}{The likelihood convergence history for the HME3M model.  If the parameters
       |     ^
checkRd: (-1) plotClassifierROC.Rd:18-19: Lost braces
    18 | item{Bottom}{The likelihood convergence history for the HME3M model.  If the parameters
       |             ^
* 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 shell scripts ... 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 ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
plotPaths 5.325   0.04   5.365
* 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/NetPathMiner.Rcheck/00check.log’
for details.


Installation output

NetPathMiner.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:27:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c handlesegfault.c -o handlesegfault.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c hme3m.c -o hme3m.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall  -c kgml_interface.cpp -o kgml_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall  -c methods.cpp -o methods.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall  -c pathScope.cpp -o pathScope.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from pathScope.cpp:34:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall  -c sbml_interface.cpp -o sbml_interface.o
sbml_interface.cpp: In function ‘SEXPREC* readsbmlfile(SEXP, SEXP, SEXP)’:
sbml_interface.cpp:44:47: warning: format not a string literal and no format arguments [-Wformat-security]
   44 |                                 Rf_warningcall(mkChar(filename), message.str().c_str());
      |                                 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sbml_interface.cpp:48:31: warning: format not a string literal and no format arguments [-Wformat-security]
   48 |                 Rf_warningcall(mkChar(filename), message.str().c_str());
      |                 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sbml_interface.cpp: In function ‘SEXPREC* readsbml_sign(SEXP, SEXP, SEXP)’:
sbml_interface.cpp:369:39: warning: format not a string literal and no format arguments [-Wformat-security]
  369 |                         Rf_warningcall(mkChar(filename), message.str().c_str());
      |                         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lsbml -lxml2 -lxml2 -lsbml -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-NetPathMiner/00new/NetPathMiner/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
Warning in fun(libname, pkgname) :
  Package 'NetPathMiner' is deprecated and will be removed from
  Bioconductor version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'NetPathMiner' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (NetPathMiner)

Tests output


Example timings

NetPathMiner.Rcheck/NetPathMiner-Ex.timings

nameusersystemelapsed
KGML2igraph0.2560.0080.264
MIRIAM0.0450.0090.053
NPMdefaults0.0060.0030.010
SBML2igraph0.1320.0120.156
assignEdgeWeights0.2190.0050.223
biopax2igraph0.3650.0080.368
colorVertexByAttr0.1140.0000.114
ex_biopax0.0140.0040.018
ex_kgml_sig0.1570.0030.161
ex_microarray0.0030.0000.003
ex_sbml0.6510.0230.675
extractPathNetwork1.0110.0121.022
getAttr0.0170.0000.016
getGeneSetNetworks0.0090.0000.009
getGeneSets0.0410.0000.041
getPathsAsEIDs1.0670.0041.072
layoutVertexByAttr0.2980.0000.298
makeGeneNetwork0.1430.0040.147
makeMetaboliteNetwork0.0650.0000.064
makeReactionNetwork0.090.000.09
pathClassifier0.4760.0360.512
pathCluster0.2700.0160.286
pathRanker0.6600.0160.676
pathsToBinary0.3240.0000.325
plotAllNetworks3.5940.0563.649
plotClusters0.570.000.57
plotCytoscape0.2400.0030.244
plotNetwork0.4720.0200.492
plotPathClassifier0.5070.0080.515
plotPathCluster0.2440.0000.244
plotPaths5.3250.0405.365
predictPathClassifier0.3880.0000.388
predictPathCluster0.2150.0000.215
reindexNetwork0.1750.0040.178
rmSmallCompounds0.0560.0040.060
samplePaths0.5170.0120.529
simplifyReactionNetwork0.1180.0040.122
toGraphNEL0.5250.0080.533
vertexDeleteReconnect0.0480.0000.048