| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-10 11:36:13 -0400 (Fri, 10 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 1421/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Ahmed Mohamed
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| 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: 2024-05-10 01:03:35 -0400 (Fri, 10 May 2024) |
| EndedAt: 2024-05-10 01:04:35 -0400 (Fri, 10 May 2024) |
| EllapsedTime: 60.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NetPathMiner.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### 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 5.617 0.016 5.632
* 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.
NetPathMiner.Rcheck/00install.out
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###
### 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)
NetPathMiner.Rcheck/NetPathMiner-Ex.timings
| name | user | system | elapsed | |
| KGML2igraph | 0.257 | 0.004 | 0.262 | |
| MIRIAM | 0.034 | 0.020 | 0.054 | |
| NPMdefaults | 0.006 | 0.004 | 0.009 | |
| SBML2igraph | 0.142 | 0.000 | 0.153 | |
| assignEdgeWeights | 0.214 | 0.004 | 0.218 | |
| biopax2igraph | 0.350 | 0.004 | 0.347 | |
| colorVertexByAttr | 0.108 | 0.004 | 0.112 | |
| ex_biopax | 0.009 | 0.008 | 0.017 | |
| ex_kgml_sig | 0.163 | 0.000 | 0.162 | |
| ex_microarray | 0.003 | 0.000 | 0.004 | |
| ex_sbml | 0.655 | 0.016 | 0.672 | |
| extractPathNetwork | 0.982 | 0.012 | 0.994 | |
| getAttr | 0.013 | 0.004 | 0.016 | |
| getGeneSetNetworks | 0.007 | 0.000 | 0.008 | |
| getGeneSets | 0.032 | 0.003 | 0.036 | |
| getPathsAsEIDs | 0.96 | 0.00 | 0.96 | |
| layoutVertexByAttr | 0.302 | 0.000 | 0.302 | |
| makeGeneNetwork | 0.162 | 0.000 | 0.162 | |
| makeMetaboliteNetwork | 0.061 | 0.000 | 0.060 | |
| makeReactionNetwork | 0.105 | 0.000 | 0.105 | |
| pathClassifier | 0.482 | 0.028 | 0.509 | |
| pathCluster | 0.241 | 0.004 | 0.244 | |
| pathRanker | 0.629 | 0.020 | 0.649 | |
| pathsToBinary | 0.323 | 0.000 | 0.324 | |
| plotAllNetworks | 3.683 | 0.040 | 3.724 | |
| plotClusters | 0.651 | 0.012 | 0.662 | |
| plotCytoscape | 0.228 | 0.000 | 0.228 | |
| plotNetwork | 0.425 | 0.000 | 0.425 | |
| plotPathClassifier | 0.476 | 0.020 | 0.495 | |
| plotPathCluster | 0.227 | 0.012 | 0.239 | |
| plotPaths | 5.617 | 0.016 | 5.632 | |
| predictPathClassifier | 0.373 | 0.000 | 0.373 | |
| predictPathCluster | 0.205 | 0.004 | 0.209 | |
| reindexNetwork | 0.137 | 0.003 | 0.140 | |
| rmSmallCompounds | 0.051 | 0.000 | 0.051 | |
| samplePaths | 0.425 | 0.012 | 0.437 | |
| simplifyReactionNetwork | 0.118 | 0.004 | 0.122 | |
| toGraphNEL | 0.460 | 0.000 | 0.459 | |
| vertexDeleteReconnect | 0.044 | 0.000 | 0.043 | |