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This page was generated on 2023-04-12 11:06:17 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for NetPathMiner on lconway


To the developers/maintainers of the NetPathMiner package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 1345/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.34.2  (landing page)
Ahmed Mohamed
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/NetPathMiner
git_branch: RELEASE_3_16
git_last_commit: 4612114
git_last_commit_date: 2023-02-14 18:44:07 -0400 (Tue, 14 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NetPathMiner
Version: 1.34.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.34.2.tar.gz
StartedAt: 2023-04-10 21:31:40 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:32:41 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 60.2 seconds
RetCode: 0
Status:   OK  
CheckDir: NetPathMiner.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.34.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/NetPathMiner.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.34.2’
* 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 ... OK
* 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 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 ... 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 ... 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 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 5.601  0.053   5.709
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.



Installation output

NetPathMiner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetPathMiner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -mmacosx-version-min=10.13
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 clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
untarring boost include tree...
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC  -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
In file included from PathRanker.cpp:25:
/usr/local/include/boost/pending/relaxed_heap.hpp:14:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("the standard heap functions")
^
/usr/local/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:26:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC  -Wall -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC  -Wall -g -O2  -c methods.cpp -o methods.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC  -Wall -g -O2  -c pathScope.cpp -o pathScope.o
In file included from pathScope.cpp:30:
/usr/local/include/boost/pending/relaxed_heap.hpp:14:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("the standard heap functions")
^
/usr/local/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:30:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC  -Wall -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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
** 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 (NetPathMiner)

Tests output


Example timings

NetPathMiner.Rcheck/NetPathMiner-Ex.timings

nameusersystemelapsed
KGML2igraph0.1850.0100.196
MIRIAM0.1500.0060.155
NPMdefaults0.0050.0090.014
SBML2igraph0.0010.0000.001
assignEdgeWeights0.2010.0160.218
biopax2igraph0.3920.0180.416
colorVertexByAttr0.1080.0080.117
ex_biopax0.0150.0040.019
ex_kgml_sig0.1610.0100.173
ex_microarray0.0020.0010.003
ex_sbml0.6190.0080.630
extractPathNetwork0.9370.0240.966
getAttr0.0120.0060.018
getGeneSetNetworks0.0040.0020.009
getGeneSets0.0430.0050.060
getPathsAsEIDs0.9290.0150.947
layoutVertexByAttr0.2420.0180.273
makeGeneNetwork0.1250.0050.132
makeMetaboliteNetwork0.0570.0020.060
makeReactionNetwork0.0770.0030.083
pathClassifier0.5160.0280.547
pathCluster0.2540.0160.274
pathRanker0.6010.0310.659
pathsToBinary0.3160.0110.344
plotAllNetworks3.7430.0443.829
plotClusters0.5050.0130.524
plotCytoscape0.2350.0050.241
plotNetwork0.3690.0190.393
plotPathClassifier0.4430.0200.490
plotPathCluster0.2250.0100.238
plotPaths5.6010.0535.709
predictPathClassifier0.4090.0090.422
predictPathCluster0.2090.0040.214
reindexNetwork0.1430.0050.149
rmSmallCompounds0.0660.0030.068
samplePaths0.4470.0220.481
simplifyReactionNetwork0.1090.0030.112
toGraphNEL0.4910.0100.502
vertexDeleteReconnect0.0470.0060.054