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CHECK report for NetPathMiner on merida1

This page was generated on 2021-01-19 11:58:00 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE NetPathMiner PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1218/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.26.0
Ahmed Mohamed
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/NetPathMiner
Branch: RELEASE_3_12
Last Commit: 57dbe8c
Last Changed Date: 2020-10-27 10:56:36 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: NetPathMiner
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.26.0.tar.gz
StartedAt: 2021-01-19 04:21:46 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 04:23:11 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 85.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NetPathMiner.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/NetPathMiner.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.26.0’
* 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:
  'config' variable 'CPP' is deprecated
  #warning \
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/NetPathMiner.Rcheck/00install.out’ for details.
* 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       11.337  0.043  11.395
plotAllNetworks  8.121  0.045   8.176
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.



Installation output

NetPathMiner.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is deprecated
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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -fPIC  -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
In file included from PathRanker.cpp:23:
In file included from /usr/local/include/boost/graph/graph_utility.hpp:26:
In file included from /usr/local/include/boost/detail/algorithm.hpp:33:
/usr/local/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/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>:112:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from PathRanker.cpp:25:
/usr/local/include/boost/pending/relaxed_heap.hpp:9:2: warning: "Use of relaxed_heap is depreciated; please use the standard heap functions." [-W#warnings]
#warning \
 ^
/usr/local/include/boost/pending/relaxed_heap.hpp:15:1: 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>:55:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
3 warnings 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -fPIC  -Wall -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -fPIC  -Wall -g -O2  -c methods.cpp -o methods.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -fPIC  -Wall -g -O2  -c pathScope.cpp -o pathScope.o
In file included from pathScope.cpp:28:
In file included from /usr/local/include/boost/graph/graph_utility.hpp:26:
In file included from /usr/local/include/boost/detail/algorithm.hpp:33:
/usr/local/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/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>:118:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from pathScope.cpp:30:
/usr/local/include/boost/pending/relaxed_heap.hpp:9:2: warning: "Use of relaxed_heap is depreciated; please use the standard heap functions." [-W#warnings]
#warning \
 ^
/usr/local/include/boost/pending/relaxed_heap.hpp:15:1: 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>:67:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -fPIC  -Wall -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/MacOSX10.14.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
installing to /Library/Frameworks/R.framework/Versions/4.0/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
KGML2igraph0.2640.0100.275
MIRIAM0.1070.0080.115
NPMdefaults0.0130.0080.022
SBML2igraph0.0010.0000.001
assignEdgeWeights0.4630.0100.474
biopax2igraph0.6780.0300.712
colorVertexByAttr0.1830.0070.190
ex_biopax0.0300.0050.034
ex_kgml_sig0.2360.0090.246
ex_microarray0.0040.0010.005
ex_sbml1.2610.0171.280
extractPathNetwork1.4520.0291.482
getAttr0.0230.0090.032
getGeneSetNetworks0.0070.0020.008
getGeneSets0.0780.0040.081
getPathsAsEIDs1.4460.0141.461
layoutVertexByAttr0.4200.0130.435
makeGeneNetwork0.1350.0050.139
makeMetaboliteNetwork0.0680.0020.071
makeReactionNetwork0.0900.0020.154
pathClassifier0.8500.0270.879
pathCluster0.3680.0090.378
pathRanker0.9580.0220.983
pathsToBinary0.6620.0070.671
plotAllNetworks8.1210.0458.176
plotClusters1.0610.0111.075
plotCytoscape0.3530.0060.359
plotNetwork0.6560.0190.676
plotPathClassifier0.7940.0190.815
plotPathCluster0.3490.0080.358
plotPaths11.337 0.04311.395
predictPathClassifier0.7410.0070.749
predictPathCluster0.3590.0050.363
reindexNetwork0.1780.0050.183
rmSmallCompounds0.0800.0030.082
samplePaths0.8020.0200.823
simplifyReactionNetwork0.1270.0030.129
toGraphNEL0.7810.0110.794
vertexDeleteReconnect0.0650.0040.069