Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1437/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.44.0  (landing page)
Ahmed Mohamed
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/NetPathMiner
git_branch: RELEASE_3_21
git_last_commit: b4383b8
git_last_commit_date: 2025-04-15 13:41:41 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for NetPathMiner on lconway

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: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2025-04-21 22:17:19 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:18:31 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 72.3 seconds
RetCode: 0
Status:   OK  
CheckDir: NetPathMiner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/NetPathMiner.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.44.0’
* 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 ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ‘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’
Undefined global functions or variables:
  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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'assignEdgeWeights.Rd':
  ‘[base:Extremes]{max}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 6.199  0.047   6.272
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘NetPathMiner’ ...
** this is package ‘NetPathMiner’ version ‘1.44.0’
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch x86_64
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 -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c kgml_interface.cpp -o kgml_interface.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c methods.cpp -o methods.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sbml_interface.cpp -o sbml_interface.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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
KGML2igraph0.2900.0160.306
MIRIAM0.1800.0150.195
NPMdefaults0.0040.0040.009
SBML2igraph0.0010.0000.001
assignEdgeWeights0.3290.0120.343
biopax2igraph0.4490.0190.472
colorVertexByAttr0.1360.0060.143
ex_biopax0.0230.0040.027
ex_kgml_sig0.1890.0070.197
ex_microarray0.0030.0020.004
ex_sbml0.7980.0100.811
extractPathNetwork1.6040.0301.641
getAttr0.0390.0040.043
getGeneSetNetworks0.0290.0020.030
getGeneSets0.0900.0050.094
getPathsAsEIDs1.6320.0161.653
layoutVertexByAttr0.3410.0140.358
makeGeneNetwork0.2400.0060.246
makeMetaboliteNetwork0.0930.0020.096
makeReactionNetwork0.1440.0020.147
pathClassifier1.0180.0301.053
pathCluster0.3790.0090.390
pathRanker0.7960.0090.808
pathsToBinary0.8700.0100.882
plotAllNetworks4.3950.0424.460
plotClusters1.0590.0161.080
plotCytoscape0.2980.0060.306
plotNetwork0.4600.0160.480
plotPathClassifier1.0090.0221.037
plotPathCluster0.3520.0080.363
plotPaths6.1990.0476.272
predictPathClassifier0.7710.0090.782
predictPathCluster0.3860.0070.397
reindexNetwork0.2100.0060.218
rmSmallCompounds0.0870.0020.090
simplifyReactionNetwork0.1610.0040.165
toGraphNEL0.5560.0120.571
vertexDeleteReconnect0.0690.0020.072