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BioC 3.2: CHECK report for NetPathMiner on oaxaca

This page was generated on 2015-08-24 10:58:23 -0700 (Mon, 24 Aug 2015).

Package 682/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.5.2
Ahmed Mohamed
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/NetPathMiner
Last Changed Rev: 105781 / Revision: 107696
Last Changed Date: 2015-07-02 14:53:52 -0700 (Thu, 02 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: NetPathMiner
Version: 1.5.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetPathMiner_1.5.2.tar.gz
StartedAt: 2015-08-24 02:14:49 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:16:48 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 119.9 seconds
RetCode: 0
Status:  OK 
CheckDir: NetPathMiner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetPathMiner_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/NetPathMiner.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.5.2’
* 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 ... [21s/25s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RCytoscape’ ‘graph’ ‘rBiopaxParser’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
plotCytoscape: no visible global function definition for
  ‘cy2.edge.names’
* 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 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 compiled code ... NOTE
File ‘NetPathMiner/libs/NetPathMiner.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘methods.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/57s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       17.356  0.054  17.840
plotAllNetworks 14.125  0.054  14.425
* 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-3.2-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.


NetPathMiner.Rcheck/00install.out:

* installing *source* package ‘NetPathMiner’ ...
checking for gcc... clang
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 accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -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.
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c PathRanker.cpp -o PathRanker.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hme3m.c -o hme3m.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c methods.cpp -o methods.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c pathScope.cpp -o pathScope.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -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 -lsbml -lxml2 -lxml2 -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/NetPathMiner.Rcheck/NetPathMiner/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NetPathMiner)

NetPathMiner.Rcheck/NetPathMiner-Ex.timings:

nameusersystemelapsed
KGML2igraph0.3210.0050.369
MIRIAM0.3570.0050.364
NPMdefaults0.0150.0030.018
SBML2igraph0.4000.0060.501
assignEdgeWeights0.5920.0100.622
biopax2igraph1.0060.0211.106
colorVertexByAttr0.2220.0030.250
ex_biopax0.0260.0020.028
ex_kgml_sig0.3090.0050.319
ex_microarray0.0040.0000.005
ex_sbml1.5430.0101.568
extractPathNetwork2.3370.0062.347
getAttr0.0430.0030.045
getGeneSetNetworks0.0140.0010.015
getGeneSets0.0960.0020.098
getPathsAsEIDs2.2890.0142.338
layoutVertexByAttr0.6150.0110.632
makeGeneNetwork0.2660.0030.270
makeReactionNetwork0.1660.0010.169
pathClassifier1.1730.0121.210
pathCluster0.4660.0030.491
pathRanker1.1790.0091.205
pathsToBinary0.8760.0080.887
plotAllNetworks14.125 0.05414.425
plotClusters1.4370.0081.471
plotCytoscape0.5220.0050.527
plotNetwork0.8910.0111.014
plotPathClassifier1.0500.0091.079
plotPathCluster0.4720.0050.477
plotPaths17.356 0.05417.840
predictPathClassifier1.0580.0041.072
predictPathCluster0.5530.0020.557
rmSmallCompounds0.1770.0010.179
samplePaths1.0720.0091.085
simplifyReactionNetwork0.2720.0040.277
toGraphNEL0.8460.0060.855
vertexDeleteReconnect0.1250.0020.128