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INSTALL 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 INSTALL NetPathMiner
StartedAt: 2021-01-18 16:18:28 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 16:19:17 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:  OK 

Command output

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