bgx 1.43.0
Ernest Turro
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bgx | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bgx
###
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* checking for file ‘bgx/DESCRIPTION’ ... OK
* preparing ‘bgx’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘bgx’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
checking for gcc architecture flag...
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306e4:3200800:7fbee3ff:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... yes
checking for gcc architecture flag... -mcpu=pentiumpro
checking for clang option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -Wall -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
In file included from bgx.cc:29:
./bgx_updates.hh:43:3: error: reference to 'array' is ambiguous
array& tau;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:44:3: error: reference to 'array' is ambiguous
array& beta;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:54:23: error: reference to 'array' is ambiguous
array2d& taug_, array& tau_, array& beta_, int* probesets_,
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:54:36: error: reference to 'array' is ambiguous
array2d& taug_, array& tau_, array& beta_, int* probesets_,
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:90:3: error: reference to 'array' is ambiguous
array& eta;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:91:3: error: reference to 'array' is ambiguous
array& tau;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:92:3: error: reference to 'array' is ambiguous
array& beta;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:96:7: error: reference to 'array' is ambiguous
array& eta_, array& tau_, array& beta_, int *categories_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:96:20: error: reference to 'array' is ambiguous
array& eta_, array& tau_, array& beta_, int *categories_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:96:33: error: reference to 'array' is ambiguous
array& eta_, array& tau_, array& beta_, int *categories_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:161:3: error: reference to 'array' is ambiguous
array& a;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:162:3: error: reference to 'array' is ambiguous
array& b;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:168:38: error: reference to 'array' is ambiguous
Sigma_T(array2d& S_, array2d& mu_, array& a_, array& b_, int* probesets_, int* samplesets_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:168:49: error: reference to 'array' is ambiguous
Sigma_T(array2d& S_, array2d& mu_, array& a_, array& b_, int* probesets_, int* samplesets_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:207:3: error: reference to 'array' is ambiguous
array& eta;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:213:25: error: reference to 'array' is ambiguous
Lambda_T(array2d& H_, array& eta_, double p_mu_, double p_tau_, vector<vector<int> > & cat_indices_)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:249:19: error: reference to 'array' is ambiguous
double operator()(array & eta, double eta2, int j/*, int cat*/)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:280:21: error: reference to 'array' is ambiguous
double operator()(array & kappa, double kappa2, int j/*, int cat*/)
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from bgx.cc:29:
./bgx_updates.hh:305:3: error: reference to 'array' is ambiguous
array& tau;
^
./bgx_updates.hh:30:26: note: candidate found by name lookup is 'array'
typedef valarray<double> array;
^
/usr/local/clang4/bin/../include/c++/v1/__tuple:222:64: note: candidate found by name lookup is 'std::__1::array'
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [bgx.o] Error 1
ERROR: compilation failed for package ‘bgx’
* removing ‘/private/tmp/Rtmp8ll3sS/Rinstbebd1ca77b7f/bgx’
-----------------------------------
ERROR: package installation failed