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BioC 3.5: BUILD report for bgx on veracruz2

This page was generated on 2017-10-18 14:28:13 -0400 (Wed, 18 Oct 2017).

Package 104/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgx 1.42.0
Ernest Turro
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/bgx
Branch: RELEASE_3_5
Last Commit: b67a03e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: bgx
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bgx
StartedAt: 2017-10-17 18:42:43 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 18:42:47 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 4.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bgx
###
##############################################################################
##############################################################################


* 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/Rtmp5ba2Ru/Rinst14ce16164fcf7/bgx’
      -----------------------------------
ERROR: package installation failed