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BUILD report for bgx on merida1

This page was generated on 2019-04-16 11:54:39 -0400 (Tue, 16 Apr 2019).

Package 122/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgx 1.48.1
Ernest Turro
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/bgx
Branch: RELEASE_3_8
Last Commit: d5674fd
Last Changed Date: 2018-11-01 12:25:59 -0400 (Thu, 01 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  ERROR [ ERROR ] skipped  skipped 

Summary

Package: bgx
Version: 1.48.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bgx
StartedAt: 2019-04-15 19:03:13 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 19:03:28 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 14.4 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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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... 306e4:200800:7fbee3ff: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
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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -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:39:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
bgx.cc:152:3: error: reference to 'array' is ambiguous
  array tau(*samples), beta(*samples), eta(*samples), eta_jmps(*samples), a(*conditions), b(*conditions);
  ^
bgx.cc:77:26: 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;
                                                               ^
bgx.cc:153:35: error: use of undeclared identifier 'eta_jmps'; did you mean 'eta_jmp'?
  for(int j=0; j < *samples; j++) eta_jmps[j] = *eta_jmp;
                                  ^˜˜˜˜˜˜˜
                                  eta_jmp
bgx.cc:115:11: note: 'eta_jmp' declared here
         double* eta_jmp, bool* adaptive, int* batch_size, double* optimalAR, 
                 ^
bgx.cc:330:5: error: use of undeclared identifier 'tau'
    tau[j]=0.0005/**/*rand.Uniform(0.5,2)/**/;
    ^
bgx.cc:331:5: error: unknown type name 'beta'; did you mean 'peta'?
    beta[j]=0;
    ^˜˜˜
    peta
/usr/local/clang4/bin/../include/c++/v1/ratio:286:43: note: 'peta' declared here
typedef ratio<   1000000000000000LL, 1LL> peta;
                                          ^
bgx.cc:331:9: warning: decomposition declarations are a C++1z extension [-Wc++1z-extensions]
    beta[j]=0;
        ^˜˜
bgx.cc:331:9: error: decomposition declaration cannot be declared with type 'peta' (aka 'ratio<1000000000000000LL, 1LL>'); declared type must be 'auto' or reference to 'auto'
bgx.cc:331:10: error: redefinition of 'j'
    beta[j]=0;
         ^
bgx.cc:329:11: note: previous definition is here
  for(int j=0; j<*samples; ++j){
          ^
bgx.cc:331:9: error: no viable conversion from 'int' to 'peta' (aka 'ratio<1000000000000000LL, 1LL>')
    beta[j]=0;
        ^   ˜
/usr/local/clang4/bin/../include/c++/v1/ratio:247:28: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'int' to 'const std::__1::ratio<1000000000000000, 1> &' for 1st argument
class _LIBCPP_TEMPLATE_VIS ratio
                           ^
bgx.cc:356:5: error: use of undeclared identifier 'eta'
    eta[j]=1.0/var_lh;
    ^
bgx.cc:436:10: error: use of undeclared identifier 'a'
         a[j] = 0;
         ^
bgx.cc:437:10: error: use of undeclared identifier 'b'
         b[j] = 3;
         ^
bgx.cc:447:9: error: use of undeclared identifier 'a'
        a[j] = tempS / double(*genes);
        ^
bgx.cc:449:9: error: use of undeclared identifier 'b'
        b[j] = (double(*genes)-1)/(tempSS-(tempS*tempS / double(*genes)));
        ^
bgx.cc:463:45: error: use of undeclared identifier 'a'
    empBayesEst_ << '\t'  << j << '\t'  <<  a[j] << '\t'  <<  b[j] << endl;
                                            ^
bgx.cc:463:63: error: use of undeclared identifier 'b'
    empBayesEst_ << '\t'  << j << '\t'  <<  a[j] << '\t'  <<  b[j] << endl;
                                                              ^
bgx.cc:530:61: error: use of undeclared identifier 'eta'
    unknownProbeSeqs, *numberOfUnknownProbeSeqs, h, lambda, eta, &rand);
                                                            ^
bgx.cc:538:39: error: use of undeclared identifier 'tau'; did you mean 'tan'?
  AccS = new S_T(PM,MM,h,phi,mu,sigma,tau,beta,probesets,samplesets,categories );
                                      ^˜˜
                                      tan
/usr/local/clang4/bin/../include/c++/v1/math.h:929:1: note: 'tan' declared here
tan(_A1 __lcpp_x) _NOEXCEPT {return tan((double)__lcpp_x);}
^
bgx.cc:538:43: error: use of undeclared identifier 'beta'; did you mean 'R::beta'?
  AccS = new S_T(PM,MM,h,phi,mu,sigma,tau,beta,probesets,samplesets,categories );
                                          ^˜˜˜
                                          R::beta
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Rmath.h:202:19: note: 'R::beta' declared here
    inline double beta(double a, double b)      { return ::Rf_beta(a, b); }
                  ^
bgx.cc:541:37: error: use of undeclared identifier 'eta'; did you mean 'eta_'?
  AccH = new H_T(PM,MM,s,phi,lambda,eta,tau,beta,categories);
                                    ^˜˜
                                    eta_
bgx.cc:158:18: note: 'eta_' declared here
    tau_, phi_,  eta_, unkcats_;
                 ^
bgx.cc:541:41: error: use of undeclared identifier 'tau'; did you mean 'tan'?
  AccH = new H_T(PM,MM,s,phi,lambda,eta,tau,beta,categories);
                                        ^˜˜
                                        tan
/usr/local/clang4/bin/../include/c++/v1/math.h:929:1: note: 'tan' declared here
tan(_A1 __lcpp_x) _NOEXCEPT {return tan((double)__lcpp_x);}
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make: *** [bgx.o] Error 1
ERROR: compilation failed for package ‘bgx’
* removing ‘/private/tmp/RtmpwjlRXB/Rinstd3984f4dfc3b/bgx’
      -----------------------------------
ERROR: package installation failed