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 | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | ERROR | [ 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... 306e4:200800:7fbee3ff: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