Package: DeMixT

Version: 0.99.9

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DeMixT

StartedAt: 2019-04-08 18:22:51 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 18:23:25 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 34.0 seconds

RetCode: 0

Status:  OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DeMixT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c DeMixT.c -o DeMixT.o
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:253:26: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
       if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\n", i+1);
                          ^˜˜˜˜˜˜
                          dprintf
DeMixT.c:43:9: warning: unused variable ‘nthread’ [-Wunused-variable]
     int nthread=*thread;
         ^˜˜˜˜˜˜
DeMixT.c:36:45: warning: variable ‘st2_sig_2’ set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                             ^˜˜˜˜˜˜˜˜
DeMixT.c:36:33: warning: variable ‘st1_sig_2’ set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                 ^˜˜˜˜˜˜˜˜
DeMixT.c:36:22: warning: variable ‘st2_mu_2’ set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                      ^˜˜˜˜˜˜˜
DeMixT.c:36:11: warning: variable ‘st1_mu_2’ set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
           ^˜˜˜˜˜˜˜
DeMixT.c: In function ‘gettumor’:
DeMixT.c:540:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^˜˜˜˜˜˜
DeMixT.c:540:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^˜˜˜˜˜˜
DeMixT.c: In function ‘getpi’:
DeMixT.c:1229:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^˜˜˜˜˜˜
DeMixT.c:1229:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^˜˜˜˜˜˜
DeMixT.c: In function ‘getpiT’:
DeMixT.c:1259:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^˜˜˜˜˜˜
DeMixT.c:1259:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^˜˜˜˜˜˜
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:188:11: warning: ‘Tavgtmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
           ^
DeMixT.c:226:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   CD = calloc(intx ,sizeof(double *));
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from DeMixT.c:8:0:
/usr/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here
 extern void *calloc (size_t __nmemb, size_t __size)
              ^˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o DeMixT.so DeMixT.o init.o registerDynamicSymbol.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DeMixT)