##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL TransView
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'TransView' ...
** this is package 'TransView' version '1.51.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c R_init_TransView.c -o R_init_TransView.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c bin_density.c -o bin_density.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c construct_dc.c -o construct_dc.o
construct_dc.c: In function 'set_filter':
construct_dc.c:58:37: warning: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration]
   58 |         ft->sequence_name = (char**)Calloc(flen,char*);
      |                                     ^~~~~~
      |                                     calloc
construct_dc.c:58:49: error: expected expression before 'char'
   58 |         ft->sequence_name = (char**)Calloc(flen,char*);
      |                                                 ^~~~
construct_dc.c:59:46: error: expected expression before 'int32_t'
   59 |         ft->values = (int32_t **)Calloc(flen,int32_t*);
      |                                              ^~~~~~~
construct_dc.c:60:51: error: expected expression before 'int32_t'
   60 |         ft->value_length = (int32_t *)Calloc(flen,int32_t);
      |                                                   ^~~~~~~
construct_dc.c:65:84: error: expected expression before 'char'
   65 |                 ft->sequence_name[j] = Calloc(strlen(CHAR(STRING_ELT(fnames, j))), char);
      |                                                                                    ^~~~
construct_dc.c: In function 'destroy_filter':
construct_dc.c:85:41: warning: implicit declaration of function 'Free'; did you mean 'free'? [-Wimplicit-function-declaration]
   85 |                 if(ft->sequence_name[j])Free(ft->sequence_name[j]);
      |                                         ^~~~
      |                                         free
construct_dc.c: In function 'write_density':
construct_dc.c:172:55: error: expected expression before 'uint32_t'
  172 |         proc_chrom=Calloc(bam_file->header->n_targets,uint32_t);
      |                                                       ^~~~~~~~
construct_dc.c:198:44: error: expected expression before 'usersize'
  198 |                 cptr = Calloc(cs.max_pos+1,usersize);
      |                                            ^~~~~~~~
construct_dc.c:199:53: error: expected expression before 'uint32_t'
  199 |                 lstart_ind=Calloc(cs.min_indexspace,uint32_t);
      |                                                     ^~~~~~~~
construct_dc.c:200:51: error: expected expression before 'uint32_t'
  200 |                 lend_ind=Calloc(cs.min_indexspace,uint32_t);
      |                                                   ^~~~~~~~
make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:289: construct_dc.o] Error 1
ERROR: compilation failed for package 'TransView'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/TransView'