############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TransView ### ############################################################################## ############################################################################## * checking for file ‘TransView/DESCRIPTION’ ... OK * preparing ‘TransView’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘TransView’ ... ** this is package ‘TransView’ version ‘1.51.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_TransView.c -o R_init_TransView.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bin_density.c -o bin_density.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c construct_dc.c -o construct_dc.o In file included from construct_dc.c:23: In file included from ./parse_sam.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include/htslib/sam.h:33: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include/htslib/hts.h:36: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes] HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); ^ /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT' #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first))) ^ construct_dc.c:58:30: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] ft->sequence_name = (char**)Calloc(flen,char*); ^ construct_dc.c:58:42: error: expected expression ft->sequence_name = (char**)Calloc(flen,char*); ^ construct_dc.c:59:39: error: unexpected type name 'int32_t': expected expression ft->values = (int32_t **)Calloc(flen,int32_t*); ^ construct_dc.c:59:47: error: expected expression ft->values = (int32_t **)Calloc(flen,int32_t*); ^ construct_dc.c:60:44: error: unexpected type name 'int32_t': expected expression ft->value_length = (int32_t *)Calloc(flen,int32_t); ^ construct_dc.c:65:70: error: expected expression ft->sequence_name[j] = Calloc(strlen(CHAR(STRING_ELT(fnames, j))), char); ^ construct_dc.c:85:27: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if(ft->sequence_name[j])Free(ft->sequence_name[j]); ^ construct_dc.c:85:27: note: did you mean 'free'? /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here void free(void *); ^ construct_dc.c:87:23: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if(ft->sequence_name)Free(ft->sequence_name); ^ construct_dc.c:122:2: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] Free(cptr); ^ construct_dc.c:172:13: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] proc_chrom=Calloc(bam_file->header->n_targets,uint32_t); ^ construct_dc.c:172:48: error: unexpected type name 'uint32_t': expected expression proc_chrom=Calloc(bam_file->header->n_targets,uint32_t); ^ construct_dc.c:198:30: error: unexpected type name 'usersize': expected expression cptr = Calloc(cs.max_pos+1,usersize); ^ construct_dc.c:199:39: error: unexpected type name 'uint32_t': expected expression lstart_ind=Calloc(cs.min_indexspace,uint32_t); ^ construct_dc.c:200:37: error: unexpected type name 'uint32_t': expected expression lend_ind=Calloc(cs.min_indexspace,uint32_t); ^ construct_dc.c:347:2: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] Free(proc_chrom); ^ 1 warning and 15 errors generated. make: *** [construct_dc.o] Error 1 ERROR: compilation failed for package ‘TransView’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpQOBMEP/Rinst127c861cd18d8/TransView’ ----------------------------------- ERROR: package installation failed