############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r qrqc -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data qrqc ### ############################################################################## ############################################################################## * checking for file 'qrqc/DESCRIPTION' ... OK * preparing 'qrqc': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package 'qrqc' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_io.c -o R_init_io.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o In file included from F:/biocbuild/bbs-3.17-bioc/R/include/R.h:78, from io.c:7: io.c: In function 'hash_seq_kmers': io.c:222:39: error: 'SINT_MAX' undeclared (first use in this function); did you mean 'WINT_MAX'? 222 | char *a_kmer = Calloc(k + 2 + log10(SINT_MAX), char), *start_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:53:56: note: in definition of macro 'Calloc' 53 | #define Calloc(n, t) (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) ) | ^ io.c:222:39: note: each undeclared identifier is reported only once for each function it appears in 222 | char *a_kmer = Calloc(k + 2 + log10(SINT_MAX), char), *start_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:53:56: note: in definition of macro 'Calloc' 53 | #define Calloc(n, t) (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) ) | ^ In file included from io.c:12: io.c: At top level: F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: 'kseq_destroy' defined but not used [-Wunused-function] 171 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:237:9: note: in expansion of macro '__KSEQ_BASIC' 237 | __KSEQ_BASIC(SCOPE, type_t) \ | ^~~~~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2' 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ io.c:29:1: note: in expansion of macro 'KSEQ_INIT' 29 | KSEQ_INIT(FILE_TYPE*, gzreadclone) | ^~~~~~~~~ make: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:257: io.o] Error 1 ERROR: compilation failed for package 'qrqc' * removing 'F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpyUwdwH/Rinst45fc3c0e1cc2/qrqc' ----------------------------------- ERROR: package installation failed