Closed martin-g closed 1 year ago
Hi,
The build of the package fails for Bioconductor 3.17 (devel):
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qrqc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘qrqc’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_io.c -o R_init_io.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c io.c -o io.o In file included from /home/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; | ^~~~~~~~ /home/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; | ^~~~~~~~ /home/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: In function ‘summarize_file’: io.c:33:25: warning: initialization of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 33 | #define FILE_OPEN(x, m) (gzopen(x, m)) | ^ io.c:348:19: note: in expansion of macro ‘FILE_OPEN’ 348 | FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r"); | ^~~~~~~~~ io.c:351:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] 351 | block = kseq_init(fp); | ^~ | | | struct gzFile_s ** In file included from io.c:12: /home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:40: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 165 | SCOPE kseq_t *kseq_init(type_t fd) \ /home/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) \ | ^~~~~~~~~~~~ /home/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:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types] 453 | block = kseq_init(fp); | ^~ | | | struct gzFile_s ** In file included from io.c:12: /home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:40: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 165 | SCOPE kseq_t *kseq_init(type_t fd) \ /home/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) \ | ^~~~~~~~~~~~ /home/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:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 454 | FILE_CLOSE(fp); | ^~ | | | struct gzFile_s ** io.c:34:32: note: in definition of macro ‘FILE_CLOSE’ 34 | #define FILE_CLOSE(x) (gzclose(x)) | ^ In file included from /usr/include/zlib.h:34, from io.c:31: /usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ In file included from io.c:12: At top level: /home/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) \ | ^~~~~~~~~~~~ /home/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) \ | ^~~~~~~~~~~~ /home/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:35:1: note: in expansion of macro ‘KSEQ_INIT’ 35 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: io.o] Error 1 ERROR: compilation failed for package ‘qrqc’ * removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/qrqc’
We've found it while testing the package for Linux ARM64.
Hi,
The build of the package fails for Bioconductor 3.17 (devel):
We've found it while testing the package for Linux ARM64.