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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data qrqc
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* 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 (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/site-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/site-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/site-library/Rhtslib/include/htslib/kseq.h:165:33: 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/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-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/site-library/Rhtslib/include/htslib/kseq.h:165:33: 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/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-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/site-library/Rhtslib/include/htslib/kseq.h:171:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:237:2: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |  __KSEQ_BASIC(SCOPE, type_t)     \
      |  ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-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 ‘/tmp/RtmpHZ5zLE/Rinst3e7ff3f59b2f3/qrqc’
      -----------------------------------
ERROR: package installation failed