=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for subread-2.0.8
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o core.o core.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o core-junction.o core-junction.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o core-indel.o core-indel.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o sambam-file.o sambam-file.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o sublog.o sublog.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o gene-algorithms.o gene-algorithms.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o hashtable.o hashtable.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:54:10: warning: implicit declaration of function 'fopen64'; did you mean 'fopen'? [-Wimplicit-function-declaration]
54 | return fopen64(fname, mode);
| ^~~~~~~
| fopen
input-files.c:54:10: warning: returning 'int' from a function with return type 'FILE *' makes pointer from integer without a cast [-Wint-conversion]
54 | return fopen64(fname, mode);
| ^~~~~~~~~~~~~~~~~~~~
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o sorted-hashtable.o sorted-hashtable.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o gene-value-index.o gene-value-index.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o exon-algorithms.o exon-algorithms.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o HelperFunctions.o HelperFunctions.c
gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -O2 -fcommon -I/usr/include -I/usr/include -c -o interval_merge.o interval_merge.c
HelperFunctions.c:51:10: fatal error: sys/sysinfo.h: No such file or directory
51 | #include <sys/sysinfo.h>
| ^~~~~~~~~~~~~~~
compilation terminated.
gmake: *** [<builtin>: HelperFunctions.o] Error 1
gmake: *** Waiting for unfinished jobs....
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5267:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
5267 | char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
/usr/include/stdlib.h:117:7: note: in a call to allocation function 'malloc' declared here
117 | void *malloc(size_t);
| ^~~~~~
*** Error code 2
Stop.
make[1]: stopped in /usr/pkgsrc/biology/subread
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/biology/subread