+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/subread-2.0.8/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/subread-2.0.8/work.log ===> Building for subread-2.0.8 gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o core.o core.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o sublog.o sublog.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o hashtable.o hashtable.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o input-files.o input-files.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/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 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o HelperFunctions.o HelperFunctions.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o interval_merge.o interval_merge.c gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o long-hashtable.o long-hashtable.c HelperFunctions.c: In function 'get_free_total_mem': HelperFunctions.c:2749:5: error: implicit declaration of function 'sysinfo' [-Wimplicit-function-declaration] 2749 | sysinfo(&sinf); | ^~~~~~~ HelperFunctions.c:2752:34: error: 'struct sysinfo' has no member named 'bufferram' 2752 | *free_mem = cached_mem + sinf.bufferram+sinf.freeram; | ^ HelperFunctions.c:2752:49: error: 'struct sysinfo' has no member named 'freeram' 2752 | *free_mem = cached_mem + sinf.bufferram+sinf.freeram; | ^ HelperFunctions.c:2753:18: error: 'struct sysinfo' has no member named 'totalram' 2753 | *total = sinf.totalram; | ^ gcc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fcommon -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/opt/pkg/include -c -o core-bigtable.o core-bigtable.c gmake: *** [: HelperFunctions.o] Error 1 gmake: *** Waiting for unfinished jobs.... input-files.c: In function 'load_exon_annotation': input-files.c:2222:43: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2222 | this_gene_name[i] = 0; | ~~~~~~~~~~~~~~~~~~^~~ input-files.c:2209:34: note: at offset 1200 into destination object 'this_gene_name' of size 128 2209 | char buff[1200], this_gene_name[MAX_GENE_NAME_LEN], chromosome_name[MAX_CHROMOSOME_NAME_LEN]; | ^~~~~~~~~~~~~~ *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread