------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libsysinfo-0.0.3_2.txz SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building ===> Extracting for subread-2.0.1 => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. Extracted Memory Use: 74.15M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for subread-2.0.1 ===> Applying ports patches for subread-2.0.1 from /xports/biology/subread/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on package: gmake>=4.3 - found ===> subread-2.0.1 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) ===> Configuring for subread-2.0.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for subread-2.0.1 gmake[1]: Entering directory '/construction/biology/subread/subread-2.0.1-source/src' cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core.o core.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-junction.o core-junction.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-indel.o core-indel.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sambam-file.o sambam-file.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sublog.o sublog.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-algorithms.o gene-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o hashtable.o hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-files.o input-files.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sorted-hashtable.o sorted-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-value-index.o gene-value-index.c sorted-hashtable.c:27:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [: sorted-hashtable.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/construction/biology/subread/subread-2.0.1-source/src' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/subread FAILED 00:00:05