jandrewrfarrell
commented
3 years ago It looks like the problems are these lines ./../runRufus.sh: line 469: /usr/bin/time: No such file or directory ./../runRufus.sh: line 469: /usr/bin/time: No such file or directory ./../runRufus.sh: line 472: /usr/bin/time: No such file or directory I assumed that all linux machines would have time installed but it looks like your system does not. If you want to just remove "/usr/bin/time -v” from those lines it should work just fine. I will remove those calls from the GitHub version of RUFUS
Andrew Farrell PhD
Director of Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine
15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Email: JAndrewRFarrell@gmail.com
http://marthlab.org/ http://marthlab.org/=====================================
On Jan 29, 2021, at 5:38 PM, Matthew J. Oldach notifications@github.com wrote:
Trying to build RUFUS with gcc version
[moldach@cedar1 TOOL_TMP_DIR]$ wget https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz --2021-01-29 11:44:34-- https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz Resolving github.com (github.com)... 140.82.114.3 Connecting to github.com (github.com)|140.82.114.3|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://codeload.github.com/jandrewrfarrell/RUFUS/tar.gz/V1.0 [following] --2021-01-29 11:44:34-- https://codeload.github.com/jandrewrfarrell/RUFUS/tar.gz/V1.0 Resolving codeload.github.com (codeload.github.com)... 140.82.114.9 Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/x-gzip] Saving to: ‘V1.0.tar.gz’
V1.0.tar.gz [ <=> ] 20.80M 4.55MB/s in 4.4s
2021-01-29 11:44:39 (4.77 MB/s) - ‘V1.0.tar.gz’ saved [21815513]
[moldach@cedar1 TOOL_TMP_DIR]$ tar -zxvf V1.0.tar.gz RUFUS-1.0/ RUFUS-1.0/.gitignore RUFUS-1.0/CMakeLists.txt RUFUS-1.0/Install.sh RUFUS-1.0/Makefile RUFUS-1.0/README.md RUFUS-1.0/bin/ RUFUS-1.0/bin/AnnotateOverlap RUFUS-1.0/bin/ConvertFASTqD.to.FASTQ RUFUS-1.0/bin/ModelDist RUFUS-1.0/bin/Overlap RUFUS-1.0/bin/OverlapRegion RUFUS-1.0/bin/RUFUS.Build RUFUS-1.0/bin/RUFUS.Filter RUFUS-1.0/bin/RUFUS.interpret RUFUS-1.0/bin/ReplaceQwithDinFASTQD RUFUS-1.0/bin/external/ RUFUS-1.0/bin/external/CMakeLists.txt RUFUS-1.0/bin/externals/ RUFUS-1.0/bin/externals/.ignore RUFUS-1.0/cloud/ RUFUS-1.0/cloud/CMakeLists.txt RUFUS-1.0/cloud/CheckJellyHashList.sh RUFUS-1.0/cloud/PassThroughSamCheck RUFUS-1.0/cloud/PassThroughSamCheck.cpp RUFUS-1.0/cloud/PassThroughSamCheck.stranded RUFUS-1.0/cloud/PassThroughSamCheck.stranded.cpp RUFUS-1.0/cloud/RUFUS.Filter.jellyPipe RUFUS-1.0/cloud/RUFUS.Filter.jellyPipe.cpp RUFUS-1.0/cloud/RUFUS.search.1kg RUFUS-1.0/cloud/RUFUS.search.1kg.cpp RUFUS-1.0/cloud/ReRunOverlap.asc.sh RUFUS-1.0/cloud/RunJellyForRUFUS RUFUS-1.0/cloud/RunJellyForRUFUS.UGP RUFUS-1.0/cloud/RunRUFUS.1000G.withDupRemoce.sh RUFUS-1.0/cloud/RunRUFUS.ASC.no1kg.sh RUFUS-1.0/cloud/RunRUFUS.ASC.sh RUFUS-1.0/cloud/RunRUFUS.Trio.sh RUFUS-1.0/cloud/jellyfish-2.2.5.tar.gz RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.a RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.la RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.lai RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so.2 RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so.2.0.0 RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/LICENSE RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile.am RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile.in RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/README RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/aclocal.m4 RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/compile RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.guess RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.h RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.h.in RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.log RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.status RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.sub RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/configure RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/configure.ac RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/depcomp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/jellyfish.man RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/jellyfish.pdf RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/gtest.mk RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/allocators_mmap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_bits_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_field.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_gcc.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/backtrace.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/binary_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_common.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_counter2.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_filter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/circular_buffer.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/compare_and_swap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cooperative_pool.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cooperative_pool2.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cpp_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/divisor.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/err.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/file_header.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/generator_manager.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/generic_file_header.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/hash_counter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/int128.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/jellyfish.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/json.h RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/large_hash_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/large_hash_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/locks_pthread.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mapped_file.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_dna.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_dna_bloom_counter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_heap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_overlap_sequence_parser.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_qual_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/misc.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/offsets_key_value.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/rectangular_binary_matrix.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/simple_circular_buffer.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/sorted_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stdio_filebuf.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/storage.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stream_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stream_manager.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/text_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/thread_exec.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/time.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/token_ring.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/whole_sequence_parser.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/allocators_mmap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_bits_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_field.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_gcc.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/backtrace.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/binary_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_common.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_counter2.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_filter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/circular_buffer.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/compare_and_swap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cooperative_pool.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cooperative_pool2.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cpp_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/divisor.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/err.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/file_header.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/generator_manager.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/generic_file_header.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/hash_counter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/int128.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/jellyfish.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/json.h RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/large_hash_array.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/large_hash_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/locks_pthread.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mapped_file.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_dna.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_dna_bloom_counter.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_heap.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_overlap_sequence_parser.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_qual_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/misc.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/offsets_key_value.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/rectangular_binary_matrix.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/simple_circular_buffer.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/sorted_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stdio_filebuf.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/storage.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stream_iterator.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stream_manager.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/text_dumper.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/thread_exec.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/time.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/token_ring.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/whole_sequence_parser.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/install-sh RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish-2.0.pc RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish-2.0.pc.in RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/.dirstamp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/backtrace.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/bin_test_all-backtrace.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/dbg.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/generate_sequence.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/merge_files.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/mersenne.Po RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.dirstamp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/backtrace.cc RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/dbg.cc RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/dbg.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/fstream_default.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/generate_sequence.cc RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/generate_sequence_cmdline.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.cc RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.hpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/mersenne.cpp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/randomc.h RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/.dirstamp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/allocators_mmap.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/generator_manager.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/int128.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/jsoncpp.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/mer_dna.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/misc.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/rectangular_binary_matrix.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/storage.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/thread_exec.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/time.Plo RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.dirstamp RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/ RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/allocators_mmap.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/generator_manager.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/int128.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/jsoncpp.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/mer_dna.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/misc.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/rectangular_binary_matrix.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/storage.o RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/thread_exec.o 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RUFUS-1.0/scripts/runRUFUSAny.sh RUFUS-1.0/scripts/sort RUFUS-1.0/scripts/test.sh RUFUS-1.0/src/ RUFUS-1.0/src/AnnotateOverlap.cpp RUFUS-1.0/src/CMakeLists.txt RUFUS-1.0/src/ConvertFASTqD.to.FASTQ.cpp RUFUS-1.0/src/ModelDist.cpp RUFUS-1.0/src/Overlap RUFUS-1.0/src/Overlap.cpp RUFUS-1.0/src/OverlapRegion RUFUS-1.0/src/OverlapRegion.cpp RUFUS-1.0/src/OverlapSam.cpp RUFUS-1.0/src/RUFUS.1kg.filter.cpp RUFUS-1.0/src/RUFUS.Build.cpp RUFUS-1.0/src/RUFUS.CheckHashFilter.cpp RUFUS-1.0/src/RUFUS.Filter.cpp RUFUS-1.0/src/RUFUS.interpret.cpp RUFUS-1.0/src/RUFUS.interpret.cpp.new.good.awesome RUFUS-1.0/src/RUFUS.interpret.cpp.save.cpp RUFUS-1.0/src/RUFUS.interpret.current.cpp RUFUS-1.0/src/RUFUS.interpret.save.cpp RUFUS-1.0/src/ReplaceQwithDinFASTQD.cpp RUFUS-1.0/src/SamRead.cpp RUFUS-1.0/src/SamRead.h RUFUS-1.0/src/SamUtil.cpp RUFUS-1.0/src/SamUtil.h RUFUS-1.0/src/Util.cpp RUFUS-1.0/src/Util.h RUFUS-1.0/src/externals/ RUFUS-1.0/src/externals/fastahack/ RUFUS-1.0/src/externals/fastahack/Fasta.cpp RUFUS-1.0/src/externals/fastahack/Fasta.h RUFUS-1.0/src/externals/fastahack/Fasta.o RUFUS-1.0/src/externals/fastahack/FastaHack.cpp RUFUS-1.0/src/externals/fastahack/LargeFileSupport.h RUFUS-1.0/src/externals/fastahack/Makefile RUFUS-1.0/src/externals/fastahack/README RUFUS-1.0/src/externals/fastahack/Region.h RUFUS-1.0/src/externals/fastahack/disorder.c RUFUS-1.0/src/externals/fastahack/disorder.h RUFUS-1.0/src/externals/fastahack/libdisorder.LICENSE RUFUS-1.0/src/externals/fastahack/split.cpp RUFUS-1.0/src/externals/fastahack/split.h RUFUS-1.0/src/externals/fastahack/tests/ RUFUS-1.0/src/externals/fastahack/tests/correct.fasta RUFUS-1.0/src/externals/fastahack/tests/embedded_newline.fasta RUFUS-1.0/src/externals/fastahack/tests/mismatched_lines.fasta RUFUS-1.0/src/externals/fastahack/tests/trailing_newlines.fasta RUFUS-1.0/src/externals/jellyfish-2.2.5.tar.gz RUFUS-1.0/src/include/ RUFUS-1.0/src/include/Fasta.o RUFUS-1.0/src/include/disorder.o RUFUS-1.0/src/include/split.o RUFUS-1.0/testRun/ RUFUS-1.0/testRun/clean.sh RUFUS-1.0/testRun/runTest.sh [moldach@cedar1 TOOL_TMP_DIR]$ cd RUFUS-1.0/ [moldach@cedar1 RUFUS-1.0]$ ll total 53 drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 bin drwxr-x--- 3 moldach moldach 4096 Sep 5 2018 cloud -rw-r----- 1 moldach moldach 381 Sep 5 2018 CMakeLists.txt -rwxr-x--- 1 moldach moldach 3249 Sep 5 2018 configure.sh drwxr-x--- 2 moldach moldach 4096 Sep 5 2018 externals -rw-r----- 1 moldach moldach 4545 Sep 5 2018 Install.sh -rw-r----- 1 moldach moldach 472 Sep 5 2018 Makefile -rw-r----- 1 moldach moldach 5769 Sep 5 2018 README.md drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 resources -rwxr-x--- 1 moldach moldach 20476 Sep 5 2018 runRufus.sh drwxr-x--- 3 moldach moldach 4096 Sep 5 2018 scripts drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 src drwxr-x--- 2 moldach moldach 4096 Sep 5 2018 testRun [moldach@cedar1 RUFUS-1.0]$ nano README.md Which version of gcc?
[moldach@cedar1 RUFUS-1.0]$ which gcc /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc Cmake with which gcc since it's not 4.9.2 (but is >)
[moldach@cedar1 RUFUS-1.0]$ cd bin/ [moldach@cedar1 bin]$ cmake ../ -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++) -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin run make
[moldach@cedar1 bin]$ make Scanning dependencies of target fastahack_project [ 1%] Creating directories for 'fastahack_project' [ 2%] Performing download step (git clone) for 'fastahack_project' Cloning into 'fastahack_project'... Checking out files: 100% (22/22), done. Already on 'master' Your branch is up to date with 'origin/master'. [ 4%] No patch step for 'fastahack_project' [ 5%] No update step for 'fastahack_project' [ 6%] Performing configure step for 'fastahack_project' loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/fastahack/tmp/fastahack_project-cache-.cmake -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/fastahack/src/fastahack_project-build [ 8%] Performing build step for 'fastahack_project' Scanning dependencies of target fastahack_src_lib [ 16%] Building C object src/CMakeFiles/fastahack_src_lib.dir/disorder.c.o [ 33%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/Fasta.cpp.o [ 50%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/split.cpp.o [ 66%] Linking CXX static library libfastahack_src_lib.a [ 66%] Built target fastahack_src_lib Scanning dependencies of target fastahack [ 83%] Building CXX object tools/CMakeFiles/fastahack.dir/FastaHack.cpp.o [100%] Linking CXX executable fastahack [100%] Built target fastahack [ 9%] No install step for 'fastahack_project' [ 10%] Completed 'fastahack_project' [ 10%] Built target fastahack_project Scanning dependencies of target bwa_project [ 12%] Creating directories for 'bwa_project' [ 13%] Performing download step (git clone) for 'bwa_project' Cloning into 'bwa_project'... Checking out files: 100% (77/77), done. Already on 'master' Your branch is up to date with 'origin/master'. [ 14%] No patch step for 'bwa_project' [ 16%] No update step for 'bwa_project' [ 17%] No configure step for 'bwa_project' [ 18%] Performing build step for 'bwa_project' bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:879:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] bgint_t oldInverseSa0RelativeRank = 0; ^ bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] unsigned int bitsInWordMinusBitPerChar; ^ ar:
u' modifier ignored sinceD' is the default (see `U') [ 20%] No install step for 'bwa_project' [ 21%] Completed 'bwa_project' [ 21%] Built target bwa_project Scanning dependencies of target rufalu_project [ 22%] Creating directories for 'rufalu_project' [ 24%] Performing download step (git clone) for 'rufalu_project' Cloning into 'rufalu_project'... Checking out files: 100% (65/65), done. Already on 'master' Your branch is up to date with 'origin/master'. [ 25%] No patch step for 'rufalu_project' [ 26%] No update step for 'rufalu_project' [ 28%] Performing configure step for 'rufalu_project' loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/tmp/rufalu_project-cache-.cmake -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done BAMTOOLS INCLUDE: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include BINARY_DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project SRC_DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project BAMTOOLS LIB DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include -- Configuring done -- Generating done -- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build [ 29%] Performing build step for 'rufalu_project' Scanning dependencies of target zlib_project [ 1%] Creating directories for 'zlib_project' [ 3%] Performing download step (git clone) for 'zlib_project' Cloning into 'zlib_project'... Checking out files: 100% (254/254), done. Note: checking out '50893291621658f355bc5b4d450a8d06a563053d'.You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:
git checkout -b
HEAD is now at 5089329 zlib 1.2.8 [ 5%] No patch step for 'zlib_project' [ 7%] No update step for 'zlib_project' [ 9%] Performing configure step for 'zlib_project' loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/tmp/zlib_project-cache-.cmake -- The C compiler identification is GNU 5.4.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Renaming -- /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project/zconf.h -- to 'zconf.h.included' because this file is included with zlib -- but CMake generates it automatically in the build directory. -- Configuring done -- Generating done -- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project-build [ 11%] Performing build step for 'zlib_project' Scanning dependencies of target zlib [ 2%] Building C object CMakeFiles/zlib.dir/adler32.o [ 5%] Building C object CMakeFiles/zlib.dir/compress.o [ 7%] Building C object CMakeFiles/zlib.dir/crc32.o [ 10%] Building C object CMakeFiles/zlib.dir/deflate.o [ 12%] Building C object CMakeFiles/zlib.dir/gzclose.o [ 15%] Building C object CMakeFiles/zlib.dir/gzlib.o [ 17%] Building C object CMakeFiles/zlib.dir/gzread.o [ 20%] Building C object CMakeFiles/zlib.dir/gzwrite.o [ 22%] Building C object CMakeFiles/zlib.dir/inflate.o [ 25%] Building C object CMakeFiles/zlib.dir/infback.o [ 27%] Building C object CMakeFiles/zlib.dir/inftrees.o [ 30%] Building C object CMakeFiles/zlib.dir/inffast.o [ 32%] Building C object CMakeFiles/zlib.dir/trees.o [ 35%] Building C object CMakeFiles/zlib.dir/uncompr.o [ 37%] Building C object CMakeFiles/zlib.dir/zutil.o [ 40%] Linking C shared library libz.so [ 40%] Built target zlib Scanning dependencies of target minigzip [ 42%] Building C object CMakeFiles/minigzip.dir/test/minigzip.o [ 45%] Linking C executable minigzip [ 45%] Built target minigzip Scanning dependencies of target example [ 47%] Building C object CMakeFiles/example.dir/test/example.o [ 50%] Linking C executable example [ 50%] Built target example Scanning dependencies of target zlibstatic [ 52%] Building C object CMakeFiles/zlibstatic.dir/adler32.o [ 55%] Building C object CMakeFiles/zlibstatic.dir/compress.o [ 57%] Building C object CMakeFiles/zlibstatic.dir/crc32.o [ 60%] Building C object CMakeFiles/zlibstatic.dir/deflate.o [ 62%] Building C object CMakeFiles/zlibstatic.dir/gzclose.o [ 65%] Building C object CMakeFiles/zlibstatic.dir/gzlib.o [ 67%] Building C object CMakeFiles/zlibstatic.dir/gzread.o [ 70%] Building C object CMakeFiles/zlibstatic.dir/gzwrite.o [ 72%] Building C object CMakeFiles/zlibstatic.dir/inflate.o [ 75%] Building C object CMakeFiles/zlibstatic.dir/infback.o [ 77%] Building C object CMakeFiles/zlibstatic.dir/inftrees.o [ 80%] Building C object CMakeFiles/zlibstatic.dir/inffast.o [ 82%] Building C object CMakeFiles/zlibstatic.dir/trees.o [ 85%] Building C object CMakeFiles/zlibstatic.dir/uncompr.o [ 87%] Building C object CMakeFiles/zlibstatic.dir/zutil.o [ 90%] Linking C static library libz.a [ 90%] Built target zlibstatic Scanning dependencies of target example64 [ 92%] Building C object CMakeFiles/example64.dir/test/example.o [ 95%] Linking C executable example64 [ 95%] Built target example64 Scanning dependencies of target minigzip64 [ 97%] Building C object CMakeFiles/minigzip64.dir/test/minigzip.o [100%] Linking C executable minigzip64 [100%] Built target minigzip64 [ 13%] No install step for 'zlib_project' [ 15%] Completed 'zlib_project' [ 15%] Built target zlib_project Scanning dependencies of target bamtools_project [ 17%] Creating directories for 'bamtools_project' [ 19%] Performing download step (git clone) for 'bamtools_project' Cloning into 'bamtools_project'... Checking out files: 100% (184/184), done. Note: checking out '45129fa9035847f54baa2c1750d4d3f526793e82'.
You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:
git checkout -b
HEAD is now at 45129fa Switched order of directory processing [ 21%] No patch step for 'bamtools_project' [ 23%] No update step for 'bamtools_project' [ 25%] Performing configure step for 'bamtools_project' loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/tmp/bamtools_project-cache-.cmake -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project-build [ 26%] Performing build step for 'bamtools_project' Scanning dependencies of target SharedHeaders [ 0%] Built target SharedHeaders Scanning dependencies of target jsoncpp [ 1%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o [ 2%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o [ 3%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o [ 4%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libjsoncpp.a [ 4%] Built target jsoncpp Scanning dependencies of target BamTools [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o [ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o [ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o [ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o [ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o [ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()sizeof(uint64_t)) ) ^ [ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o [ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ [ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o [ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o [ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o [ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o [ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o [ 42%] Linking CXX shared library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools.so [ 42%] Built target BamTools Scanning dependencies of target AlgorithmsHeaders [ 42%] Built target AlgorithmsHeaders Scanning dependencies of target BamTools-static [ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o [ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o [ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o [ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o [ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o [ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o [ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o [ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o [ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o [ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o [ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o [ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o [ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o [ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o [ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o [ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()sizeof(uint64_t)) ) ^ [ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o [ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o [ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o [ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ [ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o [ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o [ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o [ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o [ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o [ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o [ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o [ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o [ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o [ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o [ 80%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools.a [ 80%] Built target BamTools-static Scanning dependencies of target APIHeaders [ 80%] Built target APIHeaders Scanning dependencies of target BamTools-utils [ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o [ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o [ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o [ 85%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools-utils.a [ 85%] Built target BamTools-utils Scanning dependencies of target bamtools_cmd [ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.di
moldach
Trying to build RUFUS with gcc version
Which version of
gcc?Cmake with
which gccsince it's not 4.9.2 (but is >)run
makeTry to run
bash runTest.sh