install errors

[retrogenomics]

Hi, I'm trying to install Giggle on MacOsX. I went through the test procedure, and I had several blocks/errors:

• upon running giggle_tests.sh:

 /usr/local/bin/bedtools

check_intersections_per_file ran in 0 sec with 0/1411 lines to STDERR/OUT
PASS EXIT CODE (LINE 41)
 PASS "0" == "0" (LINE 42)

check_chr_v_nochr_search_1 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 0/11 lines to STDERR/OUT
PASS "11" == "11" (LINE 55)
PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 0/23 lines to STDERR/OUT
PASS "23" == "23" (LINE 79)
PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 0/72 lines to STDERR/OUT
PASS "72" == "72" (LINE 87)
PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 2/0 lines to STDERR/OUT
FAIL EXIT CODE (LINE 102)
--> expected EX_OK, observed Unknown code: 1

sshtest v0.1.5

27        Tests
1         Failures
26        Successes

• upon running cd ../unit; make

test_giggle.c:1851:test_giggle_bulk_insert:FAIL: Expected 22 Was 140239760787248 Any suggestion to fix this? Thanks in advance Gael

[ryanlayer]

Can you please go to giggle/test/data/, run the command below, and tell me the result.

../../bin/giggle index \
        -s \
         -i "../data/dense/*gz" \
         -o ../data/dense_b \
         -f \
         -s

[retrogenomics]

giggle: Could not open file '../data/dense/326.bed.gz'
: Too many open files

[ryanlayer]

Ah! Okay. Try running this before your test:

ulimit -Sn 16384

[retrogenomics]

It turns out that macOS Sierra (10.12) does not allow to modify the limit... even with sudoing. However, I found the following trick [http://blog.mact.me/2014/10/22/yosemite-upgrade-changes-open-file-limit]:

echo kern.maxfiles=65536 | sudo tee -a /etc/sysctl.conf
echo kern.maxfilesperproc=65536 | sudo tee -a /etc/sysctl.conf
sudo sysctl -w kern.maxfiles=65536
sudo sysctl -w kern.maxfilesperproc=65536
ulimit -Sn 16384

Now I can run giggle_tests.sh successfully. Unfortunately, I've got a novel error when running cd ../unit; make:

ruby ./unity/generate_test_runner.rb test_bpt_Runner.c
gcc -Werror -g -o test_bpt_Runner \
        -I./unity \
        -I../../src/ \
        -I../../lib/htslib/ \
        -DTEST ./unity/unity.c \
        -DSAMTOOLS=1 \
        -pthread \
        ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \
        test_bpt_Runner.c test_bpt_Runner_Runner.c \
        ../../lib/htslib//libhts.a \
        -lz -lm -lcurl -lcrypto -lssl
Undefined symbols for architecture x86_64:
  "_test_b_search", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_find_leaf", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_insert", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_insert_id_updated_bpt_node", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_insert_new_value", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_insert_repeat", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_insert_repeat_append", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_new_node", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_node_macros", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_rand_order_insert_new_value", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_split_node_non_root_parent_has_room", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_split_node_root", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_bpt_write_tree", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_find", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_rand_test", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_rand_test_high_order", referenced from:
      _main in test_bpt_Runner-f64dc6.o
  "_test_split_repair", referenced from:
      _main in test_bpt_Runner-f64dc6.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [test_bpt_Runner] Error 1

[ryanlayer]

Try make clean;make

[retrogenomics]

Thanks a lot for your help and quick answers! It now works perfectly and I could run the Roadmap Epigenomics example in few minutes.