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RomoL2 / RegVar

Characterize 3'UTR variants
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RegVar installation #10

Closed Madelinehazel closed 6 months ago

Madelinehazel commented 7 months ago

Hello,

I'm trying to install RegVar on an HPC. I've successfully installed the conda environment for RBPamp and have run python setup.py build. However, I run into this error:

building 'RBPamp.cy.cy_kmers' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/RBPamp creating build/temp.linux-x86_64-3.7/RBPamp/cython gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include -I/home/mcouse/.conda/envs/RBPamp/include/python3.7m -c RBPamp/cython/kmers.c -o build/temp.linux-x86_64-3.7/RBPamp/cython/kmers.o -fopenmp -O3 -ffast-math -march=native -mtune=native In file included from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from RBPamp/cython/kmers.c:746: /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~ RBPamp/cython/kmers.c: In function ‘pyx_pf_6RBPamp_2cy_8cy_kmers_3weighted_kmer_shifts’: RBPamp/cython/kmers.c:4278:3: internal compiler error: Illegal instruction 4278 | pyx_v_w = ((1. (__pyx_v_l - (2 pyx_v_x))) / pyx_v_l); | ^~~~~ 0xc10aaf crash_signal ../.././gcc/toplev.cc:322 0xb7f87d real_from_string(real_value, char const) ../.././gcc/real.cc:2110 0xb8023b real_from_string3(real_value, char const, format_helper) ../.././gcc/real.cc:2176 0x752e8c interpret_float ../.././gcc/c-family/c-lex.cc:1035 0x7542fb c_lex_with_flags(tree_node*, unsigned int, unsigned char, int) ../.././gcc/c-family/c-lex.cc:517 0x6dc563 c_lex_one_token ../.././gcc/c/c-parser.cc:279 0x6dd0a0 c_parser_peek_2nd_token(c_parser) ../.././gcc/c/c-parser.cc:500 0x6dd0a0 c_parser_peek_2nd_token(c_parser*) ../.././gcc/c/c-parser.cc:493 0x6ebe87 c_parser_cast_expression ../.././gcc/c/c-parser.cc:8064 0x6ec0f1 c_parser_binary_expression ../.././gcc/c/c-parser.cc:7906 0x6ed2eb c_parser_conditional_expression ../.././gcc/c/c-parser.cc:7606 0x6ed941 c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7521 0x6edbb1 c_parser_expression ../.././gcc/c/c-parser.cc:10697 0x6e0487 c_parser_postfix_expression ../.././gcc/c/c-parser.cc:9127 0x6ea64a c_parser_unary_expression ../.././gcc/c/c-parser.cc:8261 0x6ebe77 c_parser_cast_expression ../.././gcc/c/c-parser.cc:8103 0x6ec0f1 c_parser_binary_expression ../.././gcc/c/c-parser.cc:7906 0x6ed2eb c_parser_conditional_expression ../.././gcc/c/c-parser.cc:7606 0x6ed941 c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7521 0x6ed9ea c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7564 Please submit a full bug report, with preprocessed source (by using -freport-bug). Please include the complete backtrace with any bug report. See https://gcc.gnu.org/bugs/ for instructions. error: command 'gcc' failed with exit status 1

Any help would be greatly appreciated - thank you!

Madeline

RomoL2 commented 7 months ago

Did you include the gcc=GCC line? Looks like compiling issue. You can also try installing from the dockerfile.

Lindsay

On Fri, Mar 29, 2024 at 4:27 PM Madeline Couse @.***> wrote:

Hello,

I'm trying to install RegVar on an HPC. I've successfully installed the conda environment for RBPamp and have run python setup.py build. However, I run into this error:

building 'RBPamp.cy.cy_kmers' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/RBPamp creating build/temp.linux-x86_64-3.7/RBPamp/cython gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include -I/home/mcouse/.conda/envs/RBPamp/include/python3.7m -c RBPamp/cython/kmers.c -o build/temp.linux-x86_64-3.7/RBPamp/cython/kmers.o -fopenmp -O3 -ffast-math -march=native -mtune=native In file included from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from RBPamp/cython/kmers.c:746: /home/mcouse/.conda/envs/RBPamp/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " | ^~~ RBPamp/cython/kmers.c: In function ‘pyx_pf_6RBPamp_2cy_8cy_kmers_3weighted_kmer_shifts’: RBPamp/cython/kmers.c:4278:3: internal compiler error: Illegal instruction 4278 | pyx_v_w = ((1. (__pyx_v_l - (2 pyx_v_x))) / pyx_v_l); | ^~~~~ 0xc10aaf crash_signal ../.././gcc/toplev.cc:322 0xb7f87d real_from_string(real_value, char const) ../.././gcc/real.cc:2110 0xb8023b real_from_string3(real_value, char const, format_helper) ../.././gcc/real.cc:2176 0x752e8c interpret_float ../.././gcc/c-family/c-lex.cc:1035 0x7542fb c_lex_with_flags(tree_node*, unsigned int, unsigned char, int) ../.././gcc/c-family/c-lex.cc:517 0x6dc563 c_lex_one_token ../.././gcc/c/c-parser.cc:279 0x6dd0a0 c_parser_peek_2nd_token(c_parser) ../.././gcc/c/c-parser.cc:500 0x6dd0a0 c_parser_peek_2nd_token(c_parser*) ../.././gcc/c/c-parser.cc:493 0x6ebe87 c_parser_cast_expression ../.././gcc/c/c-parser.cc:8064 0x6ec0f1 c_parser_binary_expression ../.././gcc/c/c-parser.cc:7906 0x6ed2eb c_parser_conditional_expression ../.././gcc/c/c-parser.cc:7606 0x6ed941 c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7521 0x6edbb1 c_parser_expression ../.././gcc/c/c-parser.cc:10697 0x6e0487 c_parser_postfix_expression ../.././gcc/c/c-parser.cc:9127 0x6ea64a c_parser_unary_expression ../.././gcc/c/c-parser.cc:8261 0x6ebe77 c_parser_cast_expression ../.././gcc/c/c-parser.cc:8103 0x6ec0f1 c_parser_binary_expression ../.././gcc/c/c-parser.cc:7906 0x6ed2eb c_parser_conditional_expression ../.././gcc/c/c-parser.cc:7606 0x6ed941 c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7521 0x6ed9ea c_parser_expr_no_commas ../.././gcc/c/c-parser.cc:7564 Please submit a full bug report, with preprocessed source (by using -freport-bug). Please include the complete backtrace with any bug report. See https://gcc.gnu.org/bugs/ for instructions. error: command 'gcc' failed with exit status 1

Any help would be greatly appreciated - thank you!

Madeline

— Reply to this email directly, view it on GitHub https://github.com/RomoL2/RegVar/issues/10, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZOARDB7H5DBAPXAMRCNUNLY2XFE7AVCNFSM6AAAAABFO4LJXWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIYTKOJWGE4DOMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Madelinehazel commented 7 months ago

Hi Lindsay,

That worked, thank you! There is a small typo in the README: export CC=gcc should read export GCC=gcc.

Thanks, Madeline

RomoL2 commented 7 months ago

Oh thanks for noticing, will fix that!

Lindsay

On Mon, Apr 1, 2024 at 11:00 AM Madeline Couse @.***> wrote:

Hi Lindsay,

That worked, thank you! There is a small typo in the README: export CC=gcc should read export GCC=gcc.

Thanks, Madeline

— Reply to this email directly, view it on GitHub https://github.com/RomoL2/RegVar/issues/10#issuecomment-2029898251, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZOARDCKTN6M26C6AGROXKDY3FZAPAVCNFSM6AAAAABFO4LJXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRZHA4TQMRVGE . You are receiving this because you commented.Message ID: @.***>