Issue clipper instalation #120
Description
I have been following the instalation steps from: https://github.com/YeoLab/clipper, but I have an issue:
Processing /home/proyecto/clipper
Requirement already satisfied: setuptools in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (47.3.1.post20200622)
Requirement already satisfied: pysam>=0.15.3 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (0.15.3)
Requirement already satisfied: numpy>=1.18.5 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (1.18.5)
Requirement already satisfied: scipy>=1.5.0 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (1.5.0)
Requirement already satisfied: matplotlib>=3.2.2 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (3.2.2)
Requirement already satisfied: pybedtools>=0.8.1 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (0.8.1)
Requirement already satisfied: scikit-learn>=0.23.1 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (0.23.1)
Requirement already satisfied: HTSeq>=0.11.3 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from clipper==2.1.2) (0.11.3)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from matplotlib>=3.2.2->clipper==2.1.2) (1.2.0)
Requirement already satisfied: python-dateutil>=2.1 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from matplotlib>=3.2.2->clipper==2.1.2) (2.8.1)
Requirement already satisfied: cycler>=0.10 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from matplotlib>=3.2.2->clipper==2.1.2) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from matplotlib>=3.2.2->clipper==2.1.2) (2.4.7)
Requirement already satisfied: six in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from pybedtools>=0.8.1->clipper==2.1.2) (1.15.0)
Requirement already satisfied: joblib>=0.11 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from scikit-learn>=0.23.1->clipper==2.1.2) (0.15.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages (from scikit-learn>=0.23.1->clipper==2.1.2) (2.1.0)
Building wheels for collected packages: clipper
Building wheel for clipper (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/proyecto/miniconda3/envs/clipper3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"'; file='"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-pd2q_o9u
cwd: /tmp/pip-req-build-5gx8nfbe/
Complete output (212 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/clipper
copying clipper/init.py -> build/lib.linux-x86_64-3.7/clipper
creating build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/init.py -> build/lib.linux-x86_64-3.7/clipper/data
creating build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/call_peak.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/filter_peak.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/main.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/peak_curve.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/utils.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/init.py -> build/lib.linux-x86_64-3.7/clipper/src
creating build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_call_peak.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_filter_peak.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_main.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_peakfinder.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_peaks.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_spline.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_utils.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/init.py -> build/lib.linux-x86_64-3.7/clipper/test
creating build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/init.py -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/ce10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ce10.AS.STRUCTURE.COMPILED.gff2 -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ChlSab2.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ChlSab2_Sars.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/dm3.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38v35noalt.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_pU6_cas9.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v29.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v29e.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v40.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hb27.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19chr19.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19_VSV.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg38.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10v25.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10_vM15_VSV.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm9.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/rn6.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_genes.BED.gz -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_mRNA.lengths -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_premRNA.lengths -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/regions/ce10_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_exons.mrg.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ChlSab2_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ChlSab2_Sars_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38v35noalt_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_pU6_cas9_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_pU6_cas9_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29e_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29e_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v40_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hb27_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19chr19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19chr19_v19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_VSV_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg38_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10v25_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10_vM15_VSV_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/rn6_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
creating build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.neg.bw -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.pos.bw -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.rmdup.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/CLIP_Analysis_test.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed.exon.rand.0.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed.exon.real.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.fasta -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.fasta.compseq -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.out -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test_2.fasta -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test_2.fasta.compseq -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/data.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/data_2.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/ensembl_test.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/foo -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/FOX2Brain-05.15.09.polyATrim.adapterTrim.rmRep.sorted.rmDup.peaks.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/hg19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/indexed_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/indexed_test.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/motif_distance_test_cluster.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/motif_distance_test_motif.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/not_indexed_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/peak_results.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/peak_results_no_overlap.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/rmdup_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test.tx.1.AS.STRUCTURE -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test_bed_creation.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_cutoff.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_filter.sort.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_filter.sort.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
running build_ext
cythoning clipper/src/readsToWiggle.pyx to clipper/src/readsToWiggle.c
/home/proyecto/miniconda3/envs/clipper3/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-req-build-5gx8nfbe/clipper/src/readsToWiggle.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building 'clipper.src.readsToWiggle' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/clipper
creating build/temp.linux-x86_64-3.7/clipper/src
gcc -pthread -B /home/proyecto/miniconda3/envs/clipper3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/proyecto/miniconda3/envs/clipper3/include/python3.7m -c clipper/src/readsToWiggle.c -o build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o
gcc -pthread -shared -B /home/proyecto/miniconda3/envs/clipper3/compiler_compat -L/home/proyecto/miniconda3/envs/clipper3/lib -Wl,-rpath=/home/proyecto/miniconda3/envs/clipper3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o -o build/lib.linux-x86_64-3.7/clipper/src/readsToWiggle.cpython-37m-x86_64-linux-gnu.so
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section .relr.dyn' /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6 /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section .relr.dyn'
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: cannot find /lib/x86_64-linux-gnu/libc.so.6
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section .relr.dyn' /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2 /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section .relr.dyn'
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: cannot find /lib64/ld-linux-x86-64.so.2
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
ERROR: Failed building wheel for clipper
Running setup.py clean for clipper
Failed to build clipper
Installing collected packages: clipper
Running setup.py install for clipper ... error
ERROR: Command errored out with exit status 1:
command: /home/proyecto/miniconda3/envs/clipper3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"'; file='"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-uyrnnw1s/install-record.txt --single-version-externally-managed --compile --install-headers /home/proyecto/miniconda3/envs/clipper3/include/python3.7m/clipper
cwd: /tmp/pip-req-build-5gx8nfbe/
Complete output (210 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/clipper
copying clipper/init.py -> build/lib.linux-x86_64-3.7/clipper
creating build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/init.py -> build/lib.linux-x86_64-3.7/clipper/data
creating build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/call_peak.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/filter_peak.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/main.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/peak_curve.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/utils.py -> build/lib.linux-x86_64-3.7/clipper/src
copying clipper/src/init.py -> build/lib.linux-x86_64-3.7/clipper/src
creating build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_call_peak.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_filter_peak.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_main.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_peakfinder.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_peaks.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_spline.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/test_utils.py -> build/lib.linux-x86_64-3.7/clipper/test
copying clipper/test/init.py -> build/lib.linux-x86_64-3.7/clipper/test
creating build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/init.py -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/ce10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ce10.AS.STRUCTURE.COMPILED.gff2 -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ChlSab2.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/ChlSab2_Sars.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/dm3.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38v35noalt.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_pU6_cas9.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v29.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v29e.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/GRCh38_v40.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hb27.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19chr19.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg19_VSV.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/hg38.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10v25.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm10_vM15_VSV.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/mm9.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/rn6.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_genes.BED.gz -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_mRNA.lengths -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/test.AS.STRUCTURE_premRNA.lengths -> build/lib.linux-x86_64-3.7/clipper/data
copying clipper/data/regions/ce10_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_exons.mrg.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ce10_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ChlSab2_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/ChlSab2_Sars_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38v35noalt_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_pU6_cas9_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_pU6_cas9_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v24_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29e_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29e_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v29_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/GRCh38_v40_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hb27_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19chr19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19chr19_v19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_v19_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg19_VSV_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/hg38_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10v25_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm10_vM15_VSV_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_cds.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_distintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_five_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_five_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_genes.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_introns.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_poly_a_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_proxintron500.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_start_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_stop_codons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_three_prime_ends.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_three_prime_utrs.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/mm9_transcription_start_sites.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
copying clipper/data/regions/rn6_exons.bed -> build/lib.linux-x86_64-3.7/clipper/data/regions
creating build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.neg.bw -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.pos.bw -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/allup_test.rmdup.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/CLIP_Analysis_test.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed.exon.rand.0.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/clip_analysis_test_peak_results.bed.exon.real.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.fasta -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.fasta.compseq -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test.out -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test_2.fasta -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/compseq_test_2.fasta.compseq -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/data.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/data_2.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/ensembl_test.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/foo -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/FOX2Brain-05.15.09.polyATrim.adapterTrim.rmRep.sorted.rmDup.peaks.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/hg19_genes.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/indexed_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/indexed_test.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/motif_distance_test_cluster.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/motif_distance_test_motif.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/not_indexed_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/peak_results.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/peak_results_no_overlap.BED -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/rmdup_test.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test.gtf -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test.tx.1.AS.STRUCTURE -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/test_bed_creation.bed -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_cutoff.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_filter.sort.bam -> build/lib.linux-x86_64-3.7/clipper/test/data
copying clipper/test/data/transcriptome_filter.sort.bam.bai -> build/lib.linux-x86_64-3.7/clipper/test/data
running build_ext
skipping 'clipper/src/readsToWiggle.c' Cython extension (up-to-date)
building 'clipper.src.readsToWiggle' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/clipper
creating build/temp.linux-x86_64-3.7/clipper/src
gcc -pthread -B /home/proyecto/miniconda3/envs/clipper3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/proyecto/miniconda3/envs/clipper3/include/python3.7m -c clipper/src/readsToWiggle.c -o build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o
gcc -pthread -shared -B /home/proyecto/miniconda3/envs/clipper3/compiler_compat -L/home/proyecto/miniconda3/envs/clipper3/lib -Wl,-rpath=/home/proyecto/miniconda3/envs/clipper3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o -o build/lib.linux-x86_64-3.7/clipper/src/readsToWiggle.cpython-37m-x86_64-linux-gnu.so
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section .relr.dyn' /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6 /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section .relr.dyn'
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: cannot find /lib/x86_64-linux-gnu/libc.so.6
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section .relr.dyn' /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2 /home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section .relr.dyn'
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
/home/proyecto/miniconda3/envs/clipper3/compiler_compat/ld: cannot find /lib64/ld-linux-x86-64.so.2
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/proyecto/miniconda3/envs/clipper3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"'; file='"'"'/tmp/pip-req-build-5gx8nfbe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-uyrnnw1s/install-record.txt --single-version-externally-managed --compile --install-headers /home/proyecto/miniconda3/envs/clipper3/include/python3.7m/clipper Check the logs for full command output.