<commit_before><tool id="deseq2" name="DESeq2" version="2.11.39">
    <description>Determines differentially expressed features from count tables</description>
    <requirements>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator." /><commit_msg>Add missing r-getopt requirement for deseq2<commit_after><tool id="deseq2" name="DESeq2" version="2.11.39">
    <description>Determines differentially expressed features from count tables</description>
    <requirements>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator." />
{'fraction_non_alphanumeric': 0.11735419630156473, 'fraction_numerical': 0.020625889046941678, 'mean_word_length': 3.0901162790697674, 'pattern_counts': {'":': 0, '<': 25, '<?xml version=': 0, '>': 25, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5595601', 'n_tokens_mistral': 381, 'n_tokens_neox': 354, 'n_words': 92}