Files were found with references to the Homebrew shims directory. The offending files are: share/meme/tests/xstreme/Makefile share/meme/tests/Makefile share/meme/tests/meme-chip/Makefile share/meme/tests/psp-gen/Makefile share/meme/tests/meme/Makefile share/meme/tests/tgene/Makefile share/meme/tests/dreme/Makefile share/meme/tests/gomo/Makefile share/meme/tests/qvalue/Makefile share/meme/tests/web/Makefile share/meme/tests/mhmmscan/Makefile share/meme/tests/mhmms/Makefile share/meme/tests/scaffold/Makefile share/meme/tests/bed2fasta/Makefile share/meme/tests/spamo/Makefile share/meme/tests/mcast/Makefile share/meme/tests/momo/Makefile share/meme/tests/tomtom/Makefile share/meme/tests/mhmm/Makefile share/meme/tests/motiph/Makefile share/meme/tests/common/Makefile share/meme/tests/common/motif.crp0/Makefile share/meme/tests/common/motif.Puf3p/Makefile share/meme/tests/fimo/Makefile share/meme/tests/ame/Makefile share/meme/tests/streme/Makefile share/meme/tests/draw-mhmm/Makefile share/meme/tests/centrimo/Makefile share/meme/tests/glam2/Makefile share/meme/tests/glam2scan/Makefile share/meme/tests/clustalw2fasta/Makefile share/meme/tests/scripts/Makefile share/meme/tests/sea/Makefile share/meme/tests/create-priors/Makefile share/meme/tests/mast/Makefile share/meme/tests/fasta-center/Makefile

/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.1.0/bin/bundle clean ==> Testing brewsci/bio/meme ==> /home/linuxbrew/.linuxbrew/Cellar/meme/5.5.5/bin/meme /home/linuxbrew/.linuxbrew/Cellar/meme/5.5.5/share/meme/tests/common/At.s Writing results to output directory 'meme_out'. BACKGROUND: using background model of order 0 PRIMARY (classic): n 19 p0 19 p1 0 p2 0 SEQUENCE GROUP USAGE-- Starts/EM: p0; Trim: p0; pvalue: p0; nsites: p0,p1,p2 SEEDS: maxwords 10133 highwater mark: seq 19 pos 475 BALANCE: samples 19 chars 10133 nodes 1 chars/node 10133 Initializing the motif probability tables for 2 to 19 sites... nsites = 2 nsites = 3 nsites = 4 nsites = 5 nsites = 6 nsites = 7 nsites = 8 nsites = 9 nsites = 10 nsites = 11 nsites = 12 nsites = 13 nsites = 14 nsites = 15 nsites = 16 nsites = 17 nsites = 18 nsites = 19 Done initializing. seqs= 19, min_w= 275, max_w= 1112, total_size= 10133 motif=1 SEED DEPTHS: 2 4 8 16 19 SEED WIDTHS: 8 11 15 21 29 41 50 starts: w=8, seq=0, l=407 starts: w=8, seq=5, l=472 starts: w=8, seq=10, l=339 starts: w=8, seq=15, l=500 starts: w=11, seq=0, l=407 starts: w=11, seq=5, l=472 starts: w=11, seq=10, l=339 starts: w=11, seq=15, l=500 starts: w=15, seq=0, l=407 starts: w=15, seq=5, l=472 starts: w=15, seq=10, l=339 starts: w=15, seq=15, l=500 starts: w=21, seq=0, l=407 starts: w=21, seq=5, l=472 starts: w=21, seq=10, l=339 starts: w=21, seq=15, l=500 starts: w=29, seq=0, l=407 starts: w=29, seq=5, l=472 starts: w=29, seq=10, l=339 starts: w=29, seq=15, l=500 starts: w=41, seq=0, l=407 starts: w=41, seq=5, l=472 starts: w=41, seq=10, l=339 starts: w=41, seq=15, l=500 starts: w=50, seq=0, l=407 starts: w=50, seq=5, l=472 starts: w=50, seq=10, l=339 starts: w=50, seq=15, l=500 em: w= 8, psites= 2, iter= 0 em: w= 8, psites= 4, iter= 0 em: w= 8, psites= 8, iter= 0 em: w= 8, psites= 16, iter= 0 em: w= 8, psites= 19, iter= 0 em: w= 11, psites= 2, iter= 0 em: w= 11, psites= 4, iter= 0 em: w= 11, psites= 8, iter= 0 em: w= 11, psites= 16, iter= 0 em: w= 11, psites= 19, iter= 0 em: w= 15, psites= 2, iter= 0 em: w= 15, psites= 2, iter= 10 em: w= 15, psites= 4, iter= 0 em: w= 15, psites= 8, iter= 0 em: w= 15, psites= 16, iter= 0 em: w= 15, psites= 19, iter= 0 em: w= 21, psites= 2, iter= 0 em: w= 21, psites= 4, iter= 0 em: w= 21, psites= 8, iter= 0 em: w= 21, psites= 16, iter= 0 em: w= 21, psites= 19, iter= 0 em: w= 21, psites= 19, iter= 10 em: w= 29, psites= 2, iter= 0 em: w= 29, psites= 4, iter= 0 em: w= 29, psites= 8, iter= 0 em: w= 29, psites= 8, iter= 10 em: w= 29, psites= 16, iter= 0 em: w= 29, psites= 16, iter= 10 em: w= 29, psites= 19, iter= 0 em: w= 41, psites= 2, iter= 0 em: w= 41, psites= 4, iter= 0 em: w= 41, psites= 4, iter= 10 em: w= 41, psites= 4, iter= 20 em: w= 41, psites= 4, iter= 30 em: w= 41, psites= 8, iter= 0 em: w= 41, psites= 16, iter= 0 em: w= 41, psites= 16, iter= 10 em: w= 41, psites= 19, iter= 0 em: w= 50, psites= 2, iter= 0 em: w= 50, psites= 4, iter= 0 em: w= 50, psites= 4, iter= 10 em: w= 50, psites= 8, iter= 0 em: w= 50, psites= 16, iter= 0 em: w= 50, psites= 19, iter= 0 Can't locate XML/Parser/Expat.pm in @inc (you may need to install the XML::Parser::Expat module) (@inc entries checked: /home/linuxbrew/.linuxbrew/Cellar/meme/5.5.5/libexec/meme-5.5.5 /home/linuxbrew/.linuxbrew/Cellar/meme/5.5.5/lib/meme-5.5.5/perl /home/linuxbrew/.linuxbrew/opt/perl/lib/perl5/site_perl/5.38/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/opt/perl/lib/perl5/site_perl/5.38 /home/linuxbrew/.linuxbrew/opt/perl/lib/perl5/5.38/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/opt/perl/lib/perl5/5.38 /home/linuxbrew/.linuxbrew/lib/perl5/site_perl/5.38/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/lib/perl

Process completed with exit code 1.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.