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micans / mcl

MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.
https://micans.org/mcl
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compile on Apple M-series ARM64 processors #30

Closed stephrom closed 4 months ago

stephrom commented 4 months ago

I would like to use MCL in combination with orthofinder on my MacBook Pro. I tried to compile is but the configuration fails on a test of the gcc At the configuration it doesn't seem to detect the actual architecture: arm64

~/Downloads/mcl % bash install-this-mcl.sh --2024-06-04 21:48:39-- http://micans.org/mcl/src/mcl-22-282.tar.gz Resolving micans.org (micans.org)... 2a00:1098:82::6:1, 46.235.227.111 Connecting to micans.org (micans.org)|2a00:1098:82::6:1|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2748263 (2,6M) [application/x-gzip] Saving to: ‘mcl-22-282.tar.gz’

mcl-22-282.tar.gz 100%[====================================================================>] 2,62M 6,79MB/s in 0,4s

2024-06-04 21:48:39 (6,79 MB/s) - ‘mcl-22-282.tar.gz’ saved [2748263/2748263]

--2024-06-04 21:48:39-- http://micans.org/mcl/src/cimfomfa-22-273.tar.gz Resolving micans.org (micans.org)... 2a00:1098:82::6:1, 46.235.227.111 Connecting to micans.org (micans.org)|2a00:1098:82::6:1|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 455547 (445K) [application/x-gzip] Saving to: ‘cimfomfa-22-273.tar.gz’

cimfomfa-22-273.tar.gz 100%[====================================================================>] 444,87K --.-KB/s in 0,1s

2024-06-04 21:48:40 (3,60 MB/s) - ‘cimfomfa-22-273.tar.gz’ saved [455547/455547]

checking for a BSD-compatible install... /opt/local/bin/ginstall -c checking whether build environment is sane... yes /Users/strom/Downloads/mcl/cimfomfa-22-273/missing: Unknown --is-lightweight' option Try/Users/strom/Downloads/mcl/cimfomfa-22-273/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /opt/local/bin/gmkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-apple-darwin23.5.0 checking host system type... x86_64-apple-darwin23.5.0 checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... /opt/homebrew/bin/gcc checking whether the C compiler works... no configure: error: in /Users/strom/Downloads/mcl/cimfomfa-22-273': configure: error: C compiler cannot create executables Seeconfig.log' for more details

micans commented 4 months ago

Hello, this issue might just be that you need to do one of the following

The second is my prefered way of installing. If mcl is not found, you'd then need to do something like export PATH=${PATH}:$HOME/local/bin before running orthofinder. Let me know if this works or not.

micans commented 4 months ago

I assume this solved the issue. Comment if this was not the case.

stephrom commented 4 months ago

Dear Stijn,

It did for the configuration step.

best regards Stephane

Stephane Rombauts Principal Scientific staff

Bioinformatics & Systems Biology Division Tel:+32 <tel:+32> (0)9 331 38 21 fax:+32 (0)9 3313809 VIB-UGent Center for Plant Systems Biology, Ghent University Technologiepark 71, 9052 Gent, BELGIUM @. @.> http://bioinformatics.psb.ugent.be/

On 5 Jun 2024, at 22:55, Stijn van Dongen @.***> wrote:

I assume this solved the issue. Comment if this was not the case.

— Reply to this email directly, view it on GitHub https://github.com/micans/mcl/issues/30#issuecomment-2150946852, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEBCVA3TXKXBSALNTBD6JMTZF53LJAVCNFSM6AAAAABIZGXJE2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJQHE2DMOBVGI. You are receiving this because you authored the thread.