[Bioc-devel] extraChIPs builds failing on palamino3 and merida1 - Bioc-devel

Wed, Apr 12, 2023 5:19 AM #

Thanks Shian. Appreciate you taking the time to check that too. I'll make a
few modifications and will bump the version to see if that's the fix.

On Wed, 12 Apr 2023 at 21:17, Shian Su <su.s at wehi.edu.au> wrote:

Hey Stevie,

For what it?s worth the latest version builds fine for me on my Mac. I
don?t think you?ve bumped your version number since you removed the shared
library files, which is needed to trigger a new build.

Cheers,
Shian

On 12 Apr 2023, at 5:52 pm, Stevie Pederson <

stephen.pederson.au at gmail.com> wrote:

Hi,

I've introduced some C code, modified from FMStable on CRAN, to the
intended Bioc 3.17 release of extraChIPs. When I build using github

actions

it works for all three platforms (

https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmped%2FextraChIPs%2Factions%2Fruns%2F4669758037&data=05%7C01%7Csu.s%40wehi.edu.au%7C6a4c353e9e1a47efc19f08db3b2af477%7Caa7c72e2c5cf4a40a22aa585c04ca07c%7C0%7C0%7C638168827914859588%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ED%2FhjgRIDop2Ss%2FsxVJrzSyXvbqw3OKycWeORTduqzw%3D&reserved=0),
but fails on

palamino3 and merida1. The build report is here:

https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FextraChIPs%2F&data=05%7C01%7Csu.s%40wehi.edu.au%7C6a4c353e9e1a47efc19f08db3b2af477%7Caa7c72e2c5cf4a40a22aa585c04ca07c%7C0%7C0%7C638168827914859588%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mX27x8%2FX0xvsVPDxeaoRoH9xg89APgi1k9XtYowX3iA%3D&reserved=0.
It's

really not my C code so I'm flying a little blind as I'm very much a baby
in the world of C. I actually wish I could just import the compiled

version

directly from FMStable but can't figure out how, even after hours of
googling & trying everything within in my capacity. The speedup using

this

is >100-fold so it brings function execution time from minutes to

seconds.

As I'm trying to figure this out, one thought I had was that an early

push

erroneously contained the .o and .so files. I've since deleted these from
the repository. Are they resident on those servers still and is that
causing the problems? If so, how can I fix this? If not, does anyone have
any suggestions?

The actual functions which call the routines are at the bottom of

https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmped%2FextraChIPs%2Fblob%2Fdevel%2FR%2FmergeByHMP.R&data=05%7C01%7Csu.s%40wehi.edu.au%7C6a4c353e9e1a47efc19f08db3b2af477%7Caa7c72e2c5cf4a40a22aa585c04ca07c%7C0%7C0%7C638168827914859588%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=m96K4M9LhA7xDcscCwWjAaVKIDVKZPWZbxjbea2aTwI%3D&reserved=0

Thanks in advance,

Stevie

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