On 02/04/2019 19:10, Dey, John F wrote:
Thanks, .Rprofile was the culprit.
Sounds like we should bump priority on https://github.com/easybuilders/easybuild-easyblocks/issues/867 ?
regards, Kenneth
I am still supporting an older environment which we hope to decommission. After years of using EB, we have developed some best practices for our site which I was not following, - Create a special account to own all the software builds, do not build as yourself - Build in a container using Docker Run. (or re-image your machine between builds) Dedicated build machines tend to collect unwanted packages from unsavory build scripts. - At a minimum use the toolchain foss-2018b. 2018b only allows single versions of base libraries to be part of the toolchain. It's important to have dependency consistency across every package built with a single toolchain. - Try to use as many published EasyBuild easyconfigs as possible. Resist the urge to edit and modify easybuilds. - Contribute back when possible ( --new-pr ) - use PythonPackage and/or RPackage to extend the base R and Python packages - Use bundles to create custom versions of base packages. - Document os dependencies, not every site uses CentOS - Verify package builds with ldd John Dey On 3/30/19, 10:20 AM, "[email protected] on behalf of Lars Viklund" <[email protected] on behalf of [email protected]> wrote: The message `installing to /home/jfdey/R/minqa/libs` in your output seems a bit strange.Do you have anything (silly) in your ~/.Renviron or ~/.Rprofile? If I remember correctly, R is a bit annoying in that it honors flags anddirectories specified in those files, which has broken my builds in the past and are also somewhat documented at https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_easybuilders_easybuild-2Deasyblocks_issues_867&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=ItDTfh6Nv5MBsyLiyKrxxbdWCcJ40WvM9TYgAcQ98N4&s=Qkgy4PWPbJH4icZClT0AB_7G_PVAU_-NVpgtRRFiixs&e= .The `[1] "hello"` part almost looks like the output from shell jobcontrol, but how that'd sneak in, heaven knows.I set up a 14.04 container and installed R/3.5.3 foss/2018b from a PR,got past minqa with flying colours. That one said `installing to /home/zao/slask/eb-1404/software/R/3.5.3-foss-2018b/lib/R/library/minqa/libs`.// Lars On 2019-03-29 23:17, Dey, John F wrote:> I always install by using --install-latest-eb-release > After sending this issue I upgrade Python to 2.7.16 on our 14.04 build machine, and re-installed 3.81. Same results. I have no issue with same setup on Ubuntu 18.04 > > > John Dey > > On 3/29/19, 3:05 PM, "Kenneth Hoste" <[email protected]> wrote: > > On 29/03/2019 21:24, Dey, John F wrote: > > I have put my issue into a Gist. This issue is occurring while building > > R extensions. > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_fizwit_51f41001d5bb58a3525b5f58d84a7606&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=Qx9xK3MqqUx8uKrgUVDD4CinnEVJZB7Y0-pdU3notig&s=b1J8DqAItrUzVFPc4EbLD_Gk3c0tCPVoEglu3JPO6EM&e= > > That's positively weird, indeed... Pretty sure it's not EasyBuild itself > doing this. Is this a vanilla EasyBuild 3.8.1, or was there some editing > done to it? > > Anything in your environment that may explain this? > > env | grep hello > > > regards, > > Kenneth > > > > > *John Dey* > > > > *HPC Operations* > > > > SciComp Computing > > *O* _206.667.4308_ > > *M* _360.649.2731_ > > > > [email protected] <mailto:[email protected]> > > > > SciComp Office Hours > > > > Wed. 10-noon M4-B102 > > > > http://www.fredhutch.org/content/dam/public/email-signatures/3/fred_hutch_logo.png > > <http://www.fredhutch.org/> > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N., Mail Stop J4-402 > > Seattle, WA 98109 > > *fredhutch.org <http://www.fredhutch.org/>* > > > >
