Re: [Rd] OpenBLAS in everyday R?

On Wed, Jan 10, 2018 at 12:04 AM, Keith O'Hara wrote: > > Check if libopenblas is linked against libomp or libgomp. > > I’d be curious to see any errors that arise when an OpenMP version of > OpenBLAS is linked with R. > > Keith > The one time I tried compiling OpenBLAS for

[R-pkg-devel] (no subject)

I'm seeing: * checking re-building of vignette outputs ... [3s] WARNING > Error in re-building vignettes: > ... > Quitting from lines 24-60 (strider.Rmd) > Error: processing vignette 'strider.Rmd' failed with diagnostics: > package 'dplyr' is not installed for 'arch = x64' > Execution halted

Re: [Rd] OpenBLAS in everyday R?

Check if libopenblas is linked against libomp or libgomp. I’d be curious to see any errors that arise when an OpenMP version of OpenBLAS is linked with R. Keith > On Jan 9, 2018, at 11:01 PM, Benjamin Tyner wrote: > > I didn't do the compile; is there a way to check

Re: [Rd] OpenBLAS in everyday R?

I didn't do the compile; is there a way to check whether that was used? If not, I'll inquire with our sysadmin and report back. In any case, my suggestion was motivated by the fact that some parts of R use OpenMP while others do not, in the hope that the former could have their OpenBLAS

Re: [Rd] OpenBLAS in everyday R?

Do those issues still arise when OpenBLAS is compiled with USE_OPENMP=1 ? Keith > On Jan 9, 2018, at 6:03 PM, Benjamin Tyner wrote: > > Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely > with multi-threaded OpenMP? (for example, don't race

Re: [Rd] OpenBLAS in everyday R?

Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely with multi-threaded OpenMP? (for example, don't race conditions sometimes crop up)? If so, it might be nice to have the ability to temporarily disable multi-threaded OpenMP (effectively: omp_set_num_threads(1)) for

Re: [Rd] Fixed BLAS tests for external BLAS library

Hi Martin and Tomas, Thanks for your reasoned replies. It seems that improving this is going to take more effort in pinning down exactly what is appropriate than I anticipated. Sorry if the intention was to keep the initial discussion of this off the list, I didn't mean to cause offence by

Re: [Bioc-devel] git help

Nitesh,   I have re-cloned it, everything looks good. Thanks for your help. Can you please make sure that the duplicate commit check has been re-enabled for this repo? It was previously disabled. Kevin On 01/09/2018 10:03 AM, Turaga, Nitesh wrote: Hi Kevin, Your repository should now be

Re: [Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

Hi Raymond, I’m trying to figure out why your problem was caused. The duplicates are coming from this commit (ea6c6421b074dbc9411bd6d00547b90bb6168d31), which is a merge. But I’m what I’m trying to figure out is how you’ve been able to push with duplicate commits after that merge. Please give

Re: [Bioc-devel] git help

Hi Kevin, Your repository should now be fixed. Please re-clone your repository. Best, Nitesh > On Jan 8, 2018, at 8:39 PM, Kevin Horan wrote: > > Nitesh, > >Sorry, just saw your email now. You can go ahead and make those changes. > Thanks for all your help. > >

Re: [Rd] resolving a names conflict

Dear Terry, Why not have the required code in survival and use importFrom(survival, gchol) in bdsmatrix? Since you maintain both, that shouldn't be too complicated. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission simpleroptions 0.2.0

On 09.01.2018 09:22, Luca Cerone wrote: Dear all, I have submitted my first R package to CRAN and I have received the email below back. If I understood the log message correctly, to fix the issues is fairly simple: - correct the Title using the Title Case suggestion - change a bit the

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission simpleroptions 0.2.0

Hi Luca, On 09/01/18 09:22, Luca Cerone wrote: > I have submitted my first R package to CRAN and I have received the email > below back. > > If I understood the log message correctly, to fix the issues is fairly > simple: > - correct the Title using the Title Case suggestion > - change a bit the

[R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission simpleroptions 0.2.0

Dear all, I have submitted my first R package to CRAN and I have received the email below back. If I understood the log message correctly, to fix the issues is fairly simple: - correct the Title using the Title Case suggestion - change a bit the description so that "simpleroptions" is not the

Re: [R-pkg-devel] CRAN policy on binary submission

On 09.01.2018 03:25, Hugh Parsonage wrote: On https://cran.r-project.org/ , it says Note that we generally do not accept submissions of precompiled binaries due to security reasons I note it says 'generally', not 'always'. Are there any packages on CRAN which were submitted as precompiled