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rdrr1990 / bigKRLS

Now on CRAN, bigKRLS combines bigmemory & RcppArmadillo (C++) for speed into a new Kernel Regularized Least Squares algorithm. Slides:
https://sites.google.com/site/petemohanty/software
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Current build cannot be installed with install_github() function #38

Open brandondelacuesta opened 4 years ago

brandondelacuesta commented 4 years ago

Hi guys,

Went to install this and noticed it's off CRAN. Is it no longer being supported? Went to get the Github version and install fails. I can get it working by pulling the most recent version off CRAN but just wondered if you are still supporting the package. Thanks.

AmirhosseinModabbernia commented 4 years ago

Hi there,

I am having the same problem. The package is no longer on CRAN and if I want to install it from github I get this error

✔ checking for file ‘/private/var/folders/5x/dxzpl7lx25q69bys583w3ngr0000gn/T/RtmpgSHnPt/remotese99362858638/rdrr1990-bigKRLS-e1e030f/DESCRIPTION’ (578ms) ─ preparing ‘bigKRLS’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src E checking vignette meta-information ... Output(s) listed in ‘build/vignette.rds’ but not in package: ‘inst/doc/bigKRLS_basics.html’ Run R CMD build without --no-build-vignettes to re-create Error: Failed to install 'bigKRLS' from GitHub: System command error

Please assist Thank you Amir

rbshaffer commented 4 years ago

Hey there,

Apologies for the delay in responding! Unfortunately, the CRAN issue isn't something we can easily fix. bigKRLS depends on bigalgebra for certain mathematical operations on large matrix objects. bigalgebra, in turn, has not been updated in a couple of years, and has been removed from CRAN. I'm not completely certain, but I think the reason for this has to do with CRAN's updated memory warning standards for packages that depend on Rcpp, which is something that we ran into briefly with bigKRLS as well. As far as I know, this is something that shouldn't affect functionality for bigKRLS, but if you run into issues I'd be interested in hearing about them.

In any case, removing this dependency on bigalgebra is something that's on our list to fix, but unfortunately, we haven't gotten around to it yet. In the meantime, as far as I know, bigKRLS should still work if you install it from the github page (install_github() via devtools). If you don't already have bigalgebra installed, again, as far as I know, older versions that are up on CRAN should still work. Again, though, if you run into issues please let me know!

Since people have expressed interest here, I'll try to get the dependency removed sooner rather than later. Thanks for your patience!

On Thu, Apr 23, 2020 at 10:49 AM AmirhosseinModabbernia < notifications@github.com> wrote:

Hi there,

I am having the same problem. The package is no longer on CRAN and if I want to install it from github I get this error

✔ checking for file ‘/private/var/folders/5x/dxzpl7lx25q69bys583w3ngr0000gn/T/RtmpgSHnPt/remotese99362858638/rdrr1990-bigKRLS-e1e030f/DESCRIPTION’ (578ms) ─ preparing ‘bigKRLS’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src E checking vignette meta-information ... Output(s) listed in ‘build/vignette.rds’ but not in package: ‘inst/doc/bigKRLS_basics.html’ Run R CMD build without --no-build-vignettes to re-create Error: Failed to install 'bigKRLS' from GitHub: System command error

Please assist Thank you Amir

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AmirhosseinModabbernia commented 4 years ago

Hello Robert and thank you for your prompt reply. So I installed bigalgebra but I still get this error with install_github

E checking vignette meta-information ... Output(s) listed in ‘build/vignette.rds’ but not in package: ‘inst/doc/bigKRLS_basics.html’ Run R CMD build without --no-build-vignettes to re-create Error: Failed to install 'bigKRLS' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr: E> checking for file ‘/private/var/folders/5x/dxzpl7lx25q69bys583w3ngr0000gn/T/RtmpSrSSaz/remotes33936129ef4/rdrr1990-bigKRLS-e1e030f/DESCRIPTION’ ... OK E> preparing ‘bigKRLS’: E> checking DESCRIPTION meta-information ... OK E> cleaning src E> * checking vignette meta-information ... ERROR E> Output(s) listed in ‘build/vignette.rds’ but not in package: E> ‘inst/doc/bigKRLS_basics.html’ E> Run R CMD build without --no-build-vignettes to re-create

Any thoughts?

AmirhosseinModabbernia commented 4 years ago

Never mind I got it to work with this line of code install_github('rdrr1990/bigKRLS', build=T,build_vignettes = TRUE)

rbshaffer commented 4 years ago

Great, glad to hear it! Please let me know if you run into any issues with package functionality. In the meantime, I'll do my best to get the bigalgebra dependency fixed.

On Thu, Apr 23, 2020, 11:23 AM AmirhosseinModabbernia < notifications@github.com> wrote:

Never mind I got it to work with this line of code install_github('rdrr1990/bigKRLS', build=T,build_vignettes = TRUE)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rdrr1990/bigKRLS/issues/38#issuecomment-618460850, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNR7ZAA7TMDMIUBPGNBZD3ROBMNFANCNFSM4L6Y4HAQ .

HalcyonXie commented 4 years ago

The solution AmirhosseinModabbernia posted does not work for me.

install_github("rdrr1990/bigKRLS", build=T, build_vignettes=T) Downloading GitHub repo rdrr1990/bigKRLS@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: backports (1.1.7 -> 1.1.8) [CRAN]

Enter one or more numbers, or an empty line to skip updates:3

checking for file 'C:\Users\huili\AppData\Local\Temp\RtmpA3xDNd\remotes41305169738\rdrr1990-bigKRLS-e1e030f/DESCRIPTION' ...

checking for file 'C:\Users\huili\AppData\Local\Temp\RtmpA3xDNd\remotes41305169738\rdrr1990-bigKRLS-e1e030f/DESCRIPTION' ...

√ checking for file 'C:\Users\huili\AppData\Local\Temp\RtmpA3xDNd\remotes41305169738\rdrr1990-bigKRLS-e1e030f/DESCRIPTION' (694ms)

√ checking DESCRIPTION meta-information

E creating vignettes (1m 26.2s) --- re-building 'bigKRLS_basics.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. Loading required package: bigmemory

bigKRLS is authored by Pete Mohanty (Stanford University) and Robert Shaffer (University of Pennsylvania) under License GPL 3.

To get started, check out vignette("bigKRLS_basics").

If you use this package in your research, kindly cite:

Pete Mohanty and Robert Shaffer. 2018. 'Messy Data, Robust Inference? Navigating Obstacles to Inference with bigKRLS.' Political Analysis. Cambridge University Press. DOI=10.1017/pan.2018.33. pages 1-18. Quitting from lines 37-39 (bigKRLS_basics.Rmd) Error: processing vignette 'bigKRLS_basics.Rmd' failed with diagnostics: e2 is not a scalar --- failed re-building 'bigKRLS_basics.Rmd'

SUMMARY: processing the following file failed: 'bigKRLS_basics.Rmd'

Error: Vignette re-building failed. Execution halted

Error: Failed to install 'bigKRLS' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Quitting from lines 37-39 (bigKRLS_basics.Rmd) E> Error: processing vignette 'bigKRLS_basics.Rmd' failed with diagnostics: E> e2 is not a scalar E> --- failed re-building 'bigKRLS_basics.Rmd' E> E> SUMMARY: processing the following file failed: E> 'bigKRLS_basics.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

Please advise. Thanks.