CRAN issues

[Tabima]

After attempts to submit the package to CRAN, I received an email with a problem in CRAN:

Found the following (possibly) invalid URLs:
 URL: https://cran.r-project.org/web/packages/seqinr/seqinr.pdf
   From: inst/doc/effectR.html
   Status: 200
   Message: OK
   CRAN URL not in canonical form
 The canonical URL of the CRAN page for a package is
   https://CRAN.R-project.org/package=pkgname

I think I solved the problem, but that might just mean that I'm omitting something or that there could be more potential problems and I really don't want to get banned from CRAN.

I was wondering if @knausb, @zkamvar and @zachary-foster could help me review the package real quick and check that its fine for CRAN. So far, I've succesfully:

• Build the package locally and via winbuilder
• Passed the tests and checks locally
• Installed and passed on Travis-CI (https://travis-ci.com/Tabima/effectR/jobs/105758494)
• Build, installed and used the package in Windows, MacOSX and Linux (Ubuntu and CentOS)

Am I missing something else?

[zachary-foster]

Did you use devtools::release to submit to CRAN? It does checks that R CMD check --as-cran does not. I have gotten warnings there even though I dont get them in winbuilder, travis CI, or locally. That has caught URL errors in my package as well. I think devtools::release_checks will do those checks without submitting to CRAN.

I cant look at your Travis builds because the repo is private I think. Since you are releasing the package to CRAN soon, I think it would be best to make the repo public anyway.

I will look at this more later and get back to you

[Tabima]

Thanks, @zachary-foster, for responding so quick.

The newest commit has passed the devtools::release_checks checks. The last commit just had a small warning:

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::release_checks(pkg = ".")
Running additional devtools checks for effectR
Checking version number has three components... OK
Checking dependencies don't rely on dev versions... OK
Checking vignette titles are not placeholders...
WARNING: placeholder 'Vignette Title' detected in 'title' field and/or 'VignetteIndexEntry' for: effectR.Rmd
Checking DESCRIPTION doesn't have Remotes field... OK

Here's a screenshot of the Travis-CI build. Nik wanted the package to be private until CRAN submission.

[zkamvar]

I just made pull request #11 that may address the issue.

[knausb]

On Ubuntu, using commit 7a5bb7e462c52a0beaaaadb8388632562542eb00, I see one NOTE.

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Javier Tabima <tabimaj@oregonstate.edu>’

New submission

I think you can ignore this.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.3

[knausb]

Using

grep -i --color=always 'https://cran.r-project.org/' vignettes/effectR.Rmd | less -R

I see the only R package linked appears to be seqinr. I see two links where 'cran.r' is in lower case and one in upper. I think @zkamvar caught one of these in his PR but didn't see the other. Changing this so that all three have this in uppercase may help?

[knausb]

On OSX, using 7a5bb7e462c52a0beaaaadb8388632562542eb00, I use

 R CMD check --as-cran effectR_1.0.0.tar.gz

and see one NOTE.

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Javier Tabima <tabimaj@oregonstate.edu>’

New submission

Which I think is fine.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.3

[zachary-foster]

Yup, The "New submission" note is fine. I had it the first time I submitted.

[Tabima]

Merged #11, will test as appropriate and submit early next week. Thank you all for your help!

[Tabima]

Thank you all! effectR is live in CRAN now! @grunwald @knausb @zkamvar @zachary-foster

[zachary-foster]

Wahoo! Nice job!

[knausb]

Yay! Congrats!

[zkamvar]

CRAN-gratulations!

[knausb]

Oh no! I didn't realize solaris was back up and running. You passed, whew!