license file should be deleted

[dankelley]

(This follows some direct emails between coauthors. I'm marking the assignee as CR since he noticed some problems with build warnings, related to the license. I don't see such problems when I build, so it will be easier for CR to see if any new problems arise when we remove the LICENSE file.)

I just read in the R docs the following. So we cannot include the LICENSE file.

The optional file LICENSE/LICENCE contains a copy of the license of the package. To avoid
any confusion only include such a file if it is referred to in the ‘License’ field of the 
DESCRIPTION file.

[richardsc]

My understanding (from here) is that you can include the type of license in the DESCRIPTION, but it can also indicate the presence of a LICENSE file. That is the issue I'm seeing when I do R CMD check GSW-R.

I'm going to update DESCRIPTION to also include the LICENSE file, as provided by the TEOS org.

By the way, my R settings that produce the license note are:

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (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.

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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   

and the output of R CMD check GSW-R is:

$ R CMD check GSW-R
* using log directory ‘/Users/richardsc/src/R-kelley/GSW-R.Rcheck’
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘GSW-R/DESCRIPTION’ ... OK
* this is package ‘gsw’ version ‘0.1-1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘gsw/src’ contains apparent object files/libraries
  /Users/richardsc/src/R-kelley/GSW-R/src/gsw.so
  /Users/richardsc/src/R-kelley/GSW-R/src/gsw_format.o
  /Users/richardsc/src/R-kelley/GSW-R/src/gsw_oceanographic_toolbox.o
  /Users/richardsc/src/R-kelley/GSW-R/src/gsw_saar.o
  /Users/richardsc/src/R-kelley/GSW-R/src/gsw_saar_data.o
  /Users/richardsc/src/R-kelley/GSW-R/src/teos10.o
  /Users/richardsc/src/R-kelley/GSW-R/src/wrappers.o
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... WARNING
Found the following executable files:
  .git/objects/00/90f3b2ed9076c35b160bd913327287279b57dd
... snipped out a whole lot of git directories ...
  .git/objects/fe/ff2aa8ec97408d5e457e13099092c41a889f6c
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .gitignore
  vignettes/.gitignore
  .git
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gsw’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘gsw.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML:
   ‘gsw.Rnw’

* checking running R code from vignettes ...
   ‘gsw.Rnw’ ... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  ‘/Users/richardsc/src/R-kelley/GSW-R.Rcheck/00check.log’
for details.

[richardsc]

Commit 57d9efb has an updated DESCRIPTION and LICENSE. Let me know if you think this is sensible. It can always be reverted.

[dankelley]

That looks excellent to me. It seems short enough that whoever decides on acceptability should be able to figure it out quite quickly. The danger in doing something other than GPL-2 or other standard is that some special permissions might be required to get it into the CRAN stream. But maybe the "|" operator is sufficient, in any case.

[dankelley]

Thanks.

I think I see why we get different results. Somehow, the .Rbuildignore file not being obeyed for you. You're getting lots of files (e.g. the .o and .so files) that don't get built into my tarball. And also the LICENSE was not in my tarball because it was named in .Rbuildignore.

I don't know what's doing on, because when I do git ls-files | grep build I see that .Rbuildignore is indeed in the git repo.

We should probably figure out how the two of us are getting different behaviour on .Rbuildignore, since it's an important file that can reduce the error count dramatically. (Remember, CRAN will reject anything with an error, and they don't like "note" either. So this means that you cannot test for CRAN acceptability, as your system is presently configured.)

[dankelley]

In case it's of any use, below is the Makefile portion that I use for gsw. The inference of "most recent" is done by a whacky pipe string that may be brittle if version-numbering is altered.

GSWVSN=`ls -c1 -r -t gsw_*.tar.gz|tail|sed -e s/gsw_// -e s/.tar.gz//|tail -1`
gsw: force
        PKG_CFLAGS=--pedantic R CMD BUILD GSW-R
        R CMD CHECK --as-cran gsw_${GSWVSN}.tar.gz
        R CMD INSTALL gsw_${GSWVSN}.tar.gz

[richardsc]

Oh I see why we're seeing different things -- it's an ID10T error. I've been doing

R CMD check GSW-R/

which checks the directory, rather than the built tarball. If I build and check as you do, I now get the following note:

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Dan Kelley <Dan.Kelley@Dal.Ca>’
New submission

I just deleted some other comments about DESCRIPTION errors, because I had not pulled the latest version which you had already fixed.