Hi, Duncan:
Thanks again.
I found XQuartz-2.8.1.dmg and added the 5 lines you suggested
(modified to 2.8.1) to "R-CMD-check.yaml". However, the "GitHub Action"
status symbols disappeared, so I deleted them.
I copied the "CRAN" function from fda to sos and deleted the
reference to fda from sos.
Now I'm getting, 'could not find function "CRAN"' in "processing
vignette 'sos.Rnw'", even though CRAN is in the NAMESPACE for sos.
Suggestions?
Thanks,
Spencer
p.s. To use Sys.getenv("NOT_CRAN"), I'd have to set the environment
variable "NOT_CRAN" on all the test platforms other than CRAN, and
that's a level of complexity I'd rather not get into.
On 5/23/21 7:03 PM, Duncan Murdoch wrote:
Okay, I just worked out the chain: The fda package depends on fds. fds
depends on rainbow. rainbow imports ks. ks imports plot3D. plot3D
imports misc3d. misc3d imports tcltk. tcltk on macOS needs XQuartz.
I saw this item online:
https://github.com/actions/virtual-environments/issues/771 . It's a
suggestion to add this to the default macOS VM, but apparently they
didn't act on it. You could try adding it to yours:
if: runner.os == 'macOS'
run: |
wget https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg
sudo hdiutil attach XQuartz-2.7.11.dmg
sudo installer -package /Volumes/XQuartz-2.7.11/XQuartz.pkg
-target /
(Though the current XQuartz version is 2.8.1, and the URL above doesn't
work for me, so you'll probably have to spend some time finding one that
does.)
What should you do? I can suggest a couple of things other than
installing XQuartz:
1. Drop the fda dependency, and work around the lack of fda::CRAN. It
seems you're pulling in an awful lot of stuff for that one function. The
on_cran function in testthat has this definition:
function ()
!identical(Sys.getenv("NOT_CRAN"), "true")
so I'd copy that to your package and then define environment variable
NOT_CRAN=true on your Github machine (in the "env:" section). But this
might be inconvenient working on your own machine, where you'll also
need to define NOT_CRAN=true.
2. Leave in the fda dependency, but make the test conditional, i.e. change
if (fda::CRAN())
to
if (requireNamespace("fda") && fda::CRAN())
I'd do number 1, or just assume everything is being run on CRAN.
Duncan Murdoch
On 23/05/2021 6:49 p.m., Spencer Graves wrote:
Hi, Duncan et al.:
Thanks again. I removed fda from "suggests" and added it to
"imports" in DESCRIPTION. I also added "importFrom('fda', 'CRAN')" to
NAMESPACE. Sadly, the result was the same: It passed "R CMD check" on
Windows, ubuntu, and my local Mac but not macOS on GitHub Action.
How do you suggest I proceed from here?
You may recall that I started using "if(fda::CRAN())" as a way to
keep checks for routine testing that take too much time on CRAN. I've
looked at Wickham's "skip_on_cran" but concluded, perhaps incorrectly,
that it was not self contained and required more work to use than
"if(fda::CRAN())". If I'm incorrect in that assessment, I will happily
accept instructions on how to convert "if(fda::CRAN())" to use
"skip_on_cran".
Again, I really appreciate the help.
Spencer
On 5/23/21 4:44 PM, Duncan Murdoch wrote:
I don't see where the connection is, but it's almost certainly coming in
through your unconditional use of "fda::CRAN()". Since "fda" is not a
hard requirement, this should be conditional on having it installed.
Duncan Murdoch
On 23/05/2021 5:25 p.m., Spencer Graves wrote:
Hi, Duncan et al.:
I inserted "the lines from the rgl workflow to work around the
XQuartz issues" that Duncan provided after "env" in TWO places in
R-CMD-check.yaml with the same result: GitHub Action worked fine on
Windows and ubuntu (both release and devel) but failed on macOS
complaining, "there is no package called 'ks'".
HOWEVER, I can NOT see how I even ask for ks. The error message
says:
processing the following file failed: 'sos.Rnw'
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force ->
<Anonymous>
Execution halted
Error: Process completed with exit code 1.
I can NOT find it with "grep 'ks' sos.Rnw". It's NOT in
DESCRIPTION
nor NAMESPACE.
I do NOT see how I am even asking for it.
PROPOSED NEXT STEP: Do as outlined in
"https://github.com/ThinkR-open/prepare-for-cran"; and submit to CRAN
with a note on this problem in cran-comments.md if the package passes
all other tests.
Other suggestions?
Thanks again, Duncan.
Spencer
On 5/23/21 2:36 PM, Duncan Murdoch wrote:
For ks, if you look here:
https://github.com/sbgraves237/sos/runs/2650960959?check_suite_focus=true
in the "Install Dependencies" section, you'll see these errors:
trying URL 'https://cloud.r-project.org/src/contrib/ks_1.13.0.tar.gz'
Content type 'application/x-gzip' length 1076044 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
* installing *source* package ‘plot3D’ ...
** package ‘plot3D’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: Error: .onLoad failed in loadNamespace() for 'tcltk', details:
ERROR: lazy loading failed for package ‘plot3D’
call: fun(libname, pkgname)
* removing ‘/Users/runner/work/_temp/Library/plot3D’
error: X11 library is missing: install XQuartz from
www.xquartz.org
Execution halted
ERROR: dependency ‘plot3D’ is not available for package ‘ks’
* removing ‘/Users/runner/work/_temp/Library/ks’
so the problem is really with plot3D, and indirectly with rgl and
tcltk.
I'm familiar with problems like that! Here are the lines from the rgl
workflow to work around the XQuartz issues:
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
_R_CHECK_FORCE_SUGGESTS_: false
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RGL_USE_NULL: true
The last line might be enough for you, but I think the 2nd line
_R_CHECK_FORCE_SUGGESTS_: false
may be more important: you use ks, it imports plot3D, plot3D imports
misc3d, but it only suggests rgl and tkrplot: so that would let ks
load
without XQuartz support.
Duncan Murdoch
On 23/05/2021 3:09 p.m., Spencer Graves wrote:
Hi, Duncan et al.:
Thanks again to Duncan. Your suggestions worked for the
LaTeX
problem, though it required multiple iterations, adding a total of 7
different "tinytex::parse_install" clauses to overcome other LaTeX
and
pdfTeX errors.
However, macOS still says, "there is no package called 'ks'",
even
though I added 'install.packages("ks")' as you suggested -- to three
different places, all without solving the problem. I posted this
question to
"https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions";,
as suggested in line 2 of "~/.github/workflows/R-CMD-check.yaml".
See:
Spencer
On 5/23/21 11:03 AM, Duncan Murdoch wrote:
This page
https://bookdown.org/yihui/rmarkdown-cookbook/install-latex-pkgs.html
suggests that executing this in R should fix the tikz issue:
tinytex::parse_install(
text = "! LaTeX Error: File `tikz.sty' not found."
)
The "ks" message looks like a missing R package rather than a
missing
LaTeX package, so running install.packages("ks") would fix it.
So the only question is how to do these things in a Github
action. I
don't know if there's a pre-made recipe for this, but this one
should do
it:
- name: Install tikz.tex and ks
run: |
install.packages(c('tinytex', 'ks')) # Maybe
tinytex is
already there?
tinytex::parse_install(
text = "! LaTeX Error: File `tikz.sty' not found."
)
shell: Rscript {0}
Duncan Murdoch
On 23/05/2021 11:28 a.m., Spencer Graves wrote:
Hi, Duncan et al.:
Thanks very much to Duncan for his suggestion. I did
added the
line
Duncan suggested in three slightly different places. That fixed
the
problems with missing tex and pdflatex, but exposed two new
problems:
On Windows and ubuntu (both release and devel) I now get:
LaTeX Error: File `tikz.sty' not found.
On macOS, I got a different error:
there is no package called 'ks'
I added "ks" to "suggests" in DESCRIPTON but still got "no
package
called 'ks'. And I studied README in
https://github.com/r-lib/actions,
and I did some other searches without figuring out how to fix
"`tikz.sty' not found."
For more details, see:
https://github.com/sbgraves237/sos
Suggestions?
Thanks,
Spencer
On 5/23/21 4:43 AM, Duncan Murdoch wrote:
On 22/05/2021 10:05 p.m., Spencer Graves wrote:
Hello:
What do you suggest I do to enable GitHub Action to
process
"sos.Rnw"
properly?
The development version of my "sos" package passes
"R CMD
check" on
my Mac but fails in all four platforms under GitHub Action on
https://github.com/sbgraves237/sos
The error messages on macOS and Ubuntu release and
devel all
seems
the same:
* Error: processing vignette 'sos.Rnw' failed
with
diagnostics:
Running 'texi2dvi' on 'sos.tex' failed. Messages: You don't
have a
working TeX binary (tex) installed anywhere in your PATH, and
texi2dvi
cannot proceed without one.
The error message under Windows seemed crudely
similar but
different:
* Error: processing vignette 'sos.Rnw' failed
with
diagnostics:
pdflatex is not available
What do you suggest?
The virtual machines that run Github actions have lots of tools
installed, but apparently not LaTeX. So you need to figure out
the
"step" to install it. I'm not currently using Rnw with Github
actions,
but by looking at the README for
https://github.com/r-lib/actions, I'm
pretty sure all you need is to add
- uses: r-lib/actions/setup-tinytex@v1
somewhere after
- uses: actions/checkout@master
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