Re: [R-pkg-devel] Referring to data in R/sysdata.rda

[Spencer Graves]

On 2017-04-15 11:24 AM, Hadley Wickham wrote:

Just ignore it.
Hadley

On Friday, April 14, 2017, Roy Mendelssohn - NOAA Federal <
roy.mendelss...@noaa.gov> wrote:


In my package I have a dataframe that I use but want to hide from the
user.  In Hadley's book on R Packages,  he says:


   • If you want to store parsed data, but not make it available to

the user, put it in R/sysdata.rda. This is the best place to put data that
your functions need.
I have done that,  and sure enough when the package is loaded, the
structure is there.  However,  when I am working on debugging code, and I
refer to the  structure in a function,  RStudio gives a warning that the
structure is out of scope, say the data frame is myDF:

myFunc  <-  function(myIndex) {
  junk  <-  myDF[index]
 return(junk)
}


  Have you tried the following:



myFunc  <-  function(myIndex) {
  junk  <-  yrPkg:::myDF[index]
 return(junk)
}



  This will turn of similar messages is slightly different 
contexts.  I don't know if it will work here (and I don't have time to 
try it myself now).  Spencer Graves



RStudio will warn that myDF is out of scope.  My question is if there is a
proper way to refer to myDF so as not to get the warning,  or just ignore
it.  Basically before submission I try to remove all warnings from the
editor,  even style ones,  just to have things cleaner.

Thanks,

-Roy





**
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov <javascript:;> www:
http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK
Jr.

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Re: [R-pkg-devel] CRAN and cmake

[Spencer Graves]

On 2017-05-23 10:56 AM, Dirk Eddelbuettel wrote:

On 23 May 2017 at 10:34, Thibault Vatter wrote:
| Hi,
|
| Back in 2015, there was a discussion on this list about CRAN and cmake.
|
| As explained by Gabor at the time, it would be useful to have cmake in a R
| package.
|
| Furthermore, Gregory mentioned that there was something available on GitHub:
|
| https://github.com/stnava/cmaker
|
| Since it seems that the package was CRAN-ready two years ago, I wondered
| what happened?
|
| Would an R package containing cmake be accepted in CRAN?

Yes. Many of them do.

A nice benefit of Gabor's CRAN mirror on GitHub is access to the GitHub.
Here I constrain on user:cran (to get just that mirror, and nothing) and
CMakeLists.txt.  Seems to find 47 repos -- corresponding to 47 packages.

https://github.com/search?q=user%3Acran+CMakeLists.txt=Code=%E2%9C%93



  How did you construct that search string?


  Do you think something like this should be added to some other 
general search capability like the sos or CRANsearcher packages?



  I ask in part, because there will be a session at useR!2017 on 
"NAVIGATING THE R PACKAGE UNIVERSE", and this seems possibly relevant to 
that discussion.  (That session is scheduled for Wed. July 5, from 17:00 
- 18:30.  The organizers of that session expect that a fair portion of 
that time will be devoted to discussion of other possibilities, hoping 
we can build a team who will work to improve the ability of users to 
find what they want.  See 
"https://user2017.brussels/news/2017/navigating-the-r-package-universe;.)



  Spencer Graves


Hth, Dirk



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Re: [R-pkg-devel] Producing ß in help files.

[Spencer Graves]

On 2018-01-05 21:41, Rolf Turner wrote:

On 06/01/18 16:19, Spencer Graves wrote:



On 2018-01-05 20:52, Rolf Turner wrote:


In a help file that I am writing I wish to cite an item by a bloke 
whose surname is Weiß.



   Write it "Weiss".


   See "https://en.wikipedia.org/wiki/%C3%9F;.


   That name is written "Weiss" in Switzerland and Liechtenstein 
but "Weiß" in Germany and Austria.  German is the official language 
of Liechtenstein and the primary of four official languages of 
Switzerland.



   Standard high German has several characters that are not used 
in English but have standard transliterations using the English latin 
alphabet.  These include "ß" = "ss", "ä" = "ae", "ö" = "oe" and "ü" = 
"ue".




I'm sure that you're correct, but I find it frustrating not to be able 
to produce a symbol (which is readily available elsewhere --- e.g. in 
LaTeX or from the keyboard using the "compose key") under the ".Rd" 
system.  I'd like to be *able to produce it*, even if I shouldn't! :-)


cheers,

Rolf

P. S.  It also seems to me to be polite --- if that's the way the 
bloke writes his name, then  that's the way that I ought to write it 
when referring to him.



  Agreed -- except that people who have not studied German would 
not recognize "ß" as sounding like "ss":  They might want to pronounce 
it "Weib" -- old German for "woman", though transliterated as "wife" -- 
very different from "Weiß" = "White".



  "Solzhenitsyn" is the English and Spanish transliteration of a 
name that appears in German as "Solschenizyn", French as "Soljenitsyne", 
and Russian as "Солженицын", according to Wikipedia 
(https://en.wikipedia.org/wiki/Aleksandr_Solzhenitsyn).



  Hope this helps.
  spencer



R.



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Re: [R-pkg-devel] Producing ß in help files.

[Spencer Graves]

On 2018-01-05 20:52, Rolf Turner wrote:


In a help file that I am writing I wish to cite an item by a bloke 
whose surname is Weiß.



  Write it "Weiss".


  See "https://en.wikipedia.org/wiki/%C3%9F;.


  That name is written "Weiss" in Switzerland and Liechtenstein but 
"Weiß" in Germany and Austria.  German is the official language of 
Liechtenstein and the primary of four official languages of Switzerland.



  Standard high German has several characters that are not used in 
English but have standard transliterations using the English latin 
alphabet.  These include "ß" = "ss", "ä" = "ae", "ö" = "oe" and "ü" = "ue".



  Spencer Graves



In LaTeX I would use the macro \ss, but Rd files don't accept that.

Is there any way that I can create the ß symbol in a help file? I've 
done a bit of web-searching and found nothing helpful.


Of course I could just write "Weiss", but that's *so* non-U! :-)

Thanks for any ideas.

cheers,

Rolf Turner



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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Spencer Graves]

The fda package disables some tests on CRAN using:


if(!fda::CRAN()){
    test you don't want run on CRAN
}


  I've used this in other contexts with tests that are too long to 
run on CRAN but that I want to run otherwise during "R CMD check".



      Spencer Graves


On 2018-09-05 12:13, Peter Meissner wrote:

Hey,

Maybe webmockr (or something alike) can help:
https://cran.r-project.org/web/packages/webmockr/index.html

Best, Peter

Rainer M Krug  schrieb am Mi., 5. Sep. 2018, 15:38:


OK - thanks. I will than disable the checks for CRAN.

Thanks,

Rainer



On 5 Sep 2018, at 15:37, Uwe Ligges 

wrote:

You should not run on CRAN. Note that the checks are done almost daily

oin several platforms, hence the API key is used for about 10 check runs a
day.

Best,
Uwe Ligges



On 05.09.2018 09:28, Rainer Krug wrote:

Hi
I have a package at GitHub (https://github.com/rkrug/ROriginStamp)

which I am pre[paring for CRAN.

It creates a trusted timestamp using the API fro OriginStamp (

https://originstamp.org/home) which requires an API key. Now this API
should not be made public, as to much traffic through one API key will lead
to it’s blocking.

I have stored the key encrypted in the travis.yml, and the package

passes all tests.

But if I send it to CRAN, it would fail the tests, as the api key is

not in the package itself.

I could disable all tests for CRAN which need the API key, but I think

it would be better tu run the tests there as well (as an additional check
to travis).

My question:
Is there a way of storing the API key encrypted, so that only the CRAN

test servers can decrypt it, or is there another way can steal with this?

Thanks,
Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation

Biology, UCT), Dipl. Phys. (Germany)

University of Zürich
Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
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University of Zürich

Cell:   +41 (0)78 630 66 57
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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Spencer Graves]

On 2018-09-05 12:52, Gábor Csárdi wrote:

On Wed, Sep 5, 2018 at 6:34 PM Spencer Graves
 wrote:

The fda package disables some tests on CRAN using:


if(!fda::CRAN()){
  test you don't want run on CRAN
}

Seemingly this just checks for a couple of (5 by default) environment
variables that match "^_R_":
https://github.com/cran/fda/blob/0549e6a86aa144d8c2aade2d8704a269fb8a94ed/R/CRAN.R#L14

I am not sure if this is a good indication of the machine being a CRAN
machine, I do set  some of these
occasionally on my machine.  It would be great if CRAN machines could
set a specific environment
variable globally, e.g. ON_CRAN, or _R_ON_CRAN_, so people could skip
these tests and examples
easily.



Agreed.  Before I wrote that function, I asked this list for 
suggestions.  The suggestion I got was, "Don't do it."  I felt that was 
not acceptable so wrote what I did.  I think we need a better solution.  
Spencer


Gabor



I've used this in other contexts with tests that are too long to
run on CRAN but that I want to run otherwise during "R CMD check".


Spencer Graves


On 2018-09-05 12:13, Peter Meissner wrote:

Hey,

Maybe webmockr (or something alike) can help:
https://cran.r-project.org/web/packages/webmockr/index.html

Best, Peter

Rainer M Krug  schrieb am Mi., 5. Sep. 2018, 15:38:


OK - thanks. I will than disable the checks for CRAN.

Thanks,

Rainer



On 5 Sep 2018, at 15:37, Uwe Ligges 

wrote:

You should not run on CRAN. Note that the checks are done almost daily

oin several platforms, hence the API key is used for about 10 check runs a
day.

Best,
Uwe Ligges



On 05.09.2018 09:28, Rainer Krug wrote:

Hi
I have a package at GitHub (https://github.com/rkrug/ROriginStamp)

which I am pre[paring for CRAN.

It creates a trusted timestamp using the API fro OriginStamp (

https://originstamp.org/home) which requires an API key. Now this API
should not be made public, as to much traffic through one API key will lead
to it’s blocking.

I have stored the key encrypted in the travis.yml, and the package

passes all tests.

But if I send it to CRAN, it would fail the tests, as the api key is

not in the package itself.

I could disable all tests for CRAN which need the API key, but I think

it would be better tu run the tests there as well (as an additional check
to travis).

My question:
Is there a way of storing the API key encrypted, so that only the CRAN

test servers can decrypt it, or is there another way can steal with this?

Thanks,
Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation

Biology, UCT), Dipl. Phys. (Germany)

University of Zürich
Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug
PGP: 0x0F52F982
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Biology, UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug

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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Spencer Graves]

On 2018-09-07 12:10, Duncan Murdoch wrote:


...


I would guess because it can’t. If there would be a standardised way 
of identifying that the test is run on CRAN, I would use this 
immediately.


Then your package would fail when I ran the tests, because I don't 
have an API key, and I am not CRAN.  It makes more sense to me to 
treat CRAN the same as any other user who is not the author.



RAINER:  Have you considered writing your time stamp code so it takes it 
from originstamp if it's available, and if not switches to some other 
external source if there is an Internet connection, and then from date() 
otherwise -- with an appropriate warning if it doesn't come from 
originstamp?  You can have an option that the user can set if s/he wants 
an error rather than a warning if originstamp is not available.  Then 
people can use your package without worrying about getting an API key:  
That's optional.



  Spencer Graves



Duncan Murdoch



Cheers,

Rainer




Duncan Murdoch

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Biology, UCT), Dipl. Phys. (Germany)


University of Zürich

Cell:       +41 (0)78 630 66 57
email:      rai...@krugs.de <mailto:rai...@krugs.de>
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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Spencer Graves]

On 2018-09-08 14:02, Joshua Ulrich wrote:

Hi Rainer,

On Wed, Sep 5, 2018 at 2:28 AM, Rainer Krug  wrote:

Hi

I have a package at GitHub (https://github.com/rkrug/ROriginStamp) which I am
pre[paring for CRAN.

It creates a trusted timestamp using the API fro OriginStamp
(https://originstamp.org/home) which requires an API key. Now this API should
not be made public, as to much traffic through one API key will lead to it’s
blocking.

I have stored the key encrypted in the travis.yml, and the package passes all
tests.

But if I send it to CRAN, it would fail the tests, as the api key is not in
the package itself.

I could disable all tests for CRAN which need the API key, but I think it
would be better tu run the tests there as well (as an additional check to
travis).

My question:

Is there a way of storing the API key encrypted, so that only the CRAN test
servers can decrypt it, or is there another way can steal with this?


I have a similar issue with quantmod.  I need API keys to test some
functionality and I would like the tests run regularly, so I can know
when something breaks without having to wait for a user to report the
change.

I store the API keys in encrypted environment variable in TravisCI,
and I check for those environment variables before running the tests
that require them.

Then I added a cron job on TravisCI to run the build if there hasn't
been a build in the past 24 hours.  That solves the problem adequately
for my purposes without adding any burden to CRAN.  Hopefully it works
for your purposes too.



  So those tests don't run if the required environment variables 
are not there?



  Rainer's problem was getting a secure time stamp.  For his case, 
rather than skip the tests if the API keys were not there, one might 
take the time stamp from someplace else, perhaps with a note of the 
source of the time stamp.



  Spencer


Best,
Josh


Thanks,

Rainer



--
Rainer M. Krug, PhD (Conservation Ecology, SUN),
MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug

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Re: [R-pkg-devel] Package Etiquette

[Spencer Graves]

On 2018-09-09 09:30, Dirk Eddelbuettel wrote:

Hi Joseph,

On 8 September 2018 at 21:11, Joseph Wood wrote:
| I’m a new developer and this is my first post. I have a question regarding
| package development with regards to duplication of functionality. I read
| the posting guide (https://www.r-project.org/posting-guide.html) and didn’t
| see anything addressing this.



  I wrote and use sos::findFn to find other packages and functions 
that seem to do the same or similar things.  A search for software and 
books on splines led to an invitation to help maintain and improve the 
"fda" package, and then to another invitation to collaborate on a book 
on "Functional data analysis with R and Matlab".  Another search got me 
named the maintainer of the "Ecdat" package, in which I've since fixed 
bugs while adding my own material.



  Other searches led to functions in other packages I use in the 
FinTS package.  For that, I use, cite, and compare similar functions in 
other packages.  My philosophy, like Dirk's I think, is that if someone 
else has a function that seems to do what I want, I'd rather let them 
maintain it.  I will copy it only if I really need something different 
that they don't provide and don't want to provide.  If I copied 
something otherwise, the two copies would likely eventually get out of 
sync.  Then other users (and I myself) would have trouble determining 
which version to use.  What a mess. I'll let an existing package author 
worry about maintaining what s/he has already written and maintained.  I 
can worry about other things.



  Hope this helps.
  Spencer Graves


I sense that by actually asking the question (good move!) you already have an
inkling about the answer.  So indeed, _ex ante_ and with the caveat about
missing details and not knowing more: it is generally a bad thing.

Every now and then we manage to avoid it.  Eg I once had an (incomplete and
tentative but functional) package to have R interface the (awesome !!)
MessagePack binary serialization format (using C++ via Rcpp).  Then I spotted
a new package by Travers doing very similar things (in broader scope) via
R. So I suggested we joing forces, we did and the resulting package is much
better. So much so that we wrote a (not yet complete) paper about it too.

But it is a complex topic, and sometimes we need different approaches. And
the best person to ask may be the maintainer of the package you aim to
extend.

The best answer may be in the _Writing R Extensions_ manual that came with
your copy of R.  It is the only "official" manual for package development.

| Is this the right place to ask?

Quite possibly, as it is the list about package development. Some more
pertinent detail may help, and as mentioned, maybe first talking to the
maintainer may not be a bad idea.

But to close: it is not formally forbidden, and duplication _happens_.  Good
judgement always helps, sometimes good judgement is informed by observing
best (prior) practice. And/or by asking here.

Hope this helps, Dirk



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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Spencer Graves]

On 2018-09-07 01:18, David Hugh-Jones wrote:

On Fri, 7 Sep 2018 at 01:16, Duncan Murdoch 
wrote:



When packages delete tests just for CRAN, the quality of the repository
suffers.  Users should be able to check an install by running the tests
that passed on CRAN and seeing them pass on their system as well.


In my limited experience there are usually tests that can't run on CRAN
  because they take too long, rely on external software or configuration
that is absent, or just fail on CRAN only (which is naturally hard to
debug). This seems normal, and having the ability to turn off some tests is
useful. The fact that multiple workarounds have evolved to do this suggests
that the need is widespread.



  Almost a decade ago I was told that certain tests in the fda 
package took too much time on CRAN.  I was NOT going to hammer on my 
co-authors to make those tests shorter.  I was happy I got those tests 
at all!  So I wrote fda::CRAN() and for those tests that took too long, 
I wrapped them in



if(!CRAN()){
  (tests that took too long to run on CRAN)
}


  I did it after being told repeatedly, (a) you cannot run those 
tests on CRAN, and (b) you should not use that function "CRAN()"! Since 
then, I've had other occasions to use it.



      Spencer Graves



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Re: [R-pkg-devel] some notes

[Spencer Graves]

On 2018-04-24 09:50, Duncan Murdoch wrote:

On 24/04/2018 10:29 AM, Xubo Yue wrote:

Hey

I just got feedback from CRAN auto-checking and here are some notes I
cannot resolve:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Jian Kang <jiank...@umich.edu>'

New submission

Possibly mis-spelled words in DESCRIPTION:
   Kang (7:196)

I am not sure how to solve this.



You can ignore those.


Also, here are some running time notes:

** running examples for arch 'i386' ... [250s] NOTE
Examples with CPU or elapsed time > 10s
   user system elapsed
multipleRegion_plot 190.35   1.92  205.61
summary_kcca  1.40   0.17   14.79
permkCCA_multipleRegion   1.19   0.11   14.51
nii2RData 0.40   0.20   13.84
** running examples for arch 'x64' ... [79s] NOTE
Examples with CPU or elapsed time > 10s
  user system elapsed
multipleRegion_plot 18.36   2.06   33.66
permkCCA_multipleRegion  1.47   0.20   14.88
summary_kcca 1.48   0.16   14.85
nii2RData    0.62   0.23   14.09
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs

My total running time is less than 10 minutes. I am wondering is it 
ok to

ignore these two NOTEs?


You shouldn't ignore those.  Your package will be tested many, many 
times, and it will take more than 3 minutes for just one example.  (It 
will be tested whenever any package you depend on is changed, to make 
sure the change doesn't break yours.)


Use a smaller dataset, do less, or whatever you can to get the 
multipleRegion_plot example down to a time similar to the other ones, 
i.e. well below 10s in user+system time.



  If it becomes infeasible to find smaller datasets, etc., you can 
cut out certain tests with a construct like the following:



if(!fda::CRAN()){
# ... tests to run on other computers but to skip on CRAN.  ...
}


  Obviously, you'll need fda::CRAN.  I found it infeasible to meet 
that requirement and so disabled the tests that violated CRAN's rule on 
this.



  I've been told that this is a suboptimal solution and should be 
avoided.  I agree.



  Hope this helps.
      Spencer Graves



You don't have a lot of control of elapsed time because it will depend 
on what else is happening on the test machine, but if the other times 
are short, usually elapsed time will also be short.


Duncan Murdoch

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Re: [R-pkg-devel] some notes

[Spencer Graves]

On 2018-04-24 12:23, Uwe Ligges wrote:
>
>
> On 24.04.2018 19:15, Spencer Graves wrote:
>>
>>
>> On 2018-04-24 12:01, Duncan Murdoch wrote:
>>> On 24/04/2018 12:48 PM, Uwe Ligges wrote:
>>>>
>>>>
>>>> On 24.04.2018 18:45, Spencer Graves wrote:
>>> [... deleting irrelevant stuff...]
>>>>>
>>>>>
>>>>>     If it becomes infeasible to find smaller datasets, etc., 
>>>>> you can
>>>>> cut out certain tests with a construct like the following:
>>>>>
>>>>>
>>>>> if(!fda::CRAN()){
>>>>> # ... tests to run on other computers but to skip on CRAN. ...
>>>>> }
>>>>
>>>> Ummm, how should fda::CRAN() now that it runs on CRAN?
>>>>
>>>> CRAN prefers to ship a set of examples/tests etc. that meet our
>>>> requirements. If you want to ru addtional tests and/or examples, then
>>>> run them conditionally on something that is true for your local 
>>>> machine,
>>>> e.g. some defined environment variable.
>>
>>
>>    The fda::CRAN() function tests a "defined environmental 
>> variable", as you suggest:  It is TRUE with "R CMD check –as-cran" 
>> and FALSE if "-as-cran" (or something like that)
>
>
> The something like that is rather relevant. For example, I never use 
> --as-cran on my machine, and most CRAN machines do only on incoming 
> check but not the regular daily checks ...


   I very much appreciate your time and effort in maintaining CRAN.  
The precise code used is as follows:


CRAN <- function (CRAN_pattern, n_R_CHECK4CRAN){
     gete <- Sys.getenv()
     ngete <- names(gete)
     i <- seq(along = gete)
     if (missing(CRAN_pattern)) {
     if ("_CRAN_pattern_" %in% ngete) {
     CRAN_pattern <- gete["_CRAN_pattern_"]
     }
     else CRAN_pattern <- "^_R_"
     }
     if (missing(n_R_CHECK4CRAN)) {
     if ("_n_R_CHECK4CRAN_" %in% ngete) {
     n_R_CHECK4CRAN <- as.numeric(gete["_n_R_CHECK4CRAN_"])
     }
     else n_R_CHECK4CRAN <- 5
     }
     for (pati in CRAN_pattern) i <- i[grep(pati, ngete[i])]
     cran. <- (length(i) >= n_R_CHECK4CRAN)
     attr(cran., "Sys.getenv") <- gete
     attr(cran., "matches") <- i
     cran.
}


   This seems to do what I think we both wanted:  not run the longer 
examples on CRAN but still allow them to be run elsewhere. If you want 
something different here, Uwe, please tell me what you want.  If it's 
reasonably easy to implement, I will.


   FYI, I just checked the "CRAN Package Check Results for Package 
fda":  It returned "OK" on 8 of the 12 "flavors", but returned "ERROR" 
on the other four.  NONE of those errors were for excess time.  Instead, 
they were for <>.   The NAMESPACE file for "fda" includes both 
"export(knots.fd)" and "S3method(knots, fd)".


   What should I do about this intermittent error?


   Thanks,
   Spencer

>
> Best,
> Uwe
>  is not set.  It has been
>> several years since I wrote that code, and I'm not prepared at the 
>> moment to defend exactly how it works. It was how I resolved a 
>> conflict between Jim Ramsay, the maintainer and lead author of "fda", 
>> CRAN maintainers like Uwe, and other contributors to "fda", 
>> especially Giles Hooker and me:  It allowed us to keep examples in 
>> "fda" help files without excessive work trying to find examples that 
>> would illustrate the same points with less compute time.
>>
>>>
>>> For Xubo Yue, who may not be aware of all of the players:
>>>
>>> Uwe Ligges is one of the individuals who runs CRAN.  When you submit 
>>> a package to CRAN, you are asking Uwe and others to distribute your 
>>> work. You should listen to what he says.
>>>
>>> Spencer Graves and I are not involved in running CRAN.  We will give 
>>> you advice that we think is good advice, but if it conflicts with 
>>> Uwe's, follow his.
>>>
>>> Duncan Murdoch
>>
>>
>>    Moreover, Duncan's contributions to the R Project vastly 
>> exceed mine.  If any of my suggestions seem to conflict with Duncan's 
>> comments, follow his (unless they conflict with someone like Uwe, as 
>> Duncan noted).
>>
>>
>>    Spencer Graves
>>
>>


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Re: [R-pkg-devel] some notes

[Spencer Graves]

On 2018-04-24 12:01, Duncan Murdoch wrote:

On 24/04/2018 12:48 PM, Uwe Ligges wrote:



On 24.04.2018 18:45, Spencer Graves wrote:

[... deleting irrelevant stuff...]



    If it becomes infeasible to find smaller datasets, etc., you 
can

cut out certain tests with a construct like the following:


if(!fda::CRAN()){
# ... tests to run on other computers but to skip on CRAN. ...
}


Ummm, how should fda::CRAN() now that it runs on CRAN?

CRAN prefers to ship a set of examples/tests etc. that meet our
requirements. If you want to ru addtional tests and/or examples, then
run them conditionally on something that is true for your local machine,
e.g. some defined environment variable.



  The fda::CRAN() function tests a "defined environmental 
variable", as you suggest:  It is TRUE with "R CMD check –as-cran" and 
FALSE if "-as-cran" (or something like that) is not set.  It has been 
several years since I wrote that code, and I'm not prepared at the 
moment to defend exactly how it works.  It was how I resolved a conflict 
between Jim Ramsay, the maintainer and lead author of "fda", CRAN 
maintainers like Uwe, and other contributors to "fda", especially Giles 
Hooker and me:  It allowed us to keep examples in "fda" help files 
without excessive work trying to find examples that would illustrate the 
same points with less compute time.




For Xubo Yue, who may not be aware of all of the players:

Uwe Ligges is one of the individuals who runs CRAN.  When you submit a 
package to CRAN, you are asking Uwe and others to distribute your 
work. You should listen to what he says.


Spencer Graves and I are not involved in running CRAN.  We will give 
you advice that we think is good advice, but if it conflicts with 
Uwe's, follow his.


Duncan Murdoch



  Moreover, Duncan's contributions to the R Project vastly exceed 
mine.  If any of my suggestions seem to conflict with Duncan's comments, 
follow his (unless they conflict with someone like Uwe, as Duncan noted).



  Spencer Graves

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Re: [R-pkg-devel] library dlstats -> cran_stats()

[Spencer Graves]

On 2018-03-16 06:53, Mark van der Loo wrote:

Knut

AFAIR the download statistics are limited to downloads from RStudio's cloud
service, so none of the other CRAN mirrors are included. I think there is
no separation between updates, re-installs, or installs done automatically
by CI-services, for example.



  That's what it says in the DESCRIPTION file of the "dlstats" 
package, available at 
"http://finzi.psych.upenn.edu/R/library/dlstats/DESCRIPTION;.



  Spencer Graves


-Mark



Op vr 16 mrt. 2018 om 12:30 schreef Knut Krueger <rh...@krueger-family.de>:


Dear all,

Does anybody know whether the statistics are counting also  updates?
And if yes is it possible to get only the count of new installations?

Kind regards Knut


I

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Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

[Spencer Graves]

On 2018-03-20 06:17, Johannes Ranke wrote:

...


The idea exposed by Dirk is the same: requireNamespace will find the
package on CRAN and will set eval=TRUE. What you want though is to
avoid running a chunk on CRAN, even if the package is available. So
you need to set eval=FALSE *unconditionally*.

Or conditional on the package version (as Dirk proposed regarding tests) or on
an environment variable NOT_CRAN which you can set to true on the machine
where you do want to run the code (as used by devtools).



  The function "fda::CRAN" allows package developers to run tests 
themselves that should not run on CRAN or with "R CMD check –as-cran".  
Several of my packages have code in "\examples" that include something 
like the following:



if(!fda::CRAN()){
    #Code I do not want run if a certain parameter is in Sys.getenv()
}


  I have not tried this, but I think you could set a parameter, 
e.g., '-no-vignette' via either Sys.setenv('-no-vignette'=1) or "R CMD 
check -no-vignette", then bracket code snippets in the vignette with 
"if(!fda::CRAN('-no-vignette', '-no-vignette')){...}".



  This will NOT turn off compiling the vignette, but it will allow 
you to suppress running code snippets in the vignette that take time.



  Hope this helps.
      Spencer


p.s.  I just tested "Sys.setenv('-no-vignette'=1);  tst2 <- 
CRAN('-no-vignette', '-no-vignette')" and got TRUE, when CRAN() returned 
FALSE.  When I tried print(tst2) I got:



 [1] TRUE
attr(,"Sys.getenv")
Error in formatDL(x, ...) : unused argument (digits = 7)


  I do not understand this error message, but it does not seem to 
be a problem I have to fix right now, so I won't.



Johannes

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Re: [R-pkg-devel] How to write example results to a tempdir()?

[Spencer Graves]

On 2018-04-26 07:11, Jose A Guijarro wrote:

El 25/04/18 a las 20:21, Duncan Murdoch escribió:

On 25/04/2018 1:32 PM, Sarah Goslee wrote:

Don't change the working directory! That has all kinds of unpleasant
side effects for the unsuspecting user, possibly even more so than
writing to a file.

Instead, write the file to the temp directory, and read it from 
there, with e.g.


wd <- tempdir()
write(dat, file.path(wd, 'Ttest_1981-2000.dat'))

Using file.path() means that the appropriate path delimiter for that
OS will be used.


That's one good way to do it.  But it is possible to change directory 
and change back at the end of the example.  For example,


wd <- tempdir()
savedir <- setwd(wd)

... # the original code that writes and reads in the current dir

setwd(savedir)

There's a worry that an error in the middle of the code will leave 
the user in the wrong place.  If that's really unlikely to happen, 
then this code is a little simpler than Sarah's suggestion.


If it is likely, you can use tryCatch(..., finally = setwd(savedir)), 
but I think Sarah's solution would be preferable in most cases:  many 
users will not understand what tryCatch() does.



Hi, Duncan, et al.:


  Under what circumstances should one also use "on.exit":


wd <- tempdir()
savedir <- setwd(wd)
on.exit(setwd(savedir))?


  Even senior R programmers may miss a failure mode.  In a 
function, this works well:  I don't need to remember to "setwd(savedir)" 
later in the code, which could be a problem if I have multiple exit 
points.  I don't know how it would work in a vignette or the examples 
section of a *.Rd file.  tryCatch(..., finally = setwd(savedir)) 
condenses this into one line ... and is too terse for me in many cases.



  Spencer Graves



Duncan Murdoch


Many thanks for the suggestion! In this way I only need to apply 
slight changes in the examples and can avoid modifying all read/writes 
along the package. I will try this approach and see if it passes the 
CRAN checks.


Jose





Sarah


On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guijarro 
<jguijar...@aemet.es> wrote:

Dear all,

I am struggling to update my package climatol from version 3.0 to 3.1.
The old version had all examples under a "dontrun" section because 
they

needed files created by other examples that the user had to run first.

As this is not acceptable anymore, I made the examples runnable and
prepared small ad-hoc datasets, but then writing files to the user 
space

is against the CRAN policy rules, and I was suggested to run them on a
temporal directory. Therefore I changed all my examples to read/write
files to a tempdir(), as in:

\examples{
#Set a temporal working directory and write input files:
wd <- tempdir()
setwd(wd)
data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
write(dat,'Ttest_1981-2000.dat')
write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE) 


rm(dat,est.c) #remove loaded data from memory space
#Now run the example:
dd2m('Ttest',1981,2000)
#Input and output files can be found in directory:
print(wd)
}

But now CRAN checks return this warning ten times (one for every 
example

in the package):

Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting

Any hint on how to solve the problem will be highly appreciated...

Jose








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[R-pkg-devel] DLL 'Matrix' not found: maybe not installed for this architecture?

[Spencer Graves]

Hello:


 � "00check.log" produced by R-devel winbuilder (link below) 
includes the following:


** checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'Ecfun' in 
library.dynam(lib, package, package.lib):
 �DLL 'Matrix' not found: maybe not installed for this architecture?
In addition: Warning message:
S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 
'c.sparseVector', 'as.array.Matrix', 'as.array.sparseVector', 
'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 
'as.vector.sparseVector' were declared in NAMESPACE but not found
Execution halted


 � Is this problem with R-devel winbuilder or me?


 � This is for Ecfun on R-Forge that passed their standard tests 
plus on R 3.5.2 on macOS Mojave 10.14.3.


 � Thanks,
 ����� Spencer Graves


 Forwarded Message 
Subject:winbuilder: Package Ecfun_0.2-0.tar.gz has been checked and 
built
Date:   Mon, 25 Feb 2019 04:08:22 +0100
From:   lig...@statistik.tu-dortmund.de
To: spencer.gra...@effectivedefense.org
CC: lig...@statistik.tu-dortmund.de



Dear package maintainer,
this notification has been generated automatically.
Your package Ecfun_0.2-0.tar.gz has been built (if working) and checked 
for Windows.
Please check the log files and (if working) the binary package at:
https://win-builder.r-project.org/a5a1hg7XRQIO
The files will be removed after roughly 72 hours.
Installation time in seconds: 23
Check time in seconds: 56
Status: 1 ERROR
R Under development (unstable) (2019-02-24 r76155)
All the best,
Uwe Ligges
(CRAN maintainer of binary packages for Windows)



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[R-pkg-devel] clang: error: unsupported option '-fopenmp'

[Spencer Graves]

Hello, All:


  I'm getting "clang: error: unsupported option '-fopenmp'" when 
trying to build "https://github.com/helske/bssm; under macOS 10.14.14 
with R 3.6.0;  see below.



  What do you suggest?


  Thanks,
  Spencer Graves


p.s.  I assume I have to install compiler(s).  However, I've so far been 
unable to find instructions that are sufficiently current to convince me 
I might not do more harm than good following them.



> R CMD build bssm
* checking for file ‘bssm/DESCRIPTION’ ... OK
* preparing ‘bssm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
  ---
* installing *source* package ‘bssm’ ...
** using staged installation
** libs
clang++ -std=gnu++11 
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" 
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" 
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" 
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include" 
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include" 
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
-I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c R_approx.cpp -o 
R_approx.o

clang: error: unsupported option '-fopenmp'
make: *** [R_approx.o] Error 1
ERROR: compilation failed for package ‘bssm’
* removing 
‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’

  ---
ERROR: package installation failed

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Re: [R-pkg-devel] URL of a frame (or a vignette)?

[Spencer Graves]

  What's the difference between


https://cran.r-project.org/package=bssm/vignettes/bssm.pdf


  and


https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf


  When I tried the former, it automatically changed to the latter.  
Is the former considered to be more stable?



  Thanks,
  Spencer


On 2019-09-01 10:13, Georgi Boshnakov wrote:

Correction:

https://cran.r-project.org/package=bssm/vignettes/bssm.pdf


-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Georgi Boshnakov
Sent: 01 September 2019 15:57
To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)?

It may be better to use the canonical url, 
https://cran.r-project.org/package=bssm, as in:

https://cran.r-project.org/package=bssm/bssm.pdf

By the way, the vignettes for an installed package can be found by

vignette(package="bssm")

or

help(package="bssm", help_type = "html")

The latter has the advantage that it present links in a browser even if by 
default the help is presented in text mode.


Georgi Boshnakov



-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Spencer Graves
Sent: 01 September 2019 15:42
To: Jeff Newmiller; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)?

Hi, Jeff:


    That's what I needed.  I clicked on the vignette I wanted and got
the following:


https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf


    Thanks,
    Spencer Graves


On 2019-09-01 09:37, Jeff Newmiller wrote:

Wouldn't you just refer to [1] or one of the links mentioned there?

[1] https://cran.r-project.org/package=bssm

On September 1, 2019 7:22:43 AM PDT, Spencer Graves 
 wrote:

Hello:


    How can I get a URL for a frame?


    Specifically, I want a URL that I can cite for the "bssm:
Bayesian Inference of Non-linear and
Non-Gaussian State Space Models in R" vignette in the bssm package on
CRAN.  If the package is installed, it's available there as
"bssm.pdf".
However, I want to include it in an RMarkdown vignette I'm writing, and

I'd rather not force the reader to be on a computer with the package
installed -- and force myself to figure out a way to find it in that
case, if that can even be done.


    Thanks,
    Spencer Graves

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[R-pkg-devel] unable to run 'make clean' in 'src'

[Spencer Graves]

Hello:


  "R CMD build bssm" complains:


        unable to run 'make clean' in 'src'


  This is on a Windows 10 computer with R 3.6.1 installed with, I 
think, Rtools35.exe.  "sessionInfo()" says, "Platform: 
x86_64-w64-mingw32/x64 (64-bit)".



  This is trying to build a local clone of 
"https://github.com/sbgraves237/bssm;, which is only slightly different 
from "helske/bssm".



  What do you suggest?


  Thanks,
  Spencer Graves


p.s. 
"https://stackoverflow.com/questions/28723882/problems-installing-development-package-from-either-github-or-local#28724622; 
documents a discussion of this message from 2015.  It asks if "Rtools is 
in your PATH?"  The "path" includes "C:\RBuildTools\3.5" and "C:\Program 
Files\R\R3.6.1\bin" plus other non-R stuff.  That discussion also said, 
"The .o files in the src directory were messing things up."  bssm/src 
does not contain any *.o files.


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Re: [R-pkg-devel] unable to run 'make clean' in 'src'

[Spencer Graves]

Hi, Georgi et al.:


  Thanks to Georgi, I changed my path.  That led me to a different 
error.  A search for the new error led me to:



https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/


That recommended:


install.packages("installr")
library("installr")
install.Rtools()


  I uninstalled Rtools, then installed them using this, and that 
problem disappeared.  Now I'm dealing with '"pdflatex" not found". I'll 
discuss that in a new thread.



  Thanks,
  Spencer Graves


On 2019-09-18 06:30, Georgi Boshnakov wrote:

I don't know about Windows 10 but I think that the pointers to Rtools need to 
be to the bin subdirectory. Also, it is prudent to have these at the beginning 
of the search path, e.g.

PATH=c:\Rtools\bin;c:\Rtools\mingw_64\bin;c:\ProgramF\R\R-3.6.0patched\bin;

I am not sure if the entry for ming_w64 above is (still) needed.


Georgi Boshnakov


-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Spencer Graves
Sent: 18 September 2019 07:47
To: R Package Development
Subject: [R-pkg-devel] unable to run 'make clean' in 'src'

Hello:


    "R CMD build bssm" complains:


          unable to run 'make clean' in 'src'


    This is on a Windows 10 computer with R 3.6.1 installed with, I
think, Rtools35.exe.  "sessionInfo()" says, "Platform:
x86_64-w64-mingw32/x64 (64-bit)".


    This is trying to build a local clone of
"https://github.com/sbgraves237/bssm;, which is only slightly different
from "helske/bssm".


    What do you suggest?


    Thanks,
    Spencer Graves


p.s.
"https://stackoverflow.com/questions/28723882/problems-installing-development-package-from-either-github-or-local#28724622;  
documents a discussion of this message from 2015.  It asks if "Rtools is

in your PATH?"  The "path" includes "C:\RBuildTools\3.5" and "C:\Program
Files\R\R3.6.1\bin" plus other non-R stuff.  That discussion also said,
"The .o files in the src directory were messing things up."  bssm/src
does not contain any *.o files.

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Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found

[Spencer Graves]

On 2019-09-19 12:19, Tomas Kalibera wrote:

On 9/19/19 6:29 AM, Spencer Graves wrote:
Update: A web search for 'installing pdflatex for "R CMD" on Windows 
10?' suggested I install MiKTeX.  I did that from miktex.org, and it 
got me past that error.  Spencer


Please note these things are documented in R Installation and 
Administration Manual (see Appendix D)



  Thanks for documenting this.  It's important to have that as part 
of this thread.



  I perhaps should have thought to look there, but I didn't. And 
the web searches I tried didn't lead me there.   Spencer




Best
Tomas



On 2019-09-19 01:50, Spencer Graves wrote:

Hello, All:


  What's the recommended way to get pdflatex installed on Windows
10 to run "R CMD"?


  I ask, because "R CMD build bssm" under Windows 10 produced
'Warning in system2(..., stdout = FALSE, stderr = FALSE) : '"pdflatex"'
not found'.


  This was after installing Rtools using the following (recommended
by
"https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/;): 





install.packages("installr")
library("installr")
install.Rtools()


  Below please find the output in a commands window including
"sessionInfo()".


      Thanks,
      Spencer Graves


>R CMD build bssm
* checking for file 'bssm/DESCRIPTION' ... OK
* preparing 'bssm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
  '"pdflatex"' not found
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
Failed to compile bssm.tex. See https://yihui.name/tinytex/r/#debugging
for debugging tips.
--- failed re-building 'bssm.Rmd'

--- re-building 'growth_model.Rmd' using rmarkdown
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
  '"pdflatex"' not found
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'

SUMMARY: processing the following files failed:
  'bssm.Rmd' 'growth_model.Rmd'

Error: Vignette re-building failed.
Execution halted

C:\Users\spenc\Documents\R\bssm\bssm>
C:\Users\spenc\Documents\R\bssm\bssm>pdflatex
'pdflatex' is not recognized as an internal or external command,
operable program or batch file.

C:\Users\spenc\Documents\R\bssm\bssm>r

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1

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[R-pkg-devel] incomplete final line found on 'growth_model.log'

[Spencer Graves]

   "R CMD build bssm" on a Windows 10 machine ends by complaining, 
"  incomplete final line found on 'growth_model.log'". This problem was 
not fixed by adding a couple of blank lines to 'growth_model.Rmd'.


   Suggestions?
   Thanks,
   Spencer Graves


p.s.  The same command worked fine on a Windows 7 computer.  The "bssm" 
package used here was cloned from 
""https://github.com/sbgraves237/bssm":  This is not identical to 
helski/bssm, but close.


*EXCERPT FROM CMD: *


...
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
--- finished re-building 'bssm.Rmd'

--- re-building 'growth_model.Rmd' using rmarkdown
Warning in readLines(log) :
   incomplete final line found on 'growth_model.log'
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See 
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'

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

Error: Vignette re-building failed.
Execution halted


*PLFLATEX.LOG


*2019-09-19 08:11:08,435-0500 INFO  pdflatex - starting with command 
line: C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe -halt-on-error 
-interaction=batchmode bssm.tex
2019-09-19 08:11:08,435-0500 WARN  pdflatex - running with administrator 
privileges
2019-09-19 08:11:08,450-0500 INFO  pdflatex - running 'initexmf' to 
refresh the file name database
2019-09-19 08:11:13,734-0500 INFO  pdflatex - running 'initexmf' to 
create font map files
2019-09-19 08:11:22,735-0500 INFO  pdflatex - allowing known shell commands
2019-09-19 08:11:22,735-0500 INFO  pdflatex - enabling input (output) 
from (to) processes
2019-09-19 08:11:22,798-0500 INFO  pdflatex - going to create file: 
pdflatex.fmt
2019-09-19 08:11:31,033-0500 FATAL pdflatex - GUI framework cannot be 
initialized.
2019-09-19 08:11:31,033-0500 FATAL pdflatex - Info:
2019-09-19 08:11:31,033-0500 FATAL pdflatex - Source: 
Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2019-09-19 08:11:31,033-0500 FATAL pdflatex - Line: 77
2019-09-19 08:11:31,033-0500 INFO  pdflatex - finishing with exit code 1
2019-09-19 08:12:53,079-0500 INFO  pdflatex - starting with command 
line: C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe -halt-on-error 
-interaction=batchmode growth_model.tex
2019-09-19 08:12:53,079-0500 WARN  pdflatex - running with administrator 
privileges
2019-09-19 08:12:53,079-0500 INFO  pdflatex - allowing known shell commands
2019-09-19 08:12:53,079-0500 INFO  pdflatex - enabling input (output) 
from (to) processes
2019-09-19 08:12:53,392-0500 FATAL pdflatex - GUI framework cannot be 
initialized.
2019-09-19 08:12:53,392-0500 FATAL pdflatex - Info:
2019-09-19 08:12:53,392-0500 FATAL pdflatex - Source: 
Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2019-09-19 08:12:53,392-0500 FATAL pdflatex - Line: 77
2019-09-19 08:12:53,392-0500 INFO  pdflatex - finishing with exit code 1
2019-09-19 13:15:45,812-0500 INFO  pdflatex - starting with command 
line: C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe -halt-on-error 
-interaction=batchmode growth_model.tex
2019-09-19 13:15:45,815-0500 WARN  pdflatex - running with administrator 
privileges
2019-09-19 13:15:45,819-0500 INFO  pdflatex - allowing known shell commands
2019-09-19 13:15:45,819-0500 INFO  pdflatex - enabling input (output) 
from (to) processes
2019-09-19 13:15:46,231-0500 FATAL pdflatex - GUI framework cannot be 
initialized.
2019-09-19 13:15:46,231-0500 FATAL pdflatex - Info:
2019-09-19 13:15:46,231-0500 FATAL pdflatex - Source: 
Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2019-09-19 13:15:46,231-0500 FATAL pdflatex - Line: 77
2019-09-19 13:15:46,231-0500 INFO  pdflatex - finishing with exit code 1
2019-09-19 13:22:55,302-0500 INFO  pdflatex - starting with command 
line: C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe -halt-on-error 
-interaction=batchmode growth_model.tex
2019-09-19 13:22:55,302-0500 WARN  pdflatex - running with administrator 
privileges
2019-09-19 13:22:55,302-0500 INFO  pdflatex - allowing known shell commands
2019-09-19 13:22:55,302-0500 INFO  pdflatex - enabling input (output) 
from (to) processes
2019-09-19 13:22:55,640-0500 FATAL pdflatex - GUI framework cannot be 
initialized.
2019-09-19 13:22:55,640-0500 FATAL pdflatex - Info:
2019-09-19 13:22:55,640-0500 FATAL pdflatex - Source: 
Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2019-09-19 13:22:55,640-0500 FATAL pdflatex - Line: 77
2019-09-19 13:22:55,641-0500 INFO  pdflatex - finishing with exit code 1
2019-09-19 13:22:56,136-0500 INFO  pdflatex - starting with command 
line: C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe -halt-on-error 
-interaction=batchmode growth_model.tex
2019-09-19 13:22:56,139-0500 WARN  pdflatex - running with administrator 
privileges
2019-09-19 13:22:56,154-0500 INFO  pdflatex - allowing known shell commands
2019-09-19 13:2

Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found

[Spencer Graves]

Update:  A web search for 'installing pdflatex for "R CMD" on Windows 
10?' suggested I install MiKTeX.  I did that from miktex.org, and it got 
me past that error.  Spencer



On 2019-09-19 01:50, Spencer Graves wrote:

Hello, All:


  What's the recommended way to get pdflatex installed on Windows
10 to run "R CMD"?


  I ask, because "R CMD build bssm" under Windows 10 produced
'Warning in system2(..., stdout = FALSE, stderr = FALSE) : '"pdflatex"'
not found'.


  This was after installing Rtools using the following (recommended
by
"https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/;):



install.packages("installr")
library("installr")
install.Rtools()


  Below please find the output in a commands window including
"sessionInfo()".


      Thanks,
      Spencer Graves


>R CMD build bssm
* checking for file 'bssm/DESCRIPTION' ... OK
* preparing 'bssm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
  '"pdflatex"' not found
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
Failed to compile bssm.tex. See https://yihui.name/tinytex/r/#debugging
for debugging tips.
--- failed re-building 'bssm.Rmd'

--- re-building 'growth_model.Rmd' using rmarkdown
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
  '"pdflatex"' not found
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'

SUMMARY: processing the following files failed:
  'bssm.Rmd' 'growth_model.Rmd'

Error: Vignette re-building failed.
Execution halted

C:\Users\spenc\Documents\R\bssm\bssm>
C:\Users\spenc\Documents\R\bssm\bssm>pdflatex
'pdflatex' is not recognized as an internal or external command,
operable program or batch file.

C:\Users\spenc\Documents\R\bssm\bssm>r

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1

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[R-pkg-devel] devtools::build_win()?

[Spencer Graves]

Hello:


  Hadley Wickham's otherwise wonderful "R packages" book recommends 
using "devtools::build_win()" in the "Test environments" section of his 
chapter on "Releasing a package".  However, devtools 2.2.1, which seems 
to be the current version, contains no such "build_win" function.



  This section of "R packages" also says, says that 
"devtools::revdep_check()" "Runs R CMD check on each [reverse 
dependency] and Summarises the results in a single file."  However, the 
current version of "devtools::revdep_check()" seems only to identify the 
reverse dependencies without testing them.



  That do you suggest?
  Thanks,
  Spencer Graves

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[R-pkg-devel] default col.names from data.frame not the same as as.data.frame

[Spencer Graves]

Hello, All:


  What names should be given a matrix or data.frame that does not 
have names for use in "glm.fit"?



  I ask for two reasons:


        * "base" R is inconsistent:  "data.frame(matrix(1:2, 1))" 
defaults to "X1", "X2" but "as.data.frame(matrix(1:2, 1))" defaults to 
"V1", "V2".



        * I want to use a toy example like this in the 
documentation for "BMA:::bic.glm.matrix" and "BMA:::bic.glm.data.frame", 
and since "base" R is inconsistent, I felt a need to ask a group like 
this for their preferences.



  Thanks,
  Spencer Graves

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Re: [R-pkg-devel] compression of vignettes

[Spencer Graves]

  I encountered this or a similar problem with 
"https://github.com/sbgraves237/Ecfun/blob/master/vignettes/time2nextNuclearWeaponState.Rmd;. 
I tried both "R CMD build Ecfun" and R CMD build Ecfun 
--compact-vignettes".  With both, "R CMD check Ecfun_0.2-2.tar.gz" 
included the following:



* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb


  Suggestions?
  Thanks,
  Spencer Graves


On 2019-11-21 11:43, Dirk Eddelbuettel wrote:

On 21 November 2019 at 16:43, Joris Meys wrote:
| The workflow as described in the manual :
| 
https://cran.r-project.org/doc/manuals/R-exts.html#Checking-and-building-packages

|
| is as follows :
|
| R CMD build pkg --compact-vignettes
| R CMD check pkg_x.y.z.tar.gz --as-cran
|
| In a basic Travis script this can be used as:
|
| script:
| - R CMD build . --compact-vignettes=gs+qpdf
| - R CMD check *tar.gz --as-cran
|
| You find more information here : 
https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5


You can also call the base R helper functions directly.

I like having simple command-line wrapper, so I added one to `littler` 
which

I can call as `compactpdf.r`. All it does (besides argument checking) is
loop over either the given pdf files (or those found in the current
directory) to then call

tools::compactPDF(f, gs_quality="ebook")

for each of them. That way you can simply compare 'before' and 'after'.

Similarly, I made compacting an option to the rendering script 
`render.r` I

often call directly from my editor when working on markdown files.

Dirk



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[R-pkg-devel] How to submit to CRAN from GitHub?

[Spencer Graves]

Hello:


   Two questions:


HOW TO SUBMIT TO CRAN FROM GITHUB:  Is there a standard method for 
submitting to CRAN from GitHub?  (There's a simple protocol for 
submitting to CRAN from R-Forge, but I've experienced insurmountable 
problems using R-Forge recently.)


PACKAGE STILL FAILING TRAVIS CI:  The latest report from 
bui...@travis-ci.org on my Ecdat package for R on GitHub ends with 
"Found warnings, treating as errors (as requested)."  The word "warning" 
appears in that report over 100 times.  I didn't see anything there that 
suggested to me anything I understand how to change.


NOTE:  "R CMD build Ecdat --resave-data" followed by "R CMD check 
Ecdat_0.3.3-tar.gz" completed with no errors, warnings or notes under 
macOS 10.14.6 and Windows 7 and 10.


   Thanks,
   Spencer Graves


 Forwarded Message 
Subject:Still Failing: sbgraves237/Ecdat#9 (master - c680f08)
Date:   Sun, 22 Sep 2019 15:21:08 +
From:   Travis CI 
To: spencer.gra...@effectivedefense.org



sbgraves237

/

Ecdat

<https://travis-ci.org/sbgraves237/Ecdat?utm_medium=notification_source=email>
 


branch iconmaster <https://github.com/sbgraves237/Ecdat/tree/master>

build has failed
Build #9 is still failing 
<https://travis-ci.org/sbgraves237/Ecdat/builds/588124072?utm_medium=notification_source=email>
arrow to build time
clock icon5 mins and 8 secs

sbgraves237 avatarsbgraves237

c680f08 CHANGESET → 
<https://github.com/sbgraves237/Ecdat/compare/cd2bdef45642...c680f08d04b8>

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[R-pkg-devel] MiKTex v. TeX Live?

[Spencer Graves]

Hello, All:  Two related questions:


SHORT QUESTION:  Which version of LaTeX does the R Project prefer and 
why?  I'm having trouble with MiKTeX, and one source suggested I switch 
to TeX Live.  (e.g., "https://latex.org/forum/viewtopic.php?t=29034;)



PRESENTING PROBLEM:


   "R CMD build sos" under Windows 7 on a clone from 
"https://github.com/sbgraves237/sos; ended with, 'The required file 
tex\latex\pgf\frontendlayer\tikz.sty" is missing.'  I clicked "Install" 
and got "MiKTeX Update Wizard:  The operation could not be completed for 
the following reason:  No data.  Details:  get host by name failed in 
tcp_connect()".



  I get the same error when I try to run MiKTeX 2.9 Update and 
"Update (Admin)".  (I got the "tikz.sty is missing" message only after I 
had turned off everything I could find to turn off in "Bitdefender Total 
Security".)  I think I saw a suggestion to manually delete "C:Program 
Files (x86)\MiKTeX 2.9" and manually remove the reference from the path, 
then reinstall into a different directory that the operating system and 
anti-virus would not by default identify as part of the operating system.



  Suggestions?
  Thanks,
  Spencer Graves


p.s.  This is using R 2.6.2 immediately after running "update.packages()".

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[R-pkg-devel] Internet security software?

[Spencer Graves]

Hello, All:


  What antivirus / internet security software do you use and 
recommend?



  I've used Bitdefender for years.  However, I've been encountering 
an increasing number of problems with software I've used for years.  
Some of my problems disappear when I turn off parts of Bitdefender.  
However, I've been unable to use RStudio on my Windows 7 computer since 
early last November.  Also, when I turn off certain features of 
Bitdefender, "R CMD build sos" (with sos cloned from 
"https://github.com/sbgraves237/sos;) completes in a few minutes.  With 
Bitdefender configured normally, "R CMD build sos" stops without warning 
on "* creating vignettes".  I've left it for days like that without it 
moving beyond that point.  No error message but also no progress.



  Rather than doing a web search for alternative internet security 
software, I thought I'd ask you all:  If some of you have had similar 
problems with other antivirus / internet security software, I think I'd 
be more likely to hear it from you than from a web search.  Some of my 
problems may not be due to Bitdefender, but I know that some are, and 
Bitdefender tech support answers the phone but fails to fix these problems.



  Thanks,
  Spencer Graves

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[R-pkg-devel] CRAN rules re. web scraping?

[Spencer Graves]

Hello, All:


GOOD NEWS AND BAD NEWS:


   * First the good news:  I heard from Brian Ripley;  see below.  
His web site says, "He retired in August 2014 on grounds of ill health." 
(http://www.stats.ox.ac.uk/~ripley/)  I was pleased to see that he seems 
to be well enough to send me the email below.


   * BAD NEWS:  My Ecfun package is violating current CRAN rules 
regarding "not writing anywhere in the file space".  (See below.)


QUESTION:


   How do you suggest I respond to this?


   It's hard for me to fix, because I cannot replicate the error and 
I don't understand the rules Prof. Ripley is trying to enforce. The 
"CRAN Package Check Results for" this package show an error on 1 
platform (r-devel-linux-x86_64-fedora-gcc), NOTEs on 3 platforms 
(Fedora-clang and Debian), and "OK" on 9 others.  I can program selected 
tests not to run on CRAN, e.g., with (!fda::CRAN()).


   However, I suspect I should be able to do better than that.


       Suggestions?


   Thanks,
   Spencer Graves


p.s.  The development version of this package is available at 
"https://github.com/sbgraves237/Ecfun;.


https://cloud.r-project.org/web/checks/check_results_Ecfun.html


 Forwarded Message 
Subject:CRAN package Ecfun
Date:   Tue, 21 Jan 2020 21:26:02 +
From:   Prof Brian Ripley 
Reply-To:   CRAN 
To: Spencer Graves 
CC: CRAN 



This has been intermittently failing its checks for a week: different 
check runs failed (in the 24h prior to) the 14th, 15th, 17th and today. 
The current failure is

Check: examples
Result: ERROR
Running examples in ‘Ecfun-Ex.R’ failed
The error most likely occurred in:

 > ### Name: read.testURLs
 > ### Title: Read a file produced by testURLs
 > ### Aliases: read.testURLs
 > ### Keywords: IO
 >
 > ### ** Examples
 >
 > # Test only 2 web sites, not the default 4,
 > # and test only twice, not the default 10 times:
 > tst <- testURLs(c(
+ PVI="http://en.wikipedia.org/wiki/Cook_Partisan_Voting_Index;,
+ house="http://house.gov/representatives;),
+ n=2, maxFail=2)
1
1579634784, PVI, TRUE 0.828
1579634785, house, FALSE 0.051
1579634785, house, FALSE 0.048
2
1579634785, PVI, TRUE 0.043
1579634785, house, FALSE 0.11
1579634785, house, FALSE 0.035
 >
 > # The above should have created a file 'testURLresults.csv'
 > # in the working directory. Read it.
 >
 > dat <- read.testURLs()
Error in read.table(file = file, header = header, sep = sep, quote = 
quote, :
more columns than column names
Calls: read.testURLs -> read.csv -> read.table

That does not conform to the policy on Internet access, not least as no 
attempt is made to check if the file was created, let alone that it has 
the expected layout. Nor does it conform to the policy on not writing 
anywhere in the file space (and that shows on its CRAN results page too).

Please correct ASAP and before Feb 4 to safely retain the package on CRAN.

-- 
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford


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[R-pkg-devel] finding "logo.jpg" [was: "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC]

[Spencer Graves]

  Thanks to Iñaki Ucar for identifying a second error that 
explained why I still got an error after wrapping one in "try".



  That still leaves a question of how to find a file like 
"logo.jpg" in a platform independant way.



      The following had worked for several years and now broke on rhub 
"Ubuntu Linux 16.04 LTS, R-release, GCC" but not on several other 
computers I tried:



        logo.jpg <- paste(R.home(), "doc", "html", "logo.jpg", sep 
= .Platform$file.sep)



  On that Ubuntu platform, "readJPEG(logo.jpg)" stopped with "Error 
in readJPEG(logo.jpg) : unable to open /usr/lib/R/doc/html/logo.jpg".



  I replaced the above "paste" with the following:


RdocDir <- dir(R.home(), pattern='^doc$', full.names = TRUE)
RhtmlDir <- dir(RdocDir, pattern='^html$', full.names=TRUE)
JPGs <- dir(RhtmlDir, pattern='.jpg$', full.names=TRUE)
if(length(JPGs)>1){
  logoJPG <- paste0(.Platform$file.sep, 'logo.jpg$')
  logo.jpg <- grep(logoJPG, JPGs, value=TRUE)
  if(length(logo.jpg)>1)logo.jpg <- logo.jpg[1]
  if(length(logo.jpg)<1)logo.jpg <- JPGs[1]
} else logo.jpg <- JPGs
if(length(logo.jpg)<1){
  cat('logo.jpg not found.\n')
  print(R.home())
  print(dir(RdocDir))
  print(dir(RhtmlDir))
  if(!fda::CRAN())stop('logo.jpg not found')
} else {
# length(logo.jpg)==1 so continue:
  if(require(jpeg)){
##
## 1.  Shrink as required
##
    Rlogo <- readJPEG(logo.jpg)

...


      This gave me no error message, which I believe means that either 
length(logo.jpg) == 1 or fda::CRAN() returns TRUE.  Sadly, I could not 
find the standard test file to see which of these is the case.



  I should proceed to submit the current Ecfun package to CRAN. 
Then I might modify this test sequence to force an error, so I can see 
more what is happening.



  Suggestions?
  Thanks,
  Spencer


On 2020-02-03 03:06, Iñaki Ucar wrote:

On Mon, 3 Feb 2020 at 03:16, Spencer Graves
 wrote:

Hello, All:


devtools::check_rhub failed to trap an error wrapped in "try",
per the email below.  This came from running
devtools::check_rhub(Ecfun_dir), where Ecfun_dir = the path to a copy of
"https://github.com/sbgraves237/Ecfun;.

That's improbable.


This is the development version of Ecfun, which I want to submit
to CRAN as soon as I can do so without offending the sensibilities of
the overworked CRAN maintainers.


Suggestions?
Thanks,
Spencer Graves


 Forwarded Message 
Subject:Ecfun 0.2-2: ERROR
Date:   Sun, 02 Feb 2020 23:27:10 +
From:   R-hub builder 
To: spencer.gra...@effectivedefense.org





## 2.9.  A more complicated example with elements to eval
##
logo.jpg <- paste(R.home(), "doc", "html", "logo.jpg",

+   sep = .Platform$file.sep)

if(require(jpeg)){

+   Rlogo <- try(readJPEG(logo.jpg))
+   if(!inherits(Rlogo, 'try-error')){
+ # argument list for a call to rasterImage or rasterImageAdj
+ RlogoLoc <- list(image=Rlogo,
+   xleft.0 = c(NZ=176.5,CH=172,US=171,
+   CN=177,RU= 9.5,UK= 8),
+   xleft.1 = c(NZ=176.5,CH=  9,US=-73.5,
+   CN=125,RU= 37, UK= 2),
+   ybottom.0=c(NZ=-37,  CH=-34,US=-34,
+   CN=-33,RU= 48, UK=47),
+   ybottom.1=c(NZ=-37,  CH= 47,US= 46,
+   CN= 32,RU=55.6,UK=55),
+   xright=quote(xleft+xinch(0.6)),
+   ytop = quote(ybottom+yinch(0.6)),
+   angle.0 =0,
+   angle.1 =c(NZ=0,CH=3*360,US=5*360,
+  CN=2*360,RU=360,UK=360)
+ )
+
+ RlogoInterp <- interpPairs(RlogoLoc,
+ .proportion=rep(c(0, -1), c(2, 4)) )
+ # check
+ ## Don't show:
+ stopifnot(
+ ## End(Don't show)
+ all.equal(names(RlogoInterp),
+c('image', 'xright', 'ytop', 'xleft', 'ybottom', 'angle'))
+ ## Don't show:
+ )
+ ## End(Don't show)
+ }
+ # NOTE:  'xleft', and 'ybottom' were created in interpPairs,
+ # and therefore come after 'xright' and 'ytop', which were
+ # already there.
+
+ ##
+ ## 2.10.  using envir
+ ##
+   RlogoDiag <- list(x0=quote(Rlogo.$xleft),
+   y0=quote(Rlogo.$ybottom),
+   x1=quote(Rlogo.$xright),
+   y1=quote(Rlogo.$ytop) )
+
+   RlogoD <- interpPairs(RlogoDiag, .p=1,
+ envir=list(Rlogo.=RlogoInterp) )
+ ## Don't show:
+ stopifnot(
+ ## End(Don't show)
+ all.equal(RlogoD, RlogoDiag)
+ ## Don't show:
+ )
+ ## End(Don't show)
+ }
Loading required package: jpeg
Error in readJPEG(logo.jpg) : unable to open /usr/lib/R/doc/html/logo.jpg
Error in interpPairs.list(RlogoDiag, .p = 1, envir = list(Rlogo. = 
RlogoInterp)) :
object 'RlogoInterp' not found
Calls: interpPairs -> interpPairs.list
Execution halted

There it is: "Error in interpPairs.list [...] 'RlogoInterp' not
found". T

Re: [R-pkg-devel] "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC

[Spencer Graves]

Hi, Dirk:


  The short answer is that's part of what's on "rhub".


  When I run devtools::check_rhub, I get emails with test results 
from three platforms:  (1) Windows Server 2008 R2 SP1, R-devel, 32/64 
bit.  (2) Ubuntu Linux 16.04 LTS, R-release, GCC. And (3) Fedora Linux, 
R-devel, clang, gfortran.  I've been getting a NOTE of "Packages 
unavailable to check Rd xrefs: ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, 
‘TRAMPR’" from the Windows and Fedora tests and the "try" malfunction 
that I reported from Ubuntu 16.04 LTS.



  I don't know who maintains rhub, but I would naively think that's 
a separate issue from the "try" malfunction that I reported.



  Spencer


On 2020-02-02 23:27, Dirk Eddelbuettel wrote:

On 2 February 2020 at 21:47, Ben Bolker wrote:
|   Maybe an Rhub glitch.  I just ran R CMD check with a recent r-devel
| (2019-12-03 r77509) on Ubuntu 16.04 with no problems.

Is there a reason that keeps _both_ of you on Ubuntu 16.04 which has been
replaced _nearly two years ago_ by the subsequent LTS release 18.04 ?

Michael works hard to provide _an awesome_ experience using the current LTS
release_ 18.04 that I am really hard-pressed to see why 16.04 would matter.

Dirk



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[R-pkg-devel] "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC

[Spencer Graves]

Hello, All:


   devtools::check_rhub failed to trap an error wrapped in "try", 
per the email below.  This came from running 
devtools::check_rhub(Ecfun_dir), where Ecfun_dir = the path to a copy of 
"https://github.com/sbgraves237/Ecfun;.


   This is the development version of Ecfun, which I want to submit 
to CRAN as soon as I can do so without offending the sensibilities of 
the overworked CRAN maintainers.


   Suggestions?
   Thanks,
   Spencer Graves


 Forwarded Message 
Subject:Ecfun 0.2-2: ERROR
Date:   Sun, 02 Feb 2020 23:27:10 +
From:   R-hub builder 
To: spencer.gra...@effectivedefense.org



Ecfun 0.2-2: ERROR


Ecfun 0.2-2: ERROR
*Build ID:* |Ecfun_0.2-2.tar.gz-a5518fc2c19c4cd191a5d67b55c45603|
*Platform:* Ubuntu Linux 16.04 LTS, R-release, GCC
*Submitted:*1 hour 55 minutes 18.7 seconds ago
*Build time:*   1 hour 49 minutes 23.6 seconds


  ERRORS:

* checking examples ... ERROR
Running examples in ‘Ecfun-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interpPairs
> ### Title: interpolate between pairs of vectors in a list
> ### Aliases: interpPairs interpPairs.call interpPairs.function
> ###   interpPairs.list
> ### Keywords: manip
> 
> ### ** Examples
> 
> ###
> ###
> ### 1.  interpPairs.function
> ###
> ###
> 
> ##
> ## 1.1.  simple 
> ##
> plot0 <- quote(plot(0))
> plot0. <- interpPairs(plot0)
> # check 
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(plot0, plot0.)
+ ## Don't show:
+ )
> ## End(Don't show)
> 
> ##
> ## 1.2.  no op 
> ##
> noop <- interpPairs(plot0, iFrame=-1)
> # check
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(noop, enquote(NULL))
+ ## Don't show:
+ )
> ## End(Don't show)
> 
> ##
> ## 1.3.  a more typical example
> ## example function for interpPairs 
> tstPlot <- function(){
+   plot(1:2, 1:2, type='n')
+   lines(firstFrame=1:3,
+ lastFrame=4,
+ x.1=seq(1, 2, .5),
+ y.1=x,
+ z.0=0, z.1=1,
+ txt.1=c('CRAN is', 'good', '...'),
+ col='red')
+ }
> tstbo <- body(tstPlot)
> iPlot <- interpPairs(tstbo[[2]])
> # check 
> iP <- quote(plot(1:2, 1:2, type='n'))
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(iPlot, iP)
+ ## Don't show:
+ )
> ## End(Don't show)
> 
> iLines <- interpPairs(tstbo[[3]], nFrames=5, iFrame=2)
> # check:  
> # .proportion = (iFrame-firstFrame)/(lastFrame-firstFrame)
> #  = c(1/3, 0, -1/3)
> # if x.0 = 0 and y.0 = 0 by default:  
> iL <- quote(linex(x=c(1/3, 0), y=c(1/9, 0), z=c(1/3, 0), 
+tst=c('CR', '')))
> ##
> ## This example seems to give the wrong answer
> ## 2014-06-03:  Ignore for the moment 
> ##   
> #all.equal(iLines, iL)
> 
> ##
> ## 1.4.  Don't throw a cryptic error with NULL 
> ##
> ip0 <- interpPairs(quote(text(labels.1=NULL)))
>   
>   
> ###
> ###
> ### 2.  interpPairs.list
> ###
> ###
> 
> ##
> ## 2.1.  (x.0, y.0, x.1, y.1) -> (x,y)
> ##
> tstList <- list(x.0=1:5, y.0=5:9, y.1=9:5, x.1=9,
+ ignore=letters, col=1:5)
> xy <- interpPairs(tstList, 0.1)
> # check 
> xy. <- list(ignore=letters, col=1:5, 
+ x=1:5 + 0.1*(9-1:5),
+ y=5:9 + 0.1*(9:5-5:9) )
> # New columns, 'x' and 'y', come after 
> # columns 'col' and 'ignore' already in tstList 
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(xy, xy.)
+ ## Don't show:
+ )
> ## End(Don't show)
> 
> ##
> ## 2.2.  Select the middle 2:  
> ##  x=(1-(0,1))*3:4+0:1*0=(3,0)
> ##
> xy0 <- interpPairs(tstList[-4], c(-Inf, -1, 0, 1, 2) )
> # check 
> xy0. <- list(ignore=letters, col=3:4, x=c(3,0), y=7:6)
> 
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(xy0, xy0.)
+ ## Don't show:
+ )
> ## End(Don't show)
> ##
> ## 2.3.  Null interpolation because of absence of y.1 and x.0  
> ##
> xy02 <- interpPairs(tstList[c(2, 4)], 0.1)
> # check 
>  NOT the current default answer;  revisit later.  
> xy02. <- list(y=5:9, x=9)
> 
> # NOTE:  length(x) = 1 = length(x.1) in testList
> #all.equal(xy02, xy02.)
> 
> ##
> ## 2.4.  Select an empty list (make sure this works)
> ##
> x0 <- interpPairs(list(), 0:1)
Warning message:
In checkNames(object, avoid = pairs[c(1, 4, 2, 5)]) :
   object:  names = NULL; returning make.names(character(length(x))), TRUE)
> # check 
> x0. <- list()
> names(x0.) <- character(0)
> ## Don't show: 
> stopifnot(
+ ## End(Don't show)
+ all.equal(x0, x0.)
+ ## Don't show:
+ )
> ## End(Don't show)
> 
> ##

Re: [R-pkg-devel] CRAN rules re. web scraping?

[Spencer Graves]

  Thanks very much to Iñaki Ucar, Adam H Sparks, and Roy 
Mendelssohn for their replies that helped me understand what I needed to 
do to fix problems identified in the CRAN Checks.  I believe that those 
problems are not fixed in the development version of Ecfun available at 
"https://github.com/sbgraves237/Ecfun".  The package still needs more 
work, but I will make Prof. Ripley's Feb. 4 deadline.



  Thanks again,
      Spencer Graves


On 2020-01-23 01:55, Iñaki Ucar wrote:

On Thu, 23 Jan 2020 at 02:49, Spencer Graves
 wrote:

Hello, All:


GOOD NEWS AND BAD NEWS:


* First the good news:  I heard from Brian Ripley;  see below.
His web site says, "He retired in August 2014 on grounds of ill health."
(http://www.stats.ox.ac.uk/~ripley/)  I was pleased to see that he seems
to be well enough to send me the email below.


* BAD NEWS:  My Ecfun package is violating current CRAN rules
regarding "not writing anywhere in the file space".  (See below.)


QUESTION:


How do you suggest I respond to this?


It's hard for me to fix, because I cannot replicate the error and
I don't understand the rules Prof. Ripley is trying to enforce. The
"CRAN Package Check Results for" this package show an error on 1
platform (r-devel-linux-x86_64-fedora-gcc), NOTEs on 3 platforms
(Fedora-clang and Debian), and "OK" on 9 others.  I can program selected
tests not to run on CRAN, e.g., with (!fda::CRAN()).


However, I suspect I should be able to do better than that.


Suggestions?

The message from Prof. Ripley is crystal-clear, and exposes two issues
(Internet access, writing files) that have been discussed many times
in this list. A quick scan of the CRAN policy [1] yields:

- Packages which use Internet resources should fail gracefully with an
informative message if the resource is not available (and not give a
check warning nor error).

- Packages should not write in the user’s home filespace (including
clipboards), nor anywhere else on the file system apart from the R
session’s temporary directory.

[1] https://cran.r-project.org/web/packages/policies.html

Iñaki


Thanks,
Spencer Graves


p.s.  The development version of this package is available at
"https://github.com/sbgraves237/Ecfun;.


https://cloud.r-project.org/web/checks/check_results_Ecfun.html


 Forwarded Message 
Subject:CRAN package Ecfun
Date:   Tue, 21 Jan 2020 21:26:02 +
From:   Prof Brian Ripley 
Reply-To:   CRAN 
To: Spencer Graves 
CC: CRAN 



This has been intermittently failing its checks for a week: different
check runs failed (in the 24h prior to) the 14th, 15th, 17th and today.
The current failure is

Check: examples
Result: ERROR
Running examples in ‘Ecfun-Ex.R’ failed
The error most likely occurred in:

  > ### Name: read.testURLs
  > ### Title: Read a file produced by testURLs
  > ### Aliases: read.testURLs
  > ### Keywords: IO
  >
  > ### ** Examples
  >
  > # Test only 2 web sites, not the default 4,
  > # and test only twice, not the default 10 times:
  > tst <- testURLs(c(
+ PVI="http://en.wikipedia.org/wiki/Cook_Partisan_Voting_Index;,
+ house="http://house.gov/representatives;),
+ n=2, maxFail=2)
1
1579634784, PVI, TRUE 0.828
1579634785, house, FALSE 0.051
1579634785, house, FALSE 0.048
2
1579634785, PVI, TRUE 0.043
1579634785, house, FALSE 0.11
1579634785, house, FALSE 0.035
  >
  > # The above should have created a file 'testURLresults.csv'
  > # in the working directory. Read it.
  >
  > dat <- read.testURLs()
Error in read.table(file = file, header = header, sep = sep, quote =
quote, :
more columns than column names
Calls: read.testURLs -> read.csv -> read.table

That does not conform to the policy on Internet access, not least as no
attempt is made to check if the file was created, let alone that it has
the expected layout. Nor does it conform to the policy on not writing
anywhere in the file space (and that shows on its CRAN results page too).

Please correct ASAP and before Feb 4 to safely retain the package on CRAN.

--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford


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[R-pkg-devel] revdepcheck::revdep_check interpretation problem

[Spencer Graves]

Hello, All:


  I just ran "revdepcheck::revdep_check" on my development version 
of "https://github.com/sbgraves237/Ecdat";  copied below. It ended with 
"OK: 16, BROKEN: 0".  That sounds good, except that it also says 
"gamclass 0.58:  E: 1", so I'm confused.



  Two questions:


        1.  What does the "E: 1" for "gamclass" mean?  It sounds 
like an error to me, but that contradicts the final message,

"OK: 16, BROKEN: 0".


        2.  How can I even find gamclass?  It's not available on 
CRAN.  There, Ecdat only has 15 reverse dependencies, not 16.  I tried 
install.packages('gamclass');  it said, "package ‘gamclass’ is not 
available".  I tried githubinstall::githubinstall('gamclass'). It said:



Select a number or, hit 0 to cancel.

1: pik-piam/magclass    Tools for managing classroom organizations
2: tscheypidi/magclass  Tools for managing classroom organizations
3: rundel/ghclass   Tools for managing classroom organizations


  ** None of that sounds like "gamclass".


      What do you suggest?


  I should probably ignore this?
  Thanks,
  Spencer Graves


 revdepcheck::revdep_check(Ecdat_dir)
Registered S3 method overwritten by 'revdepcheck':
  method    from
  print.maintainers devtools
── INIT  Computing revdeps ──
── INSTALL  2 versions ──
Installing CRAN version of Ecdat
Installing DEV version of Ecdat
── CHECK ─ 16 packages ──
✓ catdata 1.2.2  ── E: 0 | W: 0 | N: 0
✓ DCchoice 0.0.15    ── E: 0 | W: 0 | N: 0
✓ discSurv 1.4.1 ── E: 0 | W: 0 | N: 0
✓ DStree 1.0 ── E: 0 | W: 0 | N: 1
✓ DWreg 2.0  ── E: 0 | W: 0 | N: 0
✓ Ecfun 0.2-2    ── E: 0 | W: 0 | N: 0
✓ flexmix 2.3-15 ── E: 0 | W: 0 | N: 0
✓ gamclass 0.58  ── E: 1 | W: 0 | N: 0
✓ gk 0.5.1   ── E: 0 | W: 0 | N: 0
✓ micEcon 0.6-14 ── E: 0 | W: 1 | N: 0
✓ micEconIndex 0.1-6 ── E: 0 | W: 0 | N: 0
✓ miscTools 0.6-26   ── E: 0 | W: 0 | N: 0
✓ mssm 0.1.3 ── E: 0 | W: 0 | N: 0
✓ plm 2.2-0  ── E: 0 | W: 0 | N: 0
✓ sampleSelection 1.2-6  ── E: 0 | W: 0 | N: 0
✓ SeleMix 1.0.1  ── E: 0 | W: 0 | N: 0
OK: 16
BROKEN: 0
Total time: 36 min

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[R-pkg-devel] Error: Symbol \textasciigrave not provided by (textcomp)

[Spencer Graves]

Hello, All:


  "R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the 
following:



! Package textcomp Error: Symbol \textasciigrave not provided by
(textcomp)    font family zi4 in TS1 encoding.
(textcomp)    Default family used instead.

See the textcomp package documentation for explanation.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE


  This is using R 3.6.2 under macOS 10.15.3 applied to the current 
development version of "https://github.com/sbgraves237/Ecfun".  Travis 
CI reported that the build passed;  see 
"https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;. 




  This looks to me like it's complaining about the use of the back 
tick character ("`", below "~" on the top left key on a standard 
American English keyboard), which I assume is equivalent to 
"\textasciigrave" in certain contexts.



  Six out of those 8 repetitions occur in the examples sections of 
files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and 
"subNonStandardNames.Rd".  Those functions were written to fix parsing 
errors with names like "Raúl" that had been mangled by different 
software before I could get it into R.



  After a day's work failed to produce a work around, I decided to 
ask this group.



  What do you suggest?
  Thanks,
  Spencer Graves

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[R-pkg-devel] How to create a new project on GitHub?

[Spencer Graves]

Hello, All:


  How can I create a new project within my GitHub account 
(https://github.com/sbgraves237/)?



  I'm trying to follow "http://r-pkgs.had.co.nz/git.html":


...
Synchronising with GitHub
...

    Open a shell, then follow the instructions on the new repo page. 
They’ll look something like this:


    git remote add origin g...@github.com:hadley/r-pkgs.git
    git push -u origin master

I tried:

...$ git remote add origin g...@github.com:sbgraves237/fda.git
...$ git push -u origin master
ERROR: Repository not found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


*** That didn't work, so I tried


...$ git remote add origin https://[my ssh code]@github.com/sbgraves237/fda
fatal: remote origin already exists.
...$ git push -u origin master
ERROR: Repository not found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


  *** What do I need to do to fix the mess I seem to have created 
and get what I want?



  *** Thanks, Spencer Graves


p.s.  If you know the fda package, you know that James Ramsay is the 
primary author, and I'm one of his long-time collaborators.  He has a 
new version he wants to clean up and submit to CRAN, and I'm trying to 
help him.  Thanks.  sg


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Re: [R-pkg-devel] How to create a new project on GitHub?

[Spencer Graves]

On 2020-01-15 17:18, Gábor Csárdi wrote:

Seems like you skipped step 1?

"1. Create a new repo on GitHub: https://github.com/new. Give it the
same name as your package, and include the package title as the repo
description. Leave all the other options as is, then click Submit."

Gabor



  Thanks.  I now have "https://github.com/sbgraves237/fda;. Then I 
did "git push --set-upstream origin master", and it seemed to work.



  Thanks again.
  Spencer


On Wed, Jan 15, 2020 at 11:15 PM Spencer Graves
 wrote:

Hello, All:


How can I create a new project within my GitHub account
(https://github.com/sbgraves237/)?


I'm trying to follow "http://r-pkgs.had.co.nz/git.html":


...
Synchronising with GitHub
...

  Open a shell, then follow the instructions on the new repo page.
They’ll look something like this:

  git remote add origin g...@github.com:hadley/r-pkgs.git
  git push -u origin master

I tried:

...$ git remote add origin g...@github.com:sbgraves237/fda.git
...$ git push -u origin master
ERROR: Repository not found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


*** That didn't work, so I tried


...$ git remote add origin https://[my ssh code]@github.com/sbgraves237/fda
fatal: remote origin already exists.
...$ git push -u origin master
ERROR: Repository not found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


*** What do I need to do to fix the mess I seem to have created
and get what I want?


*** Thanks, Spencer Graves


p.s.  If you know the fda package, you know that James Ramsay is the
primary author, and I'm one of his long-time collaborators.  He has a
new version he wants to clean up and submit to CRAN, and I'm trying to
help him.  Thanks.  sg

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Re: [R-pkg-devel] GitHub problems

[Spencer Graves]

Thanks very much.


I deleted my token.  I will forward your comment to Jim Ramsay to try to 
figure out the permissions question.


Spencer


On 2020-03-14 01:35, Hugh Parsonage wrote:
>
> You published your token. You should revoke it.
>
> You probably don’t have the right permissions associated with git.
>
>
>
> On Sat, 14 Mar 2020 at 2:14 pm, Spencer Graves 
>  <mailto:spencer.gra...@effectivedefense.org>> wrote:
>
> Hello, All:
>
>
>    What do you suggest Jim Ramsay and I do to migrate the fda
> package to GitHub?
>
>
>    Jim successfully created an empty repository:
>
>
> https://github.com/JamesRamsay5/fda
>
>
>    He told me he had officially made me a "contributor".  I did:
>
>
> git clone https://@github.com/JamesRamsay5/fda
> <http://github.com/JamesRamsay5/fda>
> Cloning into 'fda'...
> warning: You appear to have cloned an empty repository.
> Checking connectivity... done.
>
>
>    Then I copied files into this directory, did "git add" and
> "git
> commit".
>
>
>    Then I did "git push", and it wouldn't let me:
>
>
> SpenceravessMBP:fda sbgraves$ git push
> remote: Permission to JamesRamsay5/fda.git denied to sbgraves237.
> fatal: unable to access
> 
> 'https://892da70262d9a4faa857b8602145414d6b210...@github.com/JamesRamsay5/fda/':
>
> The requested URL returned error: 403
>
>
>    Suggestions?
>    Thanks,
>    Spencer Graves
>
> __
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> <mailto:R-package-devel@r-project.org> mailing list
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>


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[R-pkg-devel] More GitHub problems

[Spencer Graves]

Hello:


  Is there a way to restore the functionality of a local clone of a 
GitHub repository after the SSH key it used was replaced?



  I have a local clone that previously worked fine but now asks for 
a password that I don't think I have when I try "git push".



  Thanks,
      Spencer Graves

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Re: [R-pkg-devel] More GitHub problems

[Spencer Graves]

Hi, Ivan et al:


On 2020-04-21 02:15, Ivan Krylov wrote:

On Mon, 20 Apr 2020 23:44:43 -0500
Spencer Graves  wrote:


Is there a way to restore the functionality of a local clone of a
GitHub repository after the SSH key it used was replaced?

Does `git remote -v` in the repo directory show https://github.com/...
or g...@github.com:... or ssh://... URLs?

Can you add the new SSH key on <https://github.com/settings/keys> and
check ~/.ssh/config to make sure that it's used when connecting to
github.com? You can verify that the SSH part of the stack works by
running `ssh g...@github.com`:

PTY allocation request failed on channel 0
Hi ! You've successfully authenticated, but GitHub does not
provide shell access.
Connection to github.com closed.


    I have a local clone that previously worked fine but now asks
for a password that I don't think I have when I try "git push".

This sounds like it's using an https:// remote URL, not ssh. But I
might be mistaken.


You were absolutely correct.  The problem was fixed by copying "url = 
g...@github.com:/.git" from a repository 
where it worked properly into this one, and it worked.



      Thanks,
  Spencer Graves

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[R-pkg-devel] Warning in dir.create(vd2 <- "vign_test"): 'vign_test' already exists

[Spencer Graves]

Hello, All:


  Under Windows 10, "R CMD check sos_2.0-1.tar.gz" cloned from 
"https://github.com/sbgraves237/sos; ends with:



* checking rebuild of vignettes outputs ...Warning in dir.create(vd2 <- 
"vign_test"):  'vign_test' already exists



  Under macOS 10.15.3 it finishes fine.


  "grep 'vign_test'" failed to find anything.


  ???
  Thanks,
  Spencer Graves


p.s.  Running R 3.6.3 on both machines with "update.packates()" clean.

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[R-pkg-devel] GitHub problems

[Spencer Graves]

Hello, All:


  What do you suggest Jim Ramsay and I do to migrate the fda 
package to GitHub?



  Jim successfully created an empty repository:


https://github.com/JamesRamsay5/fda


  He told me he had officially made me a "contributor".  I did:


git clone https://@github.com/JamesRamsay5/fda
Cloning into 'fda'...
warning: You appear to have cloned an empty repository.
Checking connectivity... done.


      Then I copied files into this directory, did "git add" and "git 
commit".



  Then I did "git push", and it wouldn't let me:


SpenceravessMBP:fda sbgraves$ git push
remote: Permission to JamesRamsay5/fda.git denied to sbgraves237.
fatal: unable to access 
'https://892da70262d9a4faa857b8602145414d6b210...@github.com/JamesRamsay5/fda/': 
The requested URL returned error: 403



  Suggestions?
  Thanks,
  Spencer Graves

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Re: [R-pkg-devel] GitHub problems

[Spencer Graves]

Hello, All:


   I've been unable to get SSH to work with 
"https://github.com/JamesRamsay5/fda;, documented in my email to this 
group almost 3 weeks ago.  I've been able to do "git clone 
https://sbgraves237:@github.com/JamesRamsay5/fda", then 
change a file, do "git commit" and "git push".


   However, this has my GitHub password in a plain text ".git" file 
on my hard drive.  I think the hard drive on my computer is encrypted, 
so maybe that's not a problem.


   Am I not allowed to use SSH with a GitHub repository that's not 
my own?


   Thanks,
   Spencer Graves


p.s.  Since my previous email, Ramsay added "README.md" to that 
repository.  I can do "git clone" and get it, then edit it, then "git 
commit".  However, "git push" keeps giving me errors:


git push
remote: Invalid username or password.
fatal: Authentication failed for 
'https://@github.com/JamesRamsay5/fda/'


   A few hours ago, the owner, JamesRamsay5, went to "Settings" > 
"Manage access", then invited me as a collaborator.  I got an email 
asking me to "view invitation", which I did.  I got another email 
saying, "Hey there, we’re just writing to let you know that you’ve been 
automatically subscribed to a repository on GitHub." Sadly, I still 
couldn't access it, so I I deleted my token and created a new one.  I 
also deleted my previous local clone of "fda" and recreated it using  
"git clone https://@github.com/JamesRamsay5/fda".  Then I did a 
test edit to the one file in that repository, README.md.  I think did 
'git commit README.md -m "tst edit"'.  Then "git push" keeps giving me 
the error just mentioned.


 > sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.6/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
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3


On 2020-03-14 02:33, Spencer Graves wrote:
> Thanks very much.
>
>
> I deleted my token.  I will forward your comment to Jim Ramsay to try 
> to figure out the permissions question.
>
>
> Spencer
>
>
> On 2020-03-14 01:35, Hugh Parsonage wrote:
>>
>> You published your token. You should revoke it.
>>
>> You probably don’t have the right permissions associated with git.
>>
>>
>>
>> On Sat, 14 Mar 2020 at 2:14 pm, Spencer Graves 
>> > <mailto:spencer.gra...@effectivedefense.org>> wrote:
>>
>> Hello, All:
>>
>>
>>    What do you suggest Jim Ramsay and I do to migrate the fda
>> package to GitHub?
>>
>>
>>    Jim successfully created an empty repository:
>>
>>
>> https://github.com/JamesRamsay5/fda
>>
>>
>>    He told me he had officially made me a "contributor".  I did:
>>
>>
>> git clone https://@github.com/JamesRamsay5/fda
>> <http://github.com/JamesRamsay5/fda>
>> Cloning into 'fda'...
>> warning: You appear to have cloned an empty repository.
>> Checking connectivity... done.
>>
>>
>>    Then I copied files into this directory, did "git add" and
>> "git
>> commit".
>>
>>
>>    Then I did "git push", and it wouldn't let me:
>>
>>
>> SpenceravessMBP:fda sbgraves$ git push
>> remote: Permission to JamesRamsay5/fda.git denied to sbgraves237.
>> fatal: unable to access
>> 
>> 'https://892da70262d9a4faa857b8602145414d6b210...@github.com/JamesRamsay5/fda/':
>>
>> The requested URL returned error: 403
>>
>>
>>    Suggestions?
>>    Thanks,
>>    Spencer Graves
>>
>> __
>> R-package-devel@r-project.org
>> <mailto:R-package-devel@r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>


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Re: [R-pkg-devel] GitHub problems

[Spencer Graves]

Hi, Max et al.:


 ��� � With SSH established:


git clone g...@github.com:JamesRamsay5/fda.git


 ��� � Worked.


 � I had tried something like "git clone 
g...@github.com:JamesRamsay5/fda.git" before, but I either did not have 
that exact syntax or I tried that before I had SSH.


 � Thanks again,
 ����� Spencer Graves


On 2020-04-03 15:17, Max Turgeon wrote:
>
> Hi Spencer,
>
>
> Did you follow the instructions here? 
> https://help.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh
>
>
> Once the key is setup, you should be able to do "git clone 
> g...@github.com:JamesRamsay5/fda.git", without any need to input a 
> token or a password in the command. Similarly, git push/pull/fetch 
> should all work seamlessly.
>
>
> This is how I've used Github for many years, and it's always worked fine.
>
>
> Best,
>
> Max
>
> Connecting to GitHub with SSH - GitHub Help 
> <https://help.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh>
> help.github.com
> You can connect to GitHub using SSH.
>
>
>
>
> Max Turgeon
> Assistant Professor
> Department of Statistics
> Department of Computer Science
> University of Manitoba
> maxturgeon.ca <http://maxturgeon.ca>
>
>
> 
> *From:* R-package-devel  on 
> behalf of Spencer Graves 
> *Sent:* April 3, 2020 3:03:12 PM
> *To:* Hugh Parsonage
> *Cc:* List r-package-devel
> *Subject:* Re: [R-pkg-devel] GitHub problems
> 
> Caution: This message was sent from outside the University of Manitoba.
> 
>
> Hello, All:
>
>
> �� I've been unable to get SSH to work with
> "https://github.com/JamesRamsay5/fda;, documented in my email to this
> group almost 3 weeks ago.� I've been able to do "git clone
> https://sbgraves237:@github.com/JamesRamsay5/fda", then
> change a file, do "git commit" and "git push".
>
>
> �� However, this has my GitHub password in a plain text ".git" file
> on my hard drive.� I think the hard drive on my computer is encrypted,
> so maybe that's not a problem.
>
>
> �� Am I not allowed to use SSH with a GitHub repository that's not
> my own?
>
>
> �� Thanks,
> �� Spencer Graves
>
>
> p.s.� Since my previous email, Ramsay added "README.md" to that
> repository.� I can do "git clone" and get it, then edit it, then "git
> commit".� However, "git push" keeps giving me errors:
>
>
> git push
> remote: Invalid username or password.
> fatal: Authentication failed for
> 'https://@github.com/JamesRamsay5/fda/'
>
>
> �� A few hours ago, the owner, JamesRamsay5, went to "Settings" >
> "Manage access", then invited me as a collaborator.� I got an email
> asking me to "view invitation", which I did.� I got another email
> saying, "Hey there, we�re just writing to let you know that you�ve been
> automatically subscribed to a repository on GitHub." Sadly, I still
> couldn't access it, so I I deleted my token and created a new one.� I
> also deleted my previous local clone of "fda" and recreated it using
> "git clone https://@github.com/JamesRamsay5/fda".� Then I did a
> test edit to the one file in that repository, README.md.� I think did
> 'git commit README.md -m "tst edit"'.� Then "git push" keeps giving me
> the error just mentioned.
>
>
> �> sessionInfo()
> R version 3.6.3 (2020-02-29)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Catalina 10.15.4
>
> Matrix products: default
> BLAS:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.6/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
> [6] methods�� base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.3 tools_3.6.3
>
>
> On 2020-03-14 02:33, Spencer Graves wrote:
> > Thanks very much.
> >
> >
> > I deleted my token.� I will forward your comment to Jim Ramsay to try
> > to figure out the permissions question.
> >
> >
> > Spencer
> >
> >
> > On 2020-03-14 01:35, Hugh Parsonage wrote:
> >>
> >> You published your token. You s

Re: [R-pkg-devel] [BULK] Re: [Rd] "not a valid win32 application" with rtools40-x86_65.exe on Windows 10

[Spencer Graves]

Hi, Simon et al.


[changing to "R-package-devel, because I've heard complaints that this 
may not be appropriate for R-devel.]



  I'm still having problems.  I found that I had Java twice in the 
path and deleted both versions (~\AdoptOpenJDK\jdk-11.0.6.10-hotspot\bin 
and ~Java\jre1.8.0_241). That seemed not to change anything as far as I 
can tell.



  I have both directories for both "~Rtools" and "~rtools40", and 
the path includes "~rtools40\bin".  When running R4.0.0 within RStudio, 
"install.package('rJava', type='source', INSTALL_opts = 
'--merge-multiarch') complained, "WARNING:  Rtools is required ... but 
no version compatible ... was found.  Note that the following 
incompatible versions(s) ... were found:  - Rtools 3.5".  When I run r 
in a CMD prompt, I don't get that warning.  However, both complain,



  warning in system("sh ./configure.win") : 'sh' not found


  When I tried "install.packages('rJava')", it seemed to work OK 
(though I still got the complaint from R within RStudio that it could 
not find rtools40).



  And my primary problem is unchanged:  "R CMD check 
Ecfun_0.2-4.tar.gz" ends with the following:



Error:  package or namespace load failed for 'Ecfun':
  .onLoad failed in loadNamespace() for 'rJava', details
   call: inDL(x, as.logical(local), as.logical(now), ...)
   error:  unable to load shared object 'c:/Program
Files/R/R-4.0.0/library/rJava/libs/i386/rJava.dll':
   LoadLibrary failure: ^1 is not a valid win32 application


  The same package on my Mac quits with a LaTeX error I have yet to 
figure out how to fix.



  Suggestions?
  Thanks,
  Spencer Graves


00install.out:


* installing *source* package 'Ecfun' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'Ecfun':
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: inDL(x, as.logical(local), as.logical(now), ...)
  error: unable to load shared object 'C:/Program 
Files/R/R-4.0.0/library/rJava/libs/i386/rJava.dll':

  LoadLibrary failure:  %1 is not a valid Win32 application.

Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck/Ecfun'


On 2020-05-02 02:20, Simon Urbanek wrote:

Spencer,

you shouldn't have anything on the PATH, the location of Java is taken from the 
registry so you only need t have a valid installation of Java. Better don't set 
PATH or JAVA_HOME as it will stop rJava from working if you get it wrong. The 
errors on Windows are confusing, the actual error is shown via GUI as pop-up, 
what they report in the console is not the real error.

Re installation from source - it sooks like you either don't have Rtools40 or 
you didn't set PATH properly. If I recall the new Rtools40 no longer set the 
PATH (for whatever reason) so you have to do it by hand and the instructions it 
gives you are not working for the command shell.

Cheers,
Simon




On 1/05/2020, at 4:51 PM, Spencer Graves  wrote:

Hi, Jeroen et al.:


On 2020-04-30 03:15, Jeroen Ooms wrote:

On Thu, Apr 30, 2020 at 6:38 AM Spencer Graves
 wrote:

Hello, All:


"00install.out" from "R CMD check Ecfun_0.2-4.tar.gz" includes:


Error:  package or namespace load failed for 'Ecfun':
   .onLoad failed in loadNamespace() for 'rJava', details
call: inDL(x, as.logical(local), as.logical(now), ...)
error:  unable to load shared object 'c:/Program
Files/R/R-4.0.0/library/rJava/libs/i386/rJava.dll':
LoadLibrary failure: ^1 is not a valid win32 application


This is an error in loading the rJava package, so it is not related to
rtools40, and probably inappropriate for this mailing list.

As Simon suggested, you may have to install the 32-bit Java JDK. See
also this faq: 
https://github.com/r-windows/docs/blob/master/faq.md#how-to-install-rjava-on-windows


   In fact I had both 32- and 64-bit Java installed but only the 64-bit was in the 
path.  I added the 32-bit, but that did not fix the problem.  The last 2.5 lines in the 
section "How to install rJava on Windows?" to which you referred me reads:


to build rJava from source, you need the --merge-multiarch flag:

install.packages('rJava', type = 'source', INSTALL_opts='--merge-multiarch')


   When I tried that, I got:


Warning in system("sh ./configure.win") : 'sh' not found


*** ON THE OTHER HAND:  The error message above says 'c:/Program
Files/R/R-4.0.0/library/rJava/libs/i386/rJava.dll':
LoadLibrary failure: ^1 is not a valid win32 application



Is "rJava.dll" a valid win32 application?


   Suggestion

Re: [R-pkg-devel] How to remove rJava from Ecfun when it's not called directly or indirectly

[Spencer Graves]

On 2020-10-11 10:34, Enrico Schumann wrote:

On Sat, 10 Oct 2020, Spencer Graves writes:


Hello, All:


  "R CMD check Ecfun_0.2-4.tar.gz" fails under
Windows 10 with "Error: package or namespace load
failed for 'Ecfun': .onLoad failed in loadNamespace()
for 'rJava'".


  However, I cannot find where Ecfun calls rJava.  This is in:


https://github.com/sbgraves237/Ecfun


  I get nothing from "grep 'rJava'" in the
DESCRIPTION and NAMESPACE files plus in the man and R
subdirectories.  I ran tools:package_dependencies
recursively starting with Ecfun until I got all NULLs
and could not find rJava anywhere.


  Thanks,
  Spencer Graves


00install.out


* installing *source* package 'Ecfun' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'Ecfun':
  .onLoad failed in loadNamespace() for 'rJava', details:
   call: inDL(x, as.logical(local), as.logical(now), ...)
   error: unable to load shared object 'C:/Program
Files/R/R-4.0.2/library/rJava/libs/i386/rJava.dll':
   LoadLibrary failure:  %1 is not a valid Win32 application.

Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck/Ecfun'


00check.log


* using log directory 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'Ecfun/DESCRIPTION' ... OK
* this is package 'Ecfun' version '0.2-4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Ecfun' can be installed ... ERROR
Installation failed.
See
'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck/00install.out'
for details.
* DONE
Status: 1 ERROR



Hello Spencer

Just a wild guess: the CRAN version of your package
does not list 'xlsx'; but your GitHub version does.
Now, 'xlsx' depends on 'rJava'.  So perhaps start there?

As I said, only a wild guess; but maybe it helps.



Yes, it helps.  I removed that dependency, and the package now passes "R 
CMD check on my Mac;  it didn't before.



Thanks again, Spencer Graves



Kind regards
 Enrico



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[R-pkg-devel] How to remove rJava from Ecfun when it's not called directly or indirectly

[Spencer Graves]

Hello, All:


	  "R CMD check Ecfun_0.2-4.tar.gz" fails under Windows 10 with "Error: 
package or namespace load failed for 'Ecfun': .onLoad failed in 
loadNamespace() for 'rJava'".



  However, I cannot find where Ecfun calls rJava.  This is in:


https://github.com/sbgraves237/Ecfun


	  I get nothing from "grep 'rJava'" in the DESCRIPTION and NAMESPACE 
files plus in the man and R subdirectories.  I ran 
tools:package_dependencies recursively starting with Ecfun until I got 
all NULLs and could not find rJava anywhere.



  Thanks,
  Spencer Graves


00install.out


* installing *source* package 'Ecfun' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'Ecfun':
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: inDL(x, as.logical(local), as.logical(now), ...)
  error: unable to load shared object 'C:/Program 
Files/R/R-4.0.2/library/rJava/libs/i386/rJava.dll':

  LoadLibrary failure:  %1 is not a valid Win32 application.

Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck/Ecfun'


00check.log


* using log directory 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'Ecfun/DESCRIPTION' ... OK
* this is package 'Ecfun' version '0.2-4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Ecfun' can be installed ... ERROR
Installation failed.
See 'C:/Users/spenc/Documents/R/Ecfun/Ecfun.Rcheck/00install.out' for 
details.

* DONE
Status: 1 ERROR

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Re: [R-pkg-devel] CRAN pending status , left up in the air

[Spencer Graves]

On 2020-10-19 10:34, Rafael H. M. Pereira wrote:

Thank you  Dirk and Hugo for your responses. I guess I'll just have to be
patient and wait.

I can only imagine how the CRAN team is overwhelmed by the exponential
growth of package submissions. I wonder, though, whether the CRAN
maintainers and the R community more broadly are thinking about
alternatives to deal with such growing demand without compromising the
speed and consistency/quality of package development. Expanding the team of
CRAN maintainers would be the most obvious solution but I confess I'm not
familiar enough with the whole process to assess what would be the best
routes of action to tackle this bottleneck.



	  From my experience, it looks to me like their primary approach to 
handling the increased volume has been to improve automation.  In the 
spirit of brainstorming, I'd like to share other ideas on this:



MAKE IT EASY FOR A USER TO CHECK A DIFF FILE OF "Writing R Extensions" 
COMPARING THE CURRENT VERSION WITH ANY PREVIOUS ONE.



	  For example, every article on Wikipedia has a "View History" tab. 
That lists the dates of all the revisions with a terse summary of what 
was changed in each.  I can click on any two and then click "Compare" to 
see all the changes in that period.



	  I'm not going to reread every word of "Writing R Extensions" every 
time I submit something to CRAN.  However, I would be willing to review 
a diff file if it were easy for me to do that.  (And I'm NOT going to 
create my own private file copy of "Writing R Extensions" and manually 
create such a diff file.)



IMPROVE THE COLLABORATION BETWEEN THE CRAN TEAM AND OTHER DOCUMENTATION 
OF HOW TO PREPARE A PACKAGE FOR CRAN



  I know two sources of information on that:


		* Wickham and Bryan, R Packages (https://r-pkgs.org).  I created a 
"cran-comments.md" file based on their recommendations, and missed their 
comment that it should be in ".Rbuildignore".  My latest CRAN submission 
was rejected partly because of that.



		* Colin Fay, "Preparing your package for a CRAN submission" 
(https://github.com/ThinkR-open/prepare-for-cran).  These instructions 
follow Wickham and Bryan in recommending "devtools::revdep_check()". 
Sadly, "revdep_check" is not currently in devtools but in a package 
called revdepcheck.  Worse, that package is not available on CRAN and 
appears twice on GitHub.  The original by bbolker has not been updated 
in 5 years.  The version that is currently maintained is 
"https://github.com/r-lib/revdepcheck;.  Fortunately, Hadley Wickham is 
the leading contributor to the latter, so writing him may help correct 
that infelicity, but I should also write to Colin Fay.



CRAN REVIEW GROUPS:  There are now 41 different "CRAN Task Views".  We 
could ask the maintainer of each Task View to try to recruit a committee 
around each one to discuss coverage and integration.  Each committee 
could be asked to coordinate via email and in virtual meetings.  They 
could be asked to pick 3 standard times for their virtual meetings, so 
anyone in the world would not always be excluded from a meeting that was 
3 AM their time.  Each package maintainer would be asked to specify at 
least one "Task View" for each package and be willing to discuss 
overlap, etc., with others.  This might be a topic for the next useR 
conference.



  Comments?
  Best Wishes,
  Spencer Graves



best

Rafael H M Pereira

On Mon, Oct 19, 2020 at 5:46 AM Hugo Gruson 
wrote:


Hi all,

this is a bit tricky since the documentation on the dashboard comes from
an official, authoritative, source: the R journal [1].

"pending: if a decision is pending a response from the package
maintainer: If an additional issue was present in the package that we
cannot check for in the incoming checks (such as the BLAS issues
mentioned in the section above), the maintainer is automatically asked
whether these issues have been fixed. Same is true for change of
maintainer (or maintainer's mail address) where the old maintainer (old
address) is automatically asked to confirm the maintainer change. The
answers have to be processed manually."

As Dirk explains and as reported in
https://github.com/lockedata/cransays/issues/29, it is likely not true
anymore but in the absence of further official information, it is
difficult to issue a fix.

A later issue of the R journal [2] introduces the "waiting" and
"newbies" categories but does not expand on the new role of "pending".

Best,

Hugo

[1]: https://journal.r-project.org/archive/2018-1/cran.pdf
[2]: https://journal.r-project.org/archive/2019-1/cran.pdf

On 19/10/2020 02:18, Dirk Eddelbuettel wrote:


On 18 October 2020 at 20:56, Rafael H. M. Pereira wrote:
| The CRAN incoming Dashboard indicates that the status of my package

(r5r)

| is &qu

[R-pkg-devel] installed package size problem on Mac but not Linux nor Windows

[Spencer Graves]

Hello, All:


	  R CMD check of "https://github.com/sbgraves237/Ecfun; on Mac produces 
the following NOTE:



* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
doc   5.2Mb


	  It doesn't do that with Travis CI[1] nor on a Windows 10 computer I 
have.  "Writing R Extensions" suggested using "--compact-vignettes" with 
qpdf.  That changed nothing.



  Suggestions?
  Will this be problem on CRAN?
  Thanks,
  Spencer


[1]
https://travis-ci.org/github/sbgraves237/Ecfun/builds/727906753

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Re: [R-pkg-devel] installed package size problem on Mac but not Linux nor Windows

[Spencer Graves]

On 2020-09-22 02:22, Hugh Parsonage wrote:
One of your vignettes is a 52-page pdf. It may be more suitable to 
provide a link to it rather than distributing it with the package, or 
distribute an excerpt.


Some the images in the PDFs could be PDFs themselves, or be pngs with 
lower resolution.



	  Yes.  That's done by default by "R CMD build / check" on my Mac but 
not on Linux nor Windows 10.  I'm not sure, but I think this problem is 
fairly recent:  I think that "R CMD build / check" on Mac used to run 
like on Linux and Win10 without creating these huge PDF and HTML files 
from vignettes.  If it's only the figures, I would naively think there 
should be an option to make sure that the figures were coded in svg so 
it wouldn't take up as much space.  Or, failing that, if the problem is 
the figures, I can code it so the figures don't plot unless people run 
them manually.  Or maybe I shouldn't be trying to distribute vignettes 
like this.



  Thanks for the reply.
  Spencer



On Tue, 22 Sep 2020 at 5:04 pm, Spencer Graves 
<mailto:spencer.gra...@effectivedefense.org>> wrote:


Hello, All:


           R CMD check of "https://github.com/sbgraves237/Ecfun; on
Mac produces
the following NOTE:


* checking installed package size ... NOTE
    installed size is  5.9Mb
    sub-directories of 1Mb or more:
      doc   5.2Mb


           It doesn't do that with Travis CI[1] nor on a Windows 10
computer I
have.  "Writing R Extensions" suggested using "--compact-vignettes"
with
qpdf.  That changed nothing.


           Suggestions?
           Will this be problem on CRAN?
           Thanks,
           Spencer


[1]
https://travis-ci.org/github/sbgraves237/Ecfun/builds/727906753

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Re: [R-pkg-devel] [R] a question of etiquette

[Spencer Graves]

  Can Dr. Sharp kindly provide a credible reference, discussing the 
alleged ambiguities in GPL-2 and GPL-3 that convince some companies to 
avoid them?



  I like Wikimedia Foundation projects like Wikipedia, where almost 
anyone can change almost anything, and what stays tends to be written 
from a neutral point of view, citing credible sources.  I get several 
emails a day notifying me of changes in articles I'm "watching".  FUD, 
vandalism, etc., are generally reverted fairly quickly or moved to the 
"Talk" page associated with each article, where the world is invited to 
provide credible source(s).



  Spencer Graves


On 2020-06-02 10:12, Dirk Eddelbuettel wrote:

On 2 June 2020 at 10:06, R. Mark Sharp wrote:
| The GPL-2 and GPL-3 licenses are apparently sufficiently ambiguous in the 
legal community that some companies avoid them.

Wittgenstein:  'That whereof we cannot speak, thereof we must remain silent'

This is a mailing list of the R project. R is a GNU Project. R is licensed
under the GPL, version two or later. That has not stopped large corporations
from using R, adopting R, or starting or acquiring R related businesses.

If you have a strong urge to spread FUD about the GPL and R, could you have the
modicum of etiquette to not do it on a mailing list of the R Project?

Dirk



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Re: [R-pkg-devel] [R] a question of etiquette

[Spencer Graves]

On 2020-06-02 10:14, Adelchi Azzalini wrote:




In  general, "check the license" is a very sensible indication. In the specific 
case, the Matlab code comes with no licence indication - nothing.



  I'm not an attorney, but it's my understanding that "no license 
indication" is a legal minefield:  You can be sued for copyright 
infringement, even with anything that "comes with no license indicate - 
nothing."  For horror stories in that regard, see the Wikipedia article 
on Lawrence Lessig's "Free Culture (book) 
[https://en.wikipedia.org/wiki/Free_Culture_(book)]:  Hollywood has lots 
of money for SLAPP lawsuits, and they've used it to stifle competition.



  To me, this is in blatant violation of the Copyright Clause of 
the US Constitution, which says, "[the United States Congress shall have 
power] To promote the Progress of Science and useful Arts, by securing 
for limited Times to Authors and Inventors the exclusive Right to their 
respective Writings and Discoveries."[1]  However, as Lessig documented, 
the US Supreme Court disagreed.



QUESTION:  How much money have people on this list received for what 
they've written?  I've received not one penny for any technical article 
I've written or for software contributed to CRAN.



  Spencer


[1]
https://en.wikipedia.org/wiki/Copyright_Clause


Best regards,

Adelchi Azzalini
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[R-pkg-devel] RMarkdown vignettes with Wikiversity?

[Spencer Graves]

Hello, All:


  Two questions:


		1.  Might anyone have any thoughts on posting an RMarkdown 
vignette like an appendix to an article on Wikiversity?



		2.  In particular, might it be feasible to post a link to an 
online RStudio instance that could be provided with the RMarkdown source 
for a vignette that's posted to Wikiversity?



	  I've written Wikiversity articles for which the detailed statistical 
analysis is currently in vignettes in the Ecfun package.  However, that 
seems somewhat inconsistent with my understanding of the purpose of 
vignettes, and posting such directly like an appendix with the companion 
Wikiversity article seems to make more sense, anyway.



	  For comments about this by a Wikiversity "Bureaucrat", who is also a 
Professor of Computer Information Systems at Harper College in Palatine, 
Illinois, see:



https://en.wikiversity.org/wiki/User_talk:Dave_Braunschweig#RMarkdown_vignettes_with_Wikiversity?


  Thanks,
      Spencer Graves

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[R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

[Spencer Graves]

Hello:


   I'm getting two warnings that I don't know how to fix on both 
4.0.2 under macOS 10.15.5 and 4.0.0 under TRAVIS-CI; the email from 
Travis CI  is copied below.


NON-ASCII INPUT:


* checking Rd files ... WARNING
man/nuclearWeaponStates.Rd: non-ASCII input and no declared encoding
problem found in ‘nuclearWeaponStates.Rd’


   I'm virtually certain this comes from the following:


   \href{https://www.americansecurityproject.org/ASP Reports/Ref 0072 - 
North Korea’s Nuclear Program .pdf}{Derek Bolton (2012) North Korea's 
Nuclear Program} (2012-08, American Security Program, accessed 2020-07-15)


   If you look carefully, you see spaces and a right single quote in 
the URL.  If I copy this URL into a browser and back out again, I get 
the following:


https://www.americansecurityproject.org/ASP%20Reports/Ref%200072%20-%20North%20Korea%E2%80%99s%20Nuclear%20Program%20.pdf


   However, if I use this inside "\href", "R CMD check" doesn't 
recognize the close curly bracket because of the presence of the 
non-ASCII characters.  I could leave out the URL, but that would degrade 
the quality of the documentation.


"--DATA-COMPRESS" IGNORED


   I'm getting, " Note: significantly better compression could be 
obtained by using R CMD build --resave-data".  I get this message even 
though I use "R CMD build --data-compress Ecdat".  I also tried "R CMD 
build Ecdat --data-compress" and got the same result.


   Suggestions?
   Thanks,
   Spencer Graves


sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/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_4.0.2


 Forwarded Message 
Subject:Broken: sbgraves237/Ecdat#33 (master - a049665)
Date:   Fri, 17 Jul 2020 06:05:20 +
From:   Travis CI 
To: spencer.gra...@effectivedefense.org



sbgraves237

/

Ecdat

<https://travis-ci.org/github/sbgraves237/Ecdat?utm_medium=notification_source=email>
 


branch iconmaster <https://github.com/sbgraves237/Ecdat/tree/master>

build has failed
Build #33 was broken 
<https://travis-ci.org/github/sbgraves237/Ecdat/builds/709051085?utm_medium=notification_source=email>
arrow to build time
clock icon5 mins and 5 secs

sbgraves237 avatarsbgraves237

a049665 CHANGESET → 
<https://github.com/sbgraves237/Ecdat/compare/8b5b8b867663...a04966508ba6>

fix nuclearWeaponStates so it now has all the desired data

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Re: [R-pkg-devel] email misleading: checking CRAN incoming feasibility ... NOTE Maintainer

[Spencer Graves]

Hi, Uwe et al.:


  What's the preferred way to eliminate tests on CRAN that the 
maintainer still wants to run on other platforms?



  For several years, I've been using "if(!fda::CRAN()){...}". I've 
been told that I should NOT do that, but it has worked for me, and I 
haven't found anything better.  I've recently seen 
"testthat::skip_on_cran(...)", but I have yet to understand enough of 
how it works to actually use it.



  Thanks,
  Spencer Graves


On 2020-06-08 09:43, stefano wrote:

Hello Uwe,

OK sorry for that.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno mar 9 giu 2020 alle ore 00:40 Uwe Ligges <
lig...@statistik.tu-dortmund.de> ha scritto:



On 08.06.2020 16:26, stefano wrote:

Hello,

I would like to point out that I (and others in various forums) find that
the CRAN check with the note :


*checking CRAN incoming feasibility ... NOTEMaintainer*


Not true, it also says

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'x64', Result: NOTE
Examples with CPU (user + system) or elapsed time > 10s
  user system elapsed
lower_triangular-methods 11.48  011.5

Please reduce each example to less than 5 sec.

Best,
Uwe Ligges

Triggers an email saying


1) *package nanny_0.1.7.tar.gz does not pass the incoming checks
automatically*

2) *Please fix all problems and resubmit a fixed version via the webform*


While apparently nothing should be done, at least according to some forum
post


https://stackoverflow.com/questions/23829978/checking-cran-incoming-feasibility-note-maintainer

It would be nice to avoid this from the test side or the email side. It

is

pretty confusing for developers who think that they have to act.


Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

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Re: [R-pkg-devel] [R] a question of etiquette

[Spencer Graves]

On 2020-06-02 14:24, Avraham Adler wrote:
> 
>
> On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves 
>  <mailto:spencer.gra...@effectivedefense.org>> wrote:
> > QUESTION:  How much money have people on this list received for what
> > they've written?  I've received not one penny for any technical article
> > I've written or for software contributed to CRAN.
> >
> >        Spencer
>
> Ditto. What's even more annoying is when people clearly use one's 
> package in their published work and do not cite it, but that is for a 
> different thread.


   Might that be a copyright violation or just intellectual laziness 
or in some cases dishonesty but short of a level that could lead to some 
disciplinary action in a university or research organization?


    sg

>
> Avi
>


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Re: [R-pkg-devel] Note: information on .o files is not available / Found '_exit', possibly from '_exit' (C)

[Spencer Graves]

  Can you run the checks only on the subdirectory containing the 
compiled code?  If yes, then you can run it only on half of that 
directory and identify it with a binary search.



  Some years ago, I found a particularly difficult bug that way.  
If I recall correctly, I made a copy of the package, deleted half of the 
*.Rd files, etc., until I identified which *.Rd file. Then I deleted 
~half of the contents of that *.Rd file until I isolated the problem.  
It was neither easy nor fun, but it was what I did to find and then fix 
the problem.



  Hope this helps,
  Spencer


On 2020-07-17 07:34, Marcin Jurek wrote:

So maybe you tried that already but I noticed that sometimes when I do the
check on the package directory rather than on the tarball I get similar
errors. I don't know if that's the problem but it should be a quick thing
to try.

On Fri, Jul 17, 2020 at 5:05 AM Fabio Sigrist 
wrote:


Dear all,

I am trying to get an R package with C++ code on CRAN and I have one NOTE
remaining, for which I can't find a solution:

Note: information on .o files for x64 is not available
   File
'd:/RCompile/CRANincoming/R-devel/lib/gpboost/libs/x64/lib_gpboost.dll':
 Found '_exit', possibly from '_exit' (C)
 Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
 Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
 Found 'printf', possibly from 'printf' (C)

As much as I search through my code, I can't find the place / headers where
these calls / symbols originate. Also, I have no idea how to add
information on .o files (apart from the shared library, there are no .o
files). The .tar.gz file for the package can be found on
https://github.com/fabsig/GPBoost/blob/master/gpboost_0.2.0.tar.gz. Note
that the shared library is compiled using install.libs.R (this is a
deliberate choice) and the flag "GPB_R_BUILD" is set when compiling for the
R package (I have tried to put "#ifndef GPB_R_BUILD" around all headers
that could cause the problems with exit / abort calls, but apparently I
have not been able to find all).

Any help is greatly appreciated.

Best regards,
Fabio Sigrist

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Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

[Spencer Graves]

Hello, Ivan et al.:


  I tried escaping "%" every time it occurred without success, but 
adding "\encoding{UTF-8}" as the 4th line of nuclearWeaponStates.Rd 
eliminated that problem.



  Sadly, I tried "R CMD build --resave-data=best Ecdat", "R CMD 
build --resave-data Ecdat", "R CMD build Ecdat --resave-data", and "R 
CMD build Ecdat --resave-data=best", all without success.  I also noted 
that .travis.yml contains "r_build_args: --resave-data", which I 
remember adding some time ago to fix this problem.  And Travis reported 
this problem as well.  This suggests to me that a change was introduced 
with R 4.0.0 that disabled this option.



  I also tried loading and resaving all the files in the data 
directory.  This seemed to achieve some additional compression on 
average, but I still got, "Note: significantly better compression could 
be obtained by using "R CMD build --resave-data".  I then tried load and 
saveRDS on each one individually, but at least the first of the 
resulting *.rda files was corrupted, so I restored what I had before.



  Anyway, Ivan's suggestion fixed the UTF-8 problem and Travis 
confirmed that it can't make "--resave-data" work, either ;-)  If a CRAN 
maintainer complains about the compression problem, I can report what I 
tried and see what they suggest.



  Thanks again,
  Spencer Graves


On 2020-07-17 04:10, Ivan Krylov wrote:

On Fri, 17 Jul 2020 02:02:36 -0500
Spencer Graves  wrote:


If I copy this URL into a browser and back out again, I get
the following:


https://www.americansecurityproject.org/ASP%20Reports/Ref%200072%20-%20North%20Korea%E2%80%99s%20Nuclear%20Program%20.pdf


    However, if I use this inside "\href", "R CMD check" doesn't
recognize the close curly bracket because of the presence of the
non-ASCII characters.

WRE section 2.3 [*] provides an example of \href with RFC3986
percent-encoding. Since % is a comment character in Rd, the percent
signs have to be escaped with backslashes:

\href{https://www.americansecurityproject.org/ASP\%20Reports/Ref\%200072\%20-\%20North\%20Korea\%E2\%80\%99s\%20Nuclear\%20Program\%20.pdf}{Derek
Bolton (2012) North Korea's Nuclear Program}

This only works correctly in R >= 3.1.3, but results in correct output
in both HTML and PDF formats.

Alternatively, it should be possible to declare the encoding of the Rd
file using \encoding{UTF-8} (WRE 2.14 [**]), but in my tests (R 3.6.3,
could have been fixed in later versions) it results in a broken link in
Rd2pdf output.


    I'm getting, " Note: significantly better compression could be
obtained by using R CMD build --resave-data".  I get this message
even though I use "R CMD build --data-compress Ecdat".  I also tried
"R CMD build Ecdat --data-compress" and got the same result.

The note offers you to try adding --resave-data to R CMD build, not
--data-compress. What happens if you use --resave-data=best?
--data-compress doesn't seem to be an R CMD build option; at least
it's not mentioned in R CMD build --help.

WRE 1.1.6 [***] provides an example of --data-compress as an option of
R CMD INSTALL (not build).



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[R-pkg-devel] devtools::release() does not release

[Spencer Graves]

Hi folks,


  devtools::release() gave the following errors:


...
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?

Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
 argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
 argument should be a character vector of length 1
all but the first element will be ignored


	  Jim Ramsay got this after setwd to what seemed to be the appropriate 
working directory and then running devtools::release(), as noted above. 
As near as both of us can determine, we've followed essentially the same 
protocol here as with other package submissions.



	  In case you want the entire devtools::release() transcript, it 
appears below running under Big Sur on a Mac.



  Suggestions?
  Thanks,
      Spencer Graves & Jim Ramsay



——

devtools::release()

Have you checked for spelling errors (with `spell_check()`)?
1: Not yet
2: Nope
3: Absolutely

Selection: 3
Have you run `R CMD check` locally?
1: Yes
2: I forget
3: No

Selection: 1
── Running additional devtools checks for fda 
Checking version number has three components... OK
Checking dependencies don't rely on dev versions... OK
Checking DESCRIPTION doesn't have Remotes field... OK
──
Were devtool's checks successful?
1: I forget
2: No
3: Absolutely

Selection: 3
Have you fixed all existing problems at
https://cran.rstudio.com//web/checks/check_results_fda.html ?
1: Yes
2: Not yet
3: No

Selection: 1
Have you checked on R-hub (with `check_rhub()`)?
1: Not yet
2: I forget
3: Definitely

Selection: 3
Have you checked on win-builder (with `check_win_devel()`)?
1: No
2: Nope
3: Absolutely

Selection: 3
Have you checked the 67 reverse dependencies (with the revdepcheck 

package)?

1: Definitely
2: No
3: U... Maybe?

Selection: 1
Have you updated `NEWS.md` file?
1: U... Maybe?
2: No
3: Yeah

Selection: 3
Have you updated `DESCRIPTION`?
1: Yup
2: Nope
3: I forget

Selection: 1
Have you updated `cran-comments.md?`
1: Nope
2: Not yet
3: Yeah

Selection: 3
── Running Git checks for fda 
Current branch: master
Checking uncommitted files...
WARNING: All files should be tracked and committed before release. 

Please add and commit.

Checking synchronisation with remote branch...
ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol

──
Were Git checks successful?
1: Not yet
2: Nope
3: Yup

Selection: 3
Is your email address ram...@psych.mcgill.ca?
1: Yup
2: I forget
3: U... Maybe?

Selection: 1
Building
✓  checking for file 

‘/Users/jamesramsay/Documents/R/fda_work/fda/DESCRIPTION’ (437ms)

─  preparing ‘fda’: (5.8s)
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell 

scripts (1.6s)

─  checking for empty or unneeded directories
─  building ‘fda_5.1.7.tar.gz’

Submitting file: 

/var/folders/sc/6zzfzqbs5w7dl8q5g18tlqfcgn/T//RtmpbcSyMD/fda_5.1.7.tar.gz

File size: 102.9 Mb
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?

Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
 argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
 argument should be a character vector of length 1
all but the first element will be ignored




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Re: [R-pkg-devel] Used package not updated - needs java < V 11

[Spencer Graves]

	 I suggest NOT using "XLConnect".  "sos" now uses WriteXLS.  "Ecfun" 
now uses "openxlsx".



	  Also, I received an email from CRAN maintainers months ago saying 
that "gdata" was being obsoleted.  It's still on CRAN with a date of 
2017-06-06 and a huge number of reverse dependencies.  The CRAN 
maintainers may have gotten someone to agree to take it over who just 
hasn't finished fixing whatever deficiencies it has.  However, you might 
see how difficult it might be to do without "gdata" as well.



  Spencer Graves


On 2020-12-15 07:37, Duncan Murdoch wrote:

On 15/12/2020 8:02 a.m., Knut Krueger wrote:

I am using in my Package XlConnect. If the Computer is using Java < 11
all is working. But if not, the package can not be used.


inside teh functions tehre is an ' @importFrom XLConnect createSheet
writeWorksheet saveWorkbook

but only used for additional comfort to use excel sheets

The package is usable without XlConnect if I change

Imports:  igraph,chron,gdata, XLConnect
to
Imports:
  igraph,chron,gdata
Suggests:XLConnect

but then I get the error

checking package dependencies ... ERROR
    Namespace dependency not required: ‘XLConnect’

Just now the new version is on my private repository and working with or
without Xlconnect depending on the java version


How can I submit the package to cran  until XlConnect is working with
java > 11


You should not have

@importFrom XLConnect createSheet writeWorksheet saveWorkbook

in your ROxygen comments; that results in an unconditional import. 
Instead, you should use fully qualified calls each time, i.e.


XLConnect::createSheet, XLConnect::writeWorksheet, XLConnect::saveWorkbook

in your code.  You should also wrap every use of those functions in 
checks like


if (requireNamespace("XLConnect")) {
   run code
} else {
   report that you can't run that code
}

and make sure none of your examples or vignettes fail if XLConnect is 
not present.


Duncan Murdoch

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Re: [R-pkg-devel] Used package not updated - needs java < V 11

[Spencer Graves]

On 2020-12-17 12:22, Knut Krueger wrote:




   Also, I received an email from CRAN maintainers months ago 
saying that "gdata" was being obsoleted.  It's still on CRAN with a 
date of 2017-06-06 and a huge number of reverse dependencies.  The 
CRAN maintainers may have gotten someone to agree to take it over who 
just hasn't finished fixing whatever deficiencies it has.  However, 
you might see how difficult it might be to do without "gdata" as well.



   Spencer Graves



    Is it permissible to copy the code from rename.vars (gdata) inside 
my package with an hint:


"  Function rename.vars Source code from gdata as gdata is unmaintained 
since 2017-06-06 Rename variables in a dataframe

Author(s)
Don MacQueen (package gdata), macq\@llnl.gov."

it is the only function I am using from gdata.



	  That's definitely consistent with the GPL-2 license it carries as 
long as you aren't trying to charge royalties for use of your package. 
See:



https://CRAN.R-project.org/package=gdata


	  And the tarball is available at this link to make it easy for you to 
do that.



	  Regarding my earlier comment about to gdata being potentially 
obsoleted, I don't see evidence of that now:  There is only one "Note" 
in the "CRAN checks", and that would seem to be a problem more with that 
platform than with the gdata package.  The problem that Brian Ripley 
mentioned in his email about this 2020-09-11 may have been with 
something else that gdata used that has since been fixed.



	  I would normally prefer to let the gdata maintainers continue to 
maintain a function like this.  However, you seem to have a compelling 
reason for copying that function and only citing the original for the 
source of where you got the code.  You might include, e.g., 
\code{\link[gdata]{rename.vars}}.



	  CAVEAT:  Please ignore the above if contradicted by someone more 
knowledgeable than I am about CRAN and R policies and recommendations.



  Spencer



Knut

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Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

[Spencer Graves]

	  I have tests in my code to detect when something like that is not 
available.



	  I also have code in "\examples" to skip tests that would encounter 
that.



	  Hadley's "testthhat:skip_on_cran" is supposed to suppress tests like 
that on CRAN.  I have so far failed to understand how to use this 
function that Hadley wrote.  Instead, I use things like the following:



if(!fda::CRAN()){
# Code that I want to run everyplace that's NOT CRAN


}


	  When I wrote "fda::CRAN", I was told that I shouldn't do it, but I 
didn't see a better option, and I've been using it for several years now 
without being given a reason to discontinue using it or (better?) being 
given an alternative that seems better to me.



  Spencer


On 2020-12-12 12:40, Michael L Friendly wrote:

Thanks, Dirk

Just to clarify--
In my packages, candisc, heplots, vcdExtra I have mostly 2D graphic methods, 
but some 3D methods that use
rgl.  I therefore put rgl into Suggests:

Could I solve this by making rgl a Depends: ?

-Michael


-Original Message-
From: Dirk Eddelbuettel 
Sent: Saturday, December 12, 2020 12:46 PM
To: Michael L Friendly 
Cc: r-package-devel@R-project.org; Prof Brian Ripley 
Subject: Re: [R-pkg-devel] CRAN packages suggesting other packages but not 
using them conditionally


On 12 December 2020 at 16:24, Michael L Friendly wrote:
| I got the email below concerning 3 of my packages but wonder if they
| are false alarms or if not, how to locate & fix the problem.
|
| This concerns packages: ...
|
| Suggested packages should be used conditionally: see  1.1.3.1 of 'Writing 
R Extensions'.  Some of these are hard to install on a platform without X11 
such as M1 Macs: see the logs at https://www.stats.ox.ac.uk/pub/bdr/M1mac/.
|
| You can check all of the suggested packages by setting environment 
variable _R_CHECK_DEPENDS_ONLY_=true  -- see 
https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#Tools .
|
| Is this a false alarm?
|
| In each case, the outfile contains:
|
| * checking package namespace information ... OK
| * checking package dependencies ... NOTE
| Package suggested but not available for checking: 'rgl'
|
| indicating that rgl is not avaiable on the testing machine.  Then,
| when checking examples an error is triggered when an example calls something 
that requires rgl.
|
| >
| > heplot3d(Adopted.mod, hypotheses=list("Reg"=c("AMED", "BMIQ")),
| + col = c("red", "blue", "black", "gray"), wire=FALSE)
| Loading required namespace: rgl
| Failed with error:  'there is no package called 'rgl''
| Error in heplot3d.mlm(Adopted.mod, hypotheses = list(Reg = c("AMED", 
"BMIQ")),  :
|   rgl package is required.
| Calls: heplot3d -> heplot3d.mlm
| Execution halted
|
| Yet, heplot3d seems to contain the required way to refer to the suggested rgl 
package:
|
| if (!requireNamespace("rgl")) stop("rgl package is
| required.")
|
| So, I'm mystified.  Can anyone help?

This is not conditional use in the sense of my reading of WRE.

What you have here is essentially an "assert()" and equivalent to
   stopifnot(requireNamespace("rgl"))
which, in turn, is equivalent to a strong Depends or Imports as your package 
will experience a _critical error_ triggered by `stop()` if rgl is missing.

The idea of a conditional use is to, well, be conditional. Below I make use of 
Rcpp if is present, but it is only a suggests:

   ## see the source files in the snippets/ directory of the package
   ## check for (optional, only in Suggests:) Rcpp, and also wrapped in a
   ## dontrun as it takes 10s at CRAN (yet only 3.5 here) yielding a NOTE
   if (requireNamespace("Rcpp", quietly=TRUE)) {
   Rcpp::sourceCpp(system.file("snippets", "convolveExample.cpp", 
package="tidyCpp"))
   }

If the _suggested_ package is present, it is used. If not we quietly move on.
(It's not the full story as the compilation occassionally takes longer, Windows 
complained so all this is now in a \dontrun{} block too. But the idea is 
generic and there are many more examples to be found.)

Hope this helps,  Dirk

--
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

[Spencer Graves]

On 2020-12-12 19:50, Duncan Murdoch wrote:

On 12/12/2020 6:01 p.m., Ben Bolker wrote:



On 12/12/20 5:50 PM, Duncan Murdoch wrote:

On 12/12/2020 4:08 p.m., Spencer Graves wrote:

Hi, Ben et al.:


On 2020-12-12 13:43, Ben Bolker wrote:

     Apologies if I'm telling you something you already know:

     By default, fda::CRAN() uses the presence of environment 
variables
matched by the regexp "^_R_" as a heuristic to decide whether it's 
being

running on CRAN.

     testthat::skip_on_cran()  calls testthat::on_cran() to look 
for an

environment variable called NOT_CRAN equal to "true". The
devtools::check() machinery automatically sets this variable.



   > testthat::on_cran
Error: 'on_cran' is not an exported object from 'namespace:testthat'


   Besides, on my Mac, I get:


   > testthat:::on_cran()
[1] TRUE


   My Mac is NOT CRAN, and I don't want that function to return
TRUE on
my computer unless I explicitly run "R CMD check --on-cran".


     So: fda::CRAN() depends on breakable assumptions, defaults to 
FALSE

in an empty environment.  skip_on_cran() defaults to TRUE in an empty
environment (but defaults to FALSE in a devtools::check() 
environment).


   If future changes break fda::CRAN, I will have to deal with it
then.


   I'd be happier if the CRAN maintainers would develop a 
procedure to

make it easier for package maintainers do two things:


 * Include tests in their package that run longer than the
time
limit permitted on CRAN.


That's very easy now.  Just put them in a "slowtests" directory, and
tell R CMD check to use that.  How could it be easier?


 How would you do that?  In "R CMD check --help" I see that one can
use --test-dir= to specify the test directory, but I don't see a way to
specify _additional_ test directories; short of setting a tests/
directory with CRAN-specific tests and a slowtests/ directory with
*both* CRAN-specific and CRAN-excluded tests (thus duplicating files,
which seems clunky), I don't see how to do this within a standard R CMD
check framework (without testing a CRAN-indicating environment variable,
which gets us back where we started ...)  Or would you run R CMD check
twice, once without and once with --test-dir=slowtests ?


What I would do is have the slowtests run the regular tests.  So if I 
want both, I run slowtests.  If I want just the fast ones, I don't 
specify.  I can't think why I wouldn't want to run the slow ones without 
the fast ones, but if I did, it's not too hard to figure out a scheme 
that runs fast by default, slow when requested, and both if you request 
that instead.




    There doesn't seem to be very much in "Writing R Extensions" about
testing - a little bit in
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-subdirectories 



    What am I missing?

   Just to clarify, the ideal would be to be able to designate a separate
set of tests that were *not* run on CRAN, and to be able to run them in
the same "R CMD check" pass as the CRAN-specific tests. 


Yes, do that as described above.

There are a

bunch of ways to achieve this, but I think Spencer is saying (and I
agree) that it would be nice if it were there an official mechanism that
made this easier (and it seems pretty easy if the CRAN maintainers were
agreeable to the idea ...


There is such a mechanism, and I've just described it (and not for the 
first time; it's also described in WRE).  I think the problem is that 
you and Spencer are looking for something that's more complicated.  It 
doesn't need to be complicated.



	  I want to put all the tests of a particular function in the 
"\examples" section.  If some things are too pedantic to show to a user, 
I can put them in "\dontshow".  If they run too long for CRAN, I wrap 
them in "if(!fda::CRAN()){...}", as I previously noted.



	  Putting slow tests in a "slowtest" directory to me violates a 
sensible rule of documentation, because it makes it harder to think 
about how complete a test suite is.



	  I probably should not broaden this discussion to include "\dontrun", 
but I will:  I think any example in "\dontrun" should be made to work 
and wrapped in something like "if(!fda::CRAN()){...}" if you don't want 
it to be run on CRAN, where you don't care if it breaks or not.  I've 
read too many books with examples that didn't work!  The "fda" package 
has 76 reverse dependencies.  I think most of those are attributable to 
the quality of the fundamental ideas, but I'd like to think that some of 
them are because I insisted in included decent unit tests in the 
"\examples" -- AND because I insisted on make sure all but a couple of 
the examples in the book actually worked!



	  Thanks very much to everyone who has contributed to this thread.  I 
don't think we've reached a consensu

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

[Spencer Graves]

Hi, Ben et al.:


On 2020-12-12 13:43, Ben Bolker wrote:

   Apologies if I'm telling you something you already know:

   By default, fda::CRAN() uses the presence of environment variables 
matched by the regexp "^_R_" as a heuristic to decide whether it's being 
running on CRAN.


   testthat::skip_on_cran()  calls testthat::on_cran() to look for an 
environment variable called NOT_CRAN equal to "true". The 
devtools::check() machinery automatically sets this variable.



> testthat::on_cran
Error: 'on_cran' is not an exported object from 'namespace:testthat'


  Besides, on my Mac, I get:


> testthat:::on_cran()
[1] TRUE


	  My Mac is NOT CRAN, and I don't want that function to return TRUE on 
my computer unless I explicitly run "R CMD check --on-cran".



   So: fda::CRAN() depends on breakable assumptions, defaults to FALSE 
in an empty environment.  skip_on_cran() defaults to TRUE in an empty 
environment (but defaults to FALSE in a devtools::check() environment).


  If future changes break fda::CRAN, I will have to deal with it then.


	  I'd be happier if the CRAN maintainers would develop a procedure to 
make it easier for package maintainers do two things:



		* Include tests in their package that run longer than the time 
limit permitted on CRAN.



		* Give error messages that the package maintainer wants to see but 
that should be suppressed on CRAN or when the user decides to run "R CMD 
check --as-cran".



	  In any event, I hope that I'll be able to continue using fda::CRAN as 
I have been.  If not, I will be forced to reduce the coverage of test 
suites everywhere I use fda::CRAN.  That in turn will make the code 
harder to maintain and more easily broken in ways that I can no longer 
easily test.



      Spencer


On 12/12/20 2:19 PM, Spencer Graves wrote:
   I have tests in my code to detect when something like that is 
not available.



   I also have code in "\examples" to skip tests that would 
encounter that.



   Hadley's "testthhat:skip_on_cran" is supposed to suppress tests 
like that on CRAN.  I have so far failed to understand how to use this 
function that Hadley wrote.  Instead, I use things like the following:



if(!fda::CRAN()){
# Code that I want to run everyplace that's NOT CRAN


}


   When I wrote "fda::CRAN", I was told that I shouldn't do it, 
but I didn't see a better option, and I've been using it for several 
years now without being given a reason to discontinue using it or 
(better?) being given an alternative that seems better to me.



   Spencer


On 2020-12-12 12:40, Michael L Friendly wrote:

Thanks, Dirk

Just to clarify--
In my packages, candisc, heplots, vcdExtra I have mostly 2D graphic 
methods, but some 3D methods that use

rgl.  I therefore put rgl into Suggests:

Could I solve this by making rgl a Depends: ?

-Michael


-Original Message-
From: Dirk Eddelbuettel 
Sent: Saturday, December 12, 2020 12:46 PM
To: Michael L Friendly 
Cc: r-package-devel@R-project.org; Prof Brian Ripley 

Subject: Re: [R-pkg-devel] CRAN packages suggesting other packages 
but not using them conditionally



On 12 December 2020 at 16:24, Michael L Friendly wrote:
| I got the email below concerning 3 of my packages but wonder if they
| are false alarms or if not, how to locate & fix the problem.
|
| This concerns packages: ...
|
| Suggested packages should be used conditionally: see  1.1.3.1 
of 'Writing R Extensions'.  Some of these are hard to install on a 
platform without X11 such as M1 Macs: see the logs at 
https://www.stats.ox.ac.uk/pub/bdr/M1mac/.

|
| You can check all of the suggested packages by setting 
environment variable _R_CHECK_DEPENDS_ONLY_=true  -- see 
https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#Tools .

|
| Is this a false alarm?
|
| In each case, the outfile contains:
|
| * checking package namespace information ... OK
| * checking package dependencies ... NOTE
| Package suggested but not available for checking: 'rgl'
|
| indicating that rgl is not avaiable on the testing machine.  Then,
| when checking examples an error is triggered when an example calls 
something that requires rgl.

|
| >
| > heplot3d(Adopted.mod, hypotheses=list("Reg"=c("AMED", "BMIQ")),
| + col = c("red", "blue", "black", "gray"), wire=FALSE)
| Loading required namespace: rgl
| Failed with error:  'there is no package called 'rgl''
| Error in heplot3d.mlm(Adopted.mod, hypotheses = list(Reg = 
c("AMED", "BMIQ")),  :

|   rgl package is required.
| Calls: heplot3d -> heplot3d.mlm
| Execution halted
|
| Yet, heplot3d seems to contain the required way to refer to the 
suggested rgl package:

|
| if (!requireNamespace("rgl")) stop("rgl

[R-pkg-devel] "--resave-data" doesn't work

[Spencer Graves]

Hello:


	  With "R CMD check Ecdat_0.3-8.tar.gz" both locally (under macOS 
10.15.7 with R 4.0.3) and with Travis (below), I'm getting "Warning: 
large data files saved inefficiently: ...  significantly better 
compression could be obtained by using R CMD build --resave-data".  This 
is AFTER I do "R CMD build Ecdat --resave-data".



  What do you suggest I do to get past this problem?


  Thanks,
  Spencer Graves


p.s.  My ".travis.yml" file ends with "r_build_args: --resave-data".  I 
had trouble with this a year ago, and I think it was fixed then, as 
documented in:



https://travis-ci.community/t/how-to-add-resave-date-to-r-cmd-build-in-travis/5708


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Re: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Spencer Graves]

Have you followed the advice in chapter 20 of Wickham and Bryan, R 
Packages:



https://r-pkgs.org/release.html


	  In particular, does your package include a file "cran-comments.md", 
as described therein?



  I believe that's where the CRAN maintainers look for info like that.


	  Also, those instructions suggest you check reverse dependencies.  The 
last time I tried to follow those instructed, it didn't work.  Instead I 
needed:



https://github.com/r-lib/revdepcheck


devtools::install_github("r-lib/revdepcheck")


library(revdepcheck)


revdep_check()


  Hope this helps.
  Spencer Graves


On 6/22/21 6:53 AM, Alberto Garre wrote:

Thanks. I just "replied-to-all" again. Gmail then sends the email to
cran-submissi...@r-project.org. Is this the correct address?

El mar, 22 jun 2021 a las 12:38, Georgi Boshnakov (<
georgi.boshna...@manchester.ac.uk>) escribió:


... Hence please reply-all and explain: Have these been fixed?


Maybe 'reply-all' to CRAN team's  email?

Georgi Boshnakov

-Original Message-
From: R-package-devel  On Behalf
Of Alberto Garre
Sent: 22 June 2021 09:11
To: R-package-devel@r-project.org
Subject: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN
version of a package

Hi,

I submitted yesterday a new version of the biogrowth package (
https://cran.r-project.org/package=biogrowth). In the automatic response,
I got the following message:

The auto-check found additional issues for the *last* version released on
CRAN:
   donttest <https://www.stats.ox.ac.uk/pub/bdr/donttest/biogrowth.out>
   M1mac <https://www.stats.ox.ac.uk/pub/bdr/M1mac/biogrowth.out>
CRAN incoming checks do not test for these additional issues.
Hence please reply-all and explain: Have these been fixed?

I resubmitted mentioning in cran-comments.md that these problems had been
resolved, but I got again the same automatic response. Then, I answered
directly to the automatic email with no effect.

How should I communicate these issues have been fixed? Is there any
additional issue I am not seeing?

Thank you,
Alberto

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[R-pkg-devel] autotesting on GitHub with Travis or ...?

[Spencer Graves]

Hello, All:


	  What are the current recommendations for automatic testing of an R 
package on GitHub?



	  Section 19.3 in the current version of "R Packages" describes 
"Checking after every commit with Travis".  It recommends Travis.  It 
says to use Travis, first "Run usethis::use_travis()".[1]



	  However, 'help("use_travis", package="usethis")' says it's 
deprecated, but I don't understand what is recommended as an alternative.



  What do you suggest?


  Thanks,
  Spencer Graves


[1]
https://r-pkgs.org/r-cmd-check.html?q=travis#travis

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Re: [R-pkg-devel] autotesting on GitHub with Travis or ...?

[Spencer Graves]

Hi, Ben:


  Thanks very much.


  This fixed my problem.


	  For others who may be reading this later, I missed a couple of points 
when first working through 
"https://deanattali.com/blog/migrating-travis-to-github/":



* On first pass, I missed the need to "git add" and "git commit" .github".


* And when using "usethis::use_readme_rmd()", I initially missed the 
need to "knit" the file to produce the README.md.



  Spencer Graves


On 5/13/21 7:04 PM, Ben Bolker wrote:

   GitHub Actions

   ?usethis::use_github_action

   Probably start here if you are moving from Travis: 
https://deanattali.com/blog/migrating-travis-to-github/


On 5/13/21 8:00 PM, Spencer Graves wrote:

Hello, All:


   What are the current recommendations for automatic testing of 
an R package on GitHub?



   Section 19.3 in the current version of "R Packages" describes 
"Checking after every commit with Travis".  It recommends Travis.  It 
says to use Travis, first "Run usethis::use_travis()".[1]



   However, 'help("use_travis", package="usethis")' says it's 
deprecated, but I don't understand what is recommended as an alternative.



   What do you suggest?


   Thanks,
   Spencer Graves


[1]
https://r-pkgs.org/r-cmd-check.html?q=travis#travis

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Re: [R-pkg-devel] \donttest{} and writing outputs to tempdir()

[Spencer Graves]

	  You surely should be able to have some examples that would run in 
less than 5 seconds.



	  I almost never use "donttest".  Instead I use conditional skips, and 
those only on examples that I believe are likely to run too long.  In 
those cases, I believe the standard recommendation is:



testthat::skip_on_cran


https://testthat.r-lib.org/reference/skip.html


HOWEVER:  To use this, users must manually set Sys.getenv("NOT_CRAN") to 
"true" if they want the tests to run in environments that are not CRAN. 
 I don't perceive the documentation on this to be adequate;  I'd rather 
not have to set an environment variable in every new environment that 
I'd like to have run all the tests.  Therefore, some years ago, I added 
a CRAN function to the fda package, which I use as follows:



if(!fda::CRAN()){

# code I don't want to run on CRAN
# but do want to run elsewhere.
# You can use:
# R CMD check --as-cran
# to see if it works OK on CRAN


}


  Spencer


On 6/2/21 12:29 AM, Jeff Newmiller wrote:

Make examples shorter so they can run faster. Wrapping everything in donttest 
means that running examples() does nothing, which is counterproductive.

Techinically, vignettes are not tests or examples... but they do have the 
advantage that they don't have to run quickly. But that doesn't make a vignette 
a substitute for either examples or tests.

As for writing to the wrong place, you should probably just double check.

On June 1, 2021 9:39:43 PM PDT, Danielle Maeser  wrote:

Hello,

I received the following comments from a CRAN maintainer, and I don't
understand why they were an issue. I'd appreciate any insight you can
provide.

Danielle







*All your examples are wrapped in \donttest{} and therefore do not
gettested.Please unwrap the examples if that is feasible and if they
can
beexecuted in < 5 sec for each Rd file or create additionally small
toyexamples to allow automatic testing.*

I don't think I can unwrap the examples in \donttest{} because they
cannot
be executed in <5 seconds for each Rd file, and the automatic testing
of
toy data is satisfied in the vignettes I provide for each function.
Therefore, I am not sure what change to make here.




*Please ensure that your functions do not write by default or in
yourexamples/vignettes/tests in the user's home filespace (including
thepackage directory and getwd()). This is not allowed by CRAN
policies.In
your examples/vignettes/tests you can write to tempdir().*

Additionally, all of my vignettes write the output of each function to
tempdir(). Therefore, I am not sure why this is a problem.




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Re: [R-pkg-devel] Question about preventing CRAN package archival

[Spencer Graves]

	  The CRAN maintainers almost certainly have tried to contact the 
maintainer.  You can ask if he plans to fix the bug.  If not, if it's 
that easy to fix, you could offer to both the maintainers of both 
matrixcalc and CRAN to take over maintenance.



  Spencer


On 6/2/21 2:41 PM, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:

After looking up matrixcalc on CRAN,  I would recommend contacting the 
maintainer,  who is listed as:


Frederick Novomestky 



The reason I say this is what is blowing up the package in the nightly builds 
is a careless error in one Example:


   > x <- matrix( c( 2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3 ), nrow=4, ncol=4, 
byrow=TRUE )
 Error in matrix(c(2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3), nrow = 4, ncol = 4, 
:
  data length differs from size of matrix: [12 != 4 x 4]



That should be pretty easy for the maintainer to fix and to resubmit.

-Roy



On Jun 2, 2021, at 10:36 AM, Ben Staton  wrote:

My package uses the MIT license, so would that not meet the compatibility
requirements?

I will attempt to reach out to the package author - thanks for your help!

On Wed, Jun 2, 2021 at 10:31 AM Ben Bolker  wrote:


That all sounds exactly right.
   GPL >= 2 allows you to use the material without asking permission as
long as your package is compatibly licensed (e.g. also GPL).
   Under normal circumstances it would be polite to ask permission, but
if the reason for doing this is that the maintainer is unreachable in
the first place ...

  If you want to try a little harder, it seems quite possible that you
can reach the matrixcalc maintainer at the (personal) e-mail address
shown in this page:

https://www.facebook.com/photo/?fbid=10208324530363130=ecnf.1000413042

   (Possibly an identity confusion, but I rate that as unlikely based on
other facebook snooping)

   I don't think a short, polite e-mail request would be out of bounds,
they can always ignore it or tell you to go away.

   cheers
Ben Bolker

On 6/2/21 1:15 PM, Ben Staton wrote:

Hello,

Thank you for your detailed list of solutions.

I was initially tempted to go with option 1 (move matrixcalc to suggests
and check for its existence before using functions that rely on it), but

as

mentioned, this is not a long term fix.

I unfortunately can't take on the responsibilities of option 2 (becoming
the package maintainer) -- there is much that this package does that I do
not understand, and do not wish to feign authority!

I plan to take option 3 (copy the needed functions into my package).

There

are only three functions I need from matrixcalc, and all three are fairly
simple (is.square.matrix
,
is.symmetric.matrix
, and
is.positive.definite
) and

there

is only one function in postpack that needs them. I plan to define them
within the postpack function. matrixcalc is licensed under GPL >= 2 and
based on my scan of the license text, this is allowed. Is that correct?

Regarding option 4 (contacting the matrixcalc maintainer), the original
email from CRAN mentioned that they have attempted to contact the package
author with no response.

Thank you!

On Wed, Jun 2, 2021 at 9:52 AM J C Nash  wrote:


I just downloaded the source matrixcalc package to see what it

contained.

The functions
I looked at seem fairly straightforward and the OP could likely develop
equivalent features
in his own code, possibly avoiding a function call. Avoiding the

function

call means NAMESPACE etc. are not involved, so fewer places for getting
into
trouble, assuming the inline code works properly.

JN


On 2021-06-02 12:37 p.m., Duncan Murdoch wrote:

On 02/06/2021 12:13 p.m., Ben Staton wrote:

Hello,

I received an email notice from CRAN indicating that my R package
('postpack') will be archived soon if I do not take any action and I

want

to avoid that outcome. The issue is not caused by my package, but

instead a

package that my package depends on:

"... package 'matrixcalc' is now scheduled for archival on 2021-06-09,
and archiving this will necessitate also archiving its strong reverse
dependencies."

Evidently, xyz has been returning errors on new R builds prompting

CRAN

to

list it as a package to be archived. My package, 'postpack' has
'matrixcalc' listed in the Imports field, which I assume is why I

received

this email.

I want to keep 'postpack' active and don't want it to be archived. I

still

need package 'matrixcalc' for my package, but not for most functions.

Could

I simply move package 'matrixcalc' to the Suggests list and submit the

new

version to CRAN to remove the "Strong Reverse Dependency" issue that
triggered this email to avoid CRAN from archiving my package?


That's part of one solution, but not the best solution.

If you move it to Suggests, you should make sure that your package

checks for it 

Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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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[R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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?
  Thanks,
  Spencer Graves

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Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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:  ... build_package -> with_envvar -> force -> 
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=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

Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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=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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Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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:  ... build_package -> with_envvar -> force -> 


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=github-actions;, 



as suggested in line 2 of "~/.github/workflows/R-CMD-check.yaml".  See:


   Spencer


On 5/23/21 11:03 AM

Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

Hi, Duncan:


	  I apologize for bothering you with such an obvious thing as using 
"CRAN() before library(sos)".



	  Now I have another problem:  "zq <- ???spline(2)" now retrieves the 
default 100 pages, not the 2 requested.



	  I think the processing of "???" has changed between 4.0.3 and 4.1.0. 
 I've done "debug(`?`)" in both 4.0.3 and 4.1.0:  The condition 
(!is.call(topicExpr1) || length(topicExpr1) != 2 || topicExpr1[[1]] !=

"?" || !is.call(topicExpr1[[2]]) || length(topicExpr1[[2]]) !=
2 || topicExpr1[[2]][[1]] != "?") evaluates initially to FALSE in 
4.0.3 but TRUE in 4.1.0.



	  You graciously contributed that code several years ago when I changed 
the name of the package from RSiteSearch to sos, and it has worked 
wonderfully ... until now.  If you don't have time to look at this, I 
will try to understand it and fix it myself.  However, I really don't 
understand the code, and you certainly did when you wrote it ;-)



  Thanks,
  Spencer Graves


On 5/24/21 10:35 AM, Duncan Murdoch wrote:

On 24/05/2021 10:17 a.m., Spencer Graves wrote:

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?


This one is easy.  You use CRAN() before library(sos).




  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.

I wouldn't call it "complex", but it could be tedious.

Duncan Murdoch


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Re: [R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Spencer Graves]

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:  ... build_package -> with_envvar -> force ->

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 suggest

Re: [R-pkg-devel] Change package maintainer

[Spencer Graves]

	  I can suggest one example: multcompView:  I created it during or 
before 2006 and passed it during or before 2011 to Luciano Selzer 
.  I do not remember the exact process, and 
procedures could have changed since then.  However, I think I remember 
communicating with the CRAN maintainers after Selzer and I agreed he 
would take it over.  Beyond that, I see that the DESCRIPTION file for 
multicompView0.1-3 lists BOTH of us as Maintainer.  The version before 
that lists me only, and the one after lists him.[1]



	  Second, last September, Brian Ripley sent an email to 50 different 
people saying gdata had problems, the maintainer had not responded, and 
it was scheduled to be archived along with all its strong reverse 
dependencies on 2020-09-25.  I don't know what happened from that except 
that the package is still on CRAN with date Published: 2017-06-06, but 
my Ecfun package no longer uses it.



	  Beyond that, I'm pretty sure that anyone can adopt a package in the 
archives that is no longer on CRAN and resurrect it if you agree to fix 
the problems.  However, you should discuss with the CRAN maintainers.



  Spencer


[1]
https://cran.r-project.org/src/contrib/Archive/multcompView/


On 7/2/21 5:30 AM, Lluís Revilla wrote:

Hi,

I agree that the email handshake is the best approach (and very
reasonable to expect it).
I thought that maybe in cases like this there was a waiting period
and/or multiple attempts to contact the maintainer and someone on the
mailing list might have had some experience with the process.
When I'm ready to take over the package I will ask the CRAN team and
give them more details.

Many thanks to all.

Lluís Revilla

On Fri, 2 Jul 2021 at 08:38, Uwe Ligges  wrote:




On 01.07.2021 23:52, Duncan Murdoch wrote:

On 01/07/2021 3:11 p.m., Dirk Eddelbuettel wrote:


On 1 July 2021 at 20:00, Lluís Revilla wrote:
| I have a question related to changing maintainers.
| What happens when the old/current maintainer does not respond to
| emails or other methods of contact?
| Would the new maintainer need to wait until the package is removed
| from CRAN to submit it again?

Not speaking for CRAN here but my understanding always was that a full
and
complete 'email handshake' with both old and new maintainer was strongly
preferred / the default simply to prevent misunderstandings or
shenanigans.


I'd agree in the normal case where the package is still active on CRAN.

In the case where a package has unaddressed issues with no response to
CRAN from the maintainer, they'd probably be quite happy to have someone
volunteer to take over.


... and if in doubt, ask the CRAN team and give them details.

Best,
Uwe Ligges



Duncan Murdoch

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[R-pkg-devel] Warning in dir.create(vd2 <- "vign_test") : 'vign_test' already exists

[Spencer Graves]

Hello, All:


	  "R CMD check Ecfun_0.2-5.tar.gz" with R 4.1.0 under macOS 11.4 gave 
"Warning in dir.create(vd2 <- "vign_test") : 'vign_test' already 
exists".  It ultimately said, "Status: OK", so maybe I shouldn't worry 
about it.  It's available at:



https://github.com/sbgraves237/Ecfun


	  This passed all 4 GitHub Actions, so maybe I should not worry about 
this.



  Comments?
  Thanks,
  Spencer Graves


sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.1/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
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0

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Re: [R-pkg-devel] [External] Re: What is a "retired"package?

[Spencer Graves]

On 9/22/21 2:38 AM, Martin Maechler wrote:

Lenth, Russell V
 on Tue, 21 Sep 2021 18:43:07 + writes:


 > As I suspected, and a good point. But please note that the term "retired" causes 
angst, and it may be good to change that to "superceded" or something else.

well,  some of us will  become "retired" somewhere in the
future rather than "superseded" .. ;-)



yes, but we'll become "superseded" long before we want to admit it ;-)



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[R-pkg-devel] doi confusion and Data codoc mismatches

[Spencer Graves]

Hello, All:


	  The latest checks on 
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true; 
identify two problems I don't know how to fix:



FIRST:  Data codoc mismatches from documentation object 'USnewspapers':
  Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
  Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
  Population_M RevenuePerCap_2012 RevenuePerCap_nominal
  Revenue_G2012dollars Revenue_currentGdollars Year
  newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
  Revenue_G2012dollars Revenue_currentGdollars AdsProportion
  Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
  RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP


	  I believe that the column names in the data.frame 'USnewspapers' 
match the names in the order given in the *.Rd file and the variable 
list following "Code" here matches that following "Docs" using, e.g., 
sort(scan(what=character())).



SECOND:  Found the following URLs which should use \doi (with the DOI 
name only):

File 'AccountantsAuditorsPct.Rd':
  https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
  https://doi.org/10.18128/D010.V10.0


	  My concern here is that these two urls are in, e.g., 
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to 
link to the doi url}.  If it were, e.g., 
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with 
\doi{10.18128/D010.V8.0}.  However, if I do that, I don't know what to 
do with the "text to display to click to link to the doi url".



      Thanks,
  Spencer Graves

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[R-pkg-devel] doi confusion and Data codoc mismatches-confusing check

[Spencer Graves]

Hello, All:


	  The latest checks on 
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true; 
identify two problems I don't know how to fix:



FIRST:  Data codoc mismatches from documentation object 'USnewspapers':
  Variables in data frame 'USnewspapers'
Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
  Circ_G2012dollars Circ_currentGdollars GDP_G2012 GDP_nominalG
  Population_M RevenuePerCap_2012 RevenuePerCap_nominal
  Revenue_G2012dollars Revenue_currentGdollars Year
  newspapers_p_GDP
Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
  Revenue_G2012dollars Revenue_currentGdollars AdsProportion
  Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
  RevenuePerCap_2012 RevenuePerCap_nominal Year newspapers_p_GDP


	  I believe that the column names in the data.frame 'USnewspapers' 
match the names in the order given in the *.Rd file and the variable 
list following "Code" here matches that following "Docs" using, e.g., 
sort(scan(what=character())).



SECOND:  Found the following URLs which should use \doi (with the DOI 
name only):

File 'AccountantsAuditorsPct.Rd':
  https://doi.org/10.18128/D010.V8.0
File 'OCC1950.Rd':
  https://doi.org/10.18128/D010.V10.0


	  My concern here is that these two urls are in, e.g., 
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to 
link to the doi url}.  If it were, e.g., 
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with 
\doi{10.18128/D010.V8.0}.  However, if I do that, I don't know what to 
do with the "text to display to click to link to the doi url".



NOTE:  I tried changing \href{}{} to \doi{}{} in 
'AccountantsAuditorsPct.Rd' and got what I expected:  First, I failed to 
mention before that this complaint does NOT appear in R CMD check on my 
local computer;  see sessionInfo() below.  when I checked how that doi 
reference displayed in Ecdat-manual.pdf, I found that "doi: 
10.18128/D010.V8.0" was displayed, followed by the "text to display to 
click to link to the doi url".



Specifically, I got:


Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer, 
Jose Pacas, and Matthew Sobek (2018) doi: 10.18128/D010.V8.0IPUMS USA: 
Version 8.0 [dataset]. Minneapolis, MN: IPUMS.



	  With \href{}{}, "doi: 10.18128/D010.V8.0" does not appear, and I get 
that URL by clicking on "IPUMS USA: Version 8.0 [dataset]. Minneapolis, 
MN: IPUMS."  With this version, clicking on "IPUMS USA: Version 8.0 
[dataset]. Minneapolis, MN: IPUMS." does nothing, whild clicking on 
"doi: 10.18128/D010.V8.0" takes me to that URL.



	  This looks like a change to how *.Rd files are rendered that has 
appeared in the process on GitHub but not in my local computer.  ???



  Thanks,
  Spencer Graves


> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6.2

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.1/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
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2

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Re: [R-pkg-devel] doi confusion and Data codoc mismatches--AND THE VALUE OF GITHUB

[Spencer Graves]

	  Thanks to Duncan and Kurt for looking into this, recommending a patch 
for my code, and implementing a change to codocData.



VALUE OF GITHUB:  This exchange illustrates the value of GitHub:


	  1.  It made it easier for Duncan to diagnose the problem and 
recommend fixes both to me and to Kurt.



	  2.  I missed this email when it arrived five days after my post but 
found it after noticing a pull request from Duncan on GitHub.  I 
implemented it, and it worked!  Then I checked for a reply to my earlier 
post, and found Duncan's comment below.



  Spencer


On 1/1/22 1:11 PM, Duncan Murdoch wrote:

On 26/12/2021 8:03 a.m., Duncan Murdoch wrote:

I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.


And this patch was committed to the trunk by Kurt Hornik, so it should 
appear in R 4.2.0 or maybe some 4.1.x release.  Thanks Kurt!


Duncan Murdoch



Duncan Murdoch


On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:

On 26/12/2021 12:07 a.m., Spencer Graves wrote:

Hello, All:


  The latest checks on
"https://github.com/sbgraves237/Ecdat/runs/4634725654?check_suite_focus=true; 


identify two problems I don't know how to fix:


FIRST:  Data codoc mismatches from documentation object 'USnewspapers':
  Variables in data frame 'USnewspapers'
    Code: AdsProportion Ads_G2012dollars Ads_currentGdollars
  Circ_G2012dollars Circ_currentGdollars GDP_G2012 
GDP_nominalG

  Population_M RevenuePerCap_2012 RevenuePerCap_nominal
  Revenue_G2012dollars Revenue_currentGdollars Year
  newspapers_p_GDP
    Docs: Ads_G2012dollars Circ_G2012dollars Circ_currentGdollars
  Revenue_G2012dollars Revenue_currentGdollars 
AdsProportion

  Ads_currentGdollars GDP_G2012 GDP_nominalG Population_M
  RevenuePerCap_2012 RevenuePerCap_nominal Year 
newspapers_p_GDP



  I believe that the column names in the data.frame 'USnewspapers'
match the names in the order given in the *.Rd file and the variable
list following "Code" here matches that following "Docs" using, e.g.,
sort(scan(what=character())).


You can debug this by running tools::codocData("Ecdat") after the
package is installed.  It appears that some of the names in the docs are
picking up newlines, specifically the ones documented like this:

\item{Ads_currentGdollars,
 Ads_G2012dollars,
 Circ_currentGdollars,
 Circ_G2012dollars,
 Revenue_currentGdollars,
 Revenue_G2012dollars}

I think that's a bug in codocData.  A workaround is to put those all on
one line.  You don't get a "line too long" warning, because they'll be
reformatted in the display.




SECOND:  Found the following URLs which should use \doi (with the DOI
name only):
    File 'AccountantsAuditorsPct.Rd':
  https://doi.org/10.18128/D010.V8.0
    File 'OCC1950.Rd':
  https://doi.org/10.18128/D010.V10.0


  My concern here is that these two urls are in, e.g.,
\href{https://doi.org/10.18128/D010.V8.0}{text to display to click to
link to the doi url}.  If it were, e.g.,
\url{https://doi.org/10.18128/D010.V8.0} I would try replacing it with
\doi{10.18128/D010.V8.0}.  However, if I do that, I don't know what to
do with the "text to display to click to link to the doi url".


The first of those links to a page with this version of the reference:

Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer,
Jose Pacas, and Matthew Sobek. Integrated Public Use Microdata Series:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0


You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as

 Steven Ruggles, Sarah Flood, Ronald Goeken,
   Josiah Grover, Erin Meyer, Jose Pacas, and
   Matthew Sobek (2018)
IPUMS
   USA: Version 8.0 [dataset]. Minneapolis, MN:
   IPUMS. \doi{10.18128/D010.V8.0}

Duncan Murdoch






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Re: [R-pkg-devel] URL syntax causes R CMD build failure - a fix

[Spencer Graves]

I've encountered similar issues. However, it has been long enough ago 
that I don't remember enough details to say more without trying to 
update my CRAN packages to see what messages I get and maybe researching 
my notes from previous problems of this nature. Spencer Graves



On 9/2/23 4:23 PM, Greg Hunt wrote:

The percent encoded characters appear to be valid in that URL, suggesting
that rejecting them is an error. That kind of error could occur when the
software processing them converts them back to a non-unicode character set.

On Sun, 3 Sep 2023 at 4:34 am, J C Nash  wrote:


I'm posting this in case it helps some other developers getting build
failure.

Recently package nlsr that I maintain got a message that it failed to
build on
some platforms. The exact source of the problem is still to be illuminated,
but seems to be in knitr::render and/or pandoc or an unfortunate
interaction.
An update to pandoc triggered a failure to process a vignette that had been
happily processed for several years. The error messages are unhelpful, at
least
to me,

 Error at "nlsr-devdoc.knit.md" (line 5419, column 1):
 unexpected end of input
 Error: pandoc document conversion failed with error 64
 Execution halted

Unfortunately, adding "keep_md: TRUE" (you need upper case TRUE to save it
when
there is no error of this type), did not save the intermediate file in this
case. However, searching for "pandoc error 64" presented one web page
where the author
used brute force search of his document by removing / replacing sections
to find
the line(s) that caused trouble. This is a little tedious, but effective.
In my
case, the offending line turned out to be a copied and pasted URL

https://en.wikipedia.org/wiki/Levenberg%E2%80%93Marquardt_algorithm

The coded characters can be replaced by a hyphen, to give,

https://en.wikipedia.org/wiki/Levenberg-Marquardt_algorithm

and this, when pasted in Mozilla Firefox at least, will go to the
appropriate
wikipedia page.

I'd be interested in hearing from others who have had similar
difficulties. I
suspect this is relatively rare, and causing some sort of infelicity in the
output of knitr::render that then trips up some versions of pandoc, that
may,
for instance, be now applying stricter rules to URL syntax.

Best,

John Nash

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Spencer Graves]

On 11/2/23 2:52 PM, Rolf Turner wrote:


On Wed, 1 Nov 2023 16:10:34 +
David Hugh-Jones  wrote:


Aside from the package question, surely the other issue here is that
Prof Ripley’s email is extraordinarily rude. Any paid employee would
be sacked for that. I appreciate R and CRAN are volunteer-run
organisations, but I don’t think that should be an excuse for this
level of, frankly, toxicity. Why is he allowed to get away with it?

David


I've just had a look at the initial posting in this thread

https://stat.ethz.ch/pipermail/r-package-devel/2023q4/009810.html

and can see nothing rude or offensive in the email from Prof. Ripley
that was copied and pasted into that posting.

I find *your* email far more offensive than anything that Prof. Ripley
has ever written.  Get a life.

cheers,

Rolf Turner

P.S.  See fortunes::fortune(88).

R. T.



Hi, David:


	  You do, of course, know that "Ripley" is a verb? People on this list 
take pride in how many times they've been Ripleyed ;-)



	  I've been in the military, and I've learned to ignore the tone and 
look for the value in comments I receive. I've learned a lot from 
Professor Ripley, and others. When the tone seemed less supportive or 
even insulting, I'm very glad the person took the time to comment and 
didn't decide not to reply for fear of offending me. I'm more productive 
and a better human for all the help I've gotten from this and other 
R-related lists.



fortunes::fortune('Spencer Graves')


  sg




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Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

[Spencer Graves]

	  Chapter 15 in Wickham and Bryan, R Packages, discuss "Advanced 
Testing Techniques". Their current section "15.4.1 Skip a test" includes 
the following:



test_that("some long-running thing works", {
  skip_on_cran()
  # test code that can potentially take "a while" to run
})


	  Have you tried writing directly to Jennifer Bryan 
? She and Hadley might be able to get help from the 
CRAN maintainers in getting help with this particular problem AND 
getting more documentation on this in their book ;-)



  hope this helps.
  spencer graves


On 10/24/23 6:03 AM, Greg Hunt wrote:

In my case recently, after an hour or so’s messing about I disabled some
tests and example executions to get rid of the offending times. I doubt
that i am the only one to do that.

On Tue, 24 Oct 2023 at 9:38 pm, Helske, Jouni  wrote:


Thanks for the help, I now tried resubmitting with
Sys.setenv("OMP_THREAD_LIMIT" = 2) at the top of the exchange example, but
I still get the same note:

Examples with CPU time > 2.5 times elapsed time
   user system elapsed ratio
exchange 1.196   0.04   0.159 7.774

Not sure what to try next.

Best,
Jouni

From: Ivan Krylov 
Sent: Friday, October 20, 2023 16:54
To: Helske, Jouni 
Cc: r-package-devel@r-project.org 
Subject: Re: [R-pkg-devel] Too many cores used in examples (not caused by
data.table)

В Thu, 19 Oct 2023 05:57:54 +
"Helske, Jouni"  пишет:


But I just realised that bssm uses Armadillo via RcppArmadillo, which
uses OpenMP by default for some elementwise operations. So, I wonder
if that could be the culprit?


I wasn't able to reproduce the NOTE either, despite manually setting
the environment variable
_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD=2 before running R CMD
check, but I think I can see the code using OpenMP. Here's what I did:

0. Temporarily lower the system protections against capturing
performance traces of potentially sensitive parts:

echo -1 | sudo tee /proc/sys/kernel/perf_event_paranoid

(Set it back to 3 after you're done.)

1. Run the following command with the development version of the
package installed:

env OPENBLAS_NUM_THREADS=1 \
  perf record --call-graph drawf,4096 \
  R -e 'library(bssm); system.time(replicate(100, example(exchange)))'

OPENBLAS_NUM_THREADS=1 will prevent OpenBLAS from spawning worker
threads if you have it installed. (A different BLAS may need different
environment variables.)

2. Run `perf report` and browse collected call stack information.

The call stacks are hard to navigate, but I think they are not pointing
towards Armadillo. At least, setting ARMA_OPENMP_THREADS=1 doesn't
help, but setting OMP_THREAD_LIMIT=1 does.

--
Best regards,
Ivan

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Re: [R-pkg-devel] GitHub error

[Spencer Graves]

Hi, Andrew:  Thanks.  I think that was exactly what I needed:  I was in 
particular unsure about "git push --force".  Spencer Graves



On 4/20/22 8:22 PM, Andrew Simmons wrote:

Not really the place for this type of thing, but here's what I'd do:

add .DS_Store to your .gitignore file, this should ignore both
.DS_Store and inst/.DS_Store
delete both .DS_Store files from your repository
then try to pull again. You can use --force in git push, that should
force them to combine, ignoring the overwrite warning

On Wed, Apr 20, 2022 at 9:17 PM Spencer Graves
 wrote:


Hello, All:


   When I do "git pull", I get "error: Your local changes to the
following files would be overwritten by merge: .DS_Store .gitignore
inst/.DS_Store".


   I've done "git rm --cached .DS_Store", etc., which some web page told
me would remove ".DS_Store" from GitHub but not from my local copy.
Then when I try, "git push", I get "! [rejected] // master -> master
(non-fast-forward) // error: failed to push some refs to
'github.com:JamesRamsay5/fda.git'".


   What do you suggest?  Manually delete those files from the GitHub
repository?


   Thanks,
   Spencer Graves


p.s.  This is with "https://github.com/JamesRamsay5/fda;.

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Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs

[Spencer Graves]

On 6/13/22 5:05 PM, Duncan Murdoch wrote:

On 13/06/2022 5:11 p.m., Spencer Graves wrote:



On 6/13/22 1:26 PM, Duncan Murdoch wrote:

On 13/06/2022 12:12 p.m., Spencer Graves wrote:

Hello, All:


   How do I fix "Rd cross-references ... NOTE
Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’,
‘TRAMPR’, ‘raster’ in Rd xrefs"?


   This occurs with
"https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecfun-00check.html; 



and with
"https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecdat-00check.html;. 



    However, this error is not raised on other platforms.  My search 
for

this note produced essentially the same message for other packages but
no advice on how to fix it.


   These are references to other packages that I do not use in my
packages but that some users may wish to consider.  If needed, I will
add them to "Suggests" for the packages.  However, that seems overkill,
because I do not use them myself.  ???


Section 2.5 of Writing R Extensions says "Packages referred to by these
‘other forms’ should be declared in the DESCRIPTION file, in the
‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields."  Of those
fields, Suggests looks like the best fit.  You'd use Enhances if your
package provides "methods for classes from these packages, or ways to
handle objects from these packages".



  GitHub Actions failed after I added those packages to Suggests:


https://github.com/sbgraves237/Ecfun/runs/6869516417?check_suite_focus=true 



That log doesn't really give much info about what went wrong.  Maybe 
some of the packages in the Suggests list weren't available?



	  Is there a way in GitHub Action to NOT fail when a package is not 
available -- or at least to give a more useful diagnostic?



	  There probably is, but I don't know how to find the right manual to 
read nor any better place to ask for help with that than here.



  Thanks, sg



Duncan Murdoch


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[R-pkg-devel] NOTE: Escaped LaTeX specials: \$

[Spencer Graves]

Hello, All:


	  CRAN checks of "Ecdat" on several platforms includes multiple "NOTEs" 
complaining "Escaped LaTeX specials" highlighting use of "\$", "\_", and 
"\&".[1]



  What do you suggest I do with these?


	  I could replace "\$1,000" with "1,000 US dollars", and "R\" could 
be replaced with "R and D".



	  However, a dataset "Benefits" includes a column that is "a factor 
with levels (slack\_work,position\_abolished,seasonal\_job\_ended,other)".



  ???
  Thanks,
  Spencer Graves


[1] e.g.:


https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/Ecdat-00check.html

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Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs

[Spencer Graves]

On 6/13/22 2:22 PM, Ivan Krylov wrote:

On Mon, 13 Jun 2022 13:59:24 -0500
Spencer Graves  wrote:


I probably should have just used "Suggests" and not
bothered this list with this issue.


Why not use the \link{foo} form and let the HTML help system resolve
the link at run time? Is it considered bad form to use unqualified
links to help pages in other packages?




	  The problem is that \link{foo} cannot distinguish between 
\link[a]{foo} and \link[b]{foo}.  Using "Suggests" sounds to me more 
like how how the R Core and CRAN teams probably think the system should 
work.



  But Duncan or someone else may think differently.


  Thanks, Spencer

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Re: [R-pkg-devel] Warning... unable to translate 'Ekstrm' to a wide string; Error... input string 1 is invalid

[Spencer Graves]

Hi, Ivan et al.:


On 7/19/22 1:03 PM, Ivan Krylov wrote:

On Tue, 19 Jul 2022 12:32:20 -0500
Spencer Graves  wrote:


Can someone provide me with a link to the correct development
version of help('iconv')?  The current version includes the exact
offending "\x" strings that I have.


http://svn.r-project.org/R/trunk/src/library/base/man/iconv.Rd

It still does, because it works with byte strings the right way: by
passing them to iconv(), which is designed to work with bytes in
"unknown" encodings.

In contrast, your use of arbitrary bytes with gsub() is invalid,
because gsub() assumes that the strings match their declared encoding:
UTF-8, Latin-1, or the native locale encoding. (See ?Encoding.)

When you write "Ekstr\xf8m", you get a string that consists of Latin-1
bytes but has the wrong encoding property set. Given this string,
gsub() and friends will break on a UTF-8 system (because "r\xf8m" is
not a valid UTF-8 sequence of bytes), while iconv() will not.

Depending on the desired semantics of subNonStandardCharacters(), you
might be able to avoid the failures with the useBytes argument, or you
might silently return invalid data in some corner cases. Is the "x"
argument supposed to be bytes in arbitrary encoding, or properly decoded
characters that might include those that don't map to ASCII?



  Wow.  So what's the recommended fix?


	  If I understand correctly, "\u**" should work with ** being f8, f6, 
df, or fc [all hex digits, I assume?].  However, "\u00**" may be 
preferred over "\u**", and "\u{**}" may be better still.



	  The blog that Tomas wrote might be more useful if it included a 
recommendation like this.



	  Thanks for all your work to make R better and thereby help people 
everywhere extract better information from the data available to them.



  Spencer

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[R-pkg-devel] Thanks -- success after 4 package submissions in 3 days

[Spencer Graves]

Hello, All:


	  Thanks to Uwe Ligges, Max Turgeon, Duncan Murdoch, Ivan Krylov, Jeff 
Newmiller, Ben Bolker, Bill Dunlap, and Tomas Kalibera, Ecfun 0.3-0 is 
now available on CRAN, after three earlier versions were rejected in 
three days due to my limited ability to understand the error messages I 
saw.



	  My excuse for being so dense is that all the problems I encountered 
were changes required to meet new, more stringent standards implemented 
to reduce ambiguity and tighten coding standards to convert more subtle, 
intermittent problems that are difficult to trace into coding errors 
that are more easily fixed.



  Spencer Graves


On 7/20/22 11:50 AM, Uwe Ligges wrote:
Or simply read ?news which explains how the three formats (plain text 
NEWS, NEWS.Rd and NEWS.md) should look like.


Best,
Uwe Ligges

On 20.07.2022 03:27, Max Turgeon wrote:

Hi Spencer,

This NOTE was discussed a couple weeks ago on this list, it's (as you 
may expect) a new check in R-devel. Here's what Ivan had to say: 
https://stat.ethz.ch/pipermail/r-package-devel/2022q3/008239.html


Others also chimed in, you can see the first message of the thread 
here: https://stat.ethz.ch/pipermail/r-package-devel/2022q3/008235.html


Good luck!


Max Turgeon<https://www.name-coach.com/maxime-turgeon>
Assistant Professor

Department of Statistics
University of Manitoba

maxturgeon.ca<http://maxturgeon.ca/>


From: R-package-devel  on 
behalf of Spencer Graves 

Sent: Tuesday, July 19, 2022 8:05 PM
To: List r-package-devel 
Subject: [R-pkg-devel] NOTE, Problems with news in 'NEWS.md':, No news 
entries found.



Caution: This message was sent from outside the University of Manitoba.


Hello, All:


   Winbuilder with R-Devel complains, " NOTE
Problems with news in 'NEWS.md': No news entries found." See below.


   What should I do with this?  Document it in 
"cran-comments.md" and

not worry about it otherwise?  Thanks,


   Spencer Graves


 Forwarded Message 
Subject: winbuilder: Package Ecfun_0.2-7.tar.gz has been checked and 
built

Date: Wed, 20 Jul 2022 00:22:40 +0200
From: lig...@statistik.tu-dortmund.de
To: spencer.gra...@effectivedefense.org
CC: lig...@statistik.tu-dortmund.de

Dear package maintainer,
   this notification has been generated automatically.
Your package Ecfun_0.2-7.tar.gz has been built (if working) and checked
for Windows.
Please check the log files and (if working) the binary package at:
https://win-builder.r-project.org/e3NjJDDwiq0Z
The files will be removed after roughly 72 hours.
Installation time in seconds: 16
Check time in seconds: 141
Status: 1 NOTE
R Under development (unstable) (2022-07-18 r82603 ucrt)
   All the best,
Uwe Ligges
(CRAN maintainer of binary packages for Windows)

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[R-pkg-devel] Problems with news in ‘NEWS’

[Spencer Graves]

Hello, All:


  devtools::check_rhub("Ecdat") complained:


Problems with news in ‘NEWS’:
   Cannot process chunk/lines:
 2022-10-12:
   Cannot process chunk/lines:
 Ecdat 0.4-2 updated "terrorism" to 2020.
...


  For more see below.  This is with the current version of


https://github.com/sbgraves237/Ecdat


  I copied NEWS to NEWS.md and tried to format it as described in:


https://r-pkgs.org/other-markdown.html#news


	  Sadly, I still get the same error.  It seems to be ignoring my 
NEWS.md file and continuing to tell me I haven't fixed NEWS.



  What do you suggest?
  Thanks,
  Spencer Graves


 Forwarded Message 
Subject:Ecdat 0.4-2: NOTE
Date:   Thu, 13 Oct 2022 00:55:10 +
From:   R-hub builder 
To: spencer.gra...@effectivedefense.org



Ecdat 0.4-2: NOTE

Ecdat 0.4-2: NOTE
*Build ID:* |Ecdat_0.4-2.tar.gz-aec6a2cb4b8a43cfbab0405f54e67c64|
*Platform:* Windows Server 2022, R-devel, 64 bit
*Submitted:*5 minutes 25 seconds ago
*Build time:*   5 minutes 16.2 seconds


  NOTES:

* checking package subdirectories ... NOTE
Problems with news in 'NEWS':
   Cannot process chunk/lines:
 2022-10-12:
   Cannot process chunk/lines:
 Ecdat 0.4-2 updated "terrorism" to 2020.
   Cannot process chunk/lines:
 2022-07-01:
   Cannot process chunk/lines:
 Ecdat 0.4-1 replaced non-breaking spaces that used Latin-1 
encoding with " " in 4 "demoFiles/NIPA6.16*.csv" files, because the said 
non-breaking spaces were not valid in UTF-8 and were rejected by a 
development version of R.

 2022-06-14:
   Cannot process chunk/lines:
 Ecdat 0.4-0 adds new datasets USnewspapers and USPS (US Postal 
Service) while adding federal government budget data to USGDPpresidents.

   Cannot process chunk/lines:
 2020-11-01:
   Cannot process chunk/lines:
 Ecdat 0.3-9 deletes ~demoFiles/*_data.xls, because they were used 
to test Ecfun::financialDataFiles and Ecfun::readFinancialDataFiles, and 
those two functions were removed, because they used gdata, which was not 
being maintained, and the work required to maintain them exceeded the 
current need of the maintainer.

   Cannot process chunk/lines:
 2020-02-08:  Ecdat 0.3-6 adds variables popM, popYr, GDP_B, and 
GDPyr to data set "nuclearWeaponStates".

   Cannot process chunk/lines:
 2019-12-05:  Ecdat 0.3-5 corrects the description of Crime$density 
to read, "hundreds of people per square mile" from "people per square 
mile".  Thanks to Yungfong "Frank" Tang for identifying this error and 
confirming the needed correction.

   Cannot process chunk/lines:
 2019-11-05:  Ecdat 0.3-4 adds variable 'firstTestYr' to 
'nuclearWeaponStates'.  It also corrects an error in the 'Mroz' data 
set, in that "work" had the names of the levels incorrectly swapped.

   Cannot process chunk/lines:
 Ecdat 0.3-3 adds data set "nuclearWeaponStates", which might be 
used to model the probability distribution of the time to the next new 
nuclear weapon state.

   Cannot process chunk/lines:

* checking for detritus in the temp directory ... NOTE
Found the following files/directories:
   'lastMiKTeXException'

See the full build log: HTML 
<https://builder.r-hub.io/status/Ecdat_0.4-2.tar.gz-aec6a2cb4b8a43cfbab0405f54e67c64>, 
text 
<https://builder.r-hub.io/status/original/Ecdat_0.4-2.tar.gz-aec6a2cb4b8a43cfbab0405f54e67c64>, 
artifacts 
<https://artifacts.r-hub.io/Ecdat_0.4-2.tar.gz-aec6a2cb4b8a43cfbab0405f54e67c64>. 

Have questions, suggestions or want to report a bug? Please file an 
issue ticket at GitHub <https://github.com/r-hub/rhub/issues>. Thank You 
for using the R-hub builder.


(c) 2016 The R Consortium

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Re: [R-pkg-devel] Problems with news in ‘NEWS’

[Spencer Graves]

On 10/13/22 4:34 AM, Ivan Krylov wrote:

В Wed, 12 Oct 2022 20:16:20 -0500
Spencer Graves  пишет:


I copied NEWS to NEWS.md and tried to format it as described in:


https://r-pkgs.org/other-markdown.html#news


  Sadly, I still get the same error.  It seems to be ignoring
my NEWS.md file and continuing to tell me I haven't fixed NEWS.


Does it help to remove the NEWS after you've created NEWS.md in the
root directory of your package? In theory, NEWS.md takes precedence
over everything except inst/NEWS.Rd, but maybe that's not the case when
checking the package.



Thanks.  I did that, and it worked.



For the record, both the plain text format R expects in the NEWS file
and the Markdown format for NEWS.md are described in help(news).



Thanks, I missed that reference but managed to find something that worked.


  Spencer

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Re: [R-pkg-devel] Misspelled words in descrition and tar.gz inside folder

[Spencer Graves]

Hello, Edward Wei:


	  Are you familiar with R Packages (2nd edition) Hadley Wickham and 
Jenny Bryan?



https://r-pkgs.org


	  This book is the most up-to-date information I know on preparing 
something for CRAN.  To your question specifically, I have a "WORDLIST" 
file in an "inst" folder.



	  Below please find notes I've prepared for myself on the various tests 
I've gotten from their book, etc.  The section numbers refer to an 
earlier version of this book.  Ignore or use with caution.



  Hope this helps.
  Spencer Graves


# File > "Open Project..." > [parent of Package file]

# https://r-pkgs.org/release.html

#20.1.  Pick a version number:
#   in DESCRIPTION: must be later than any version on CRAN
#20.3.  The submission process
#   Store submission comments in cran-comments.md
#20.3.1.  Test environments
# devtools::check_win_*()
dir()

PkgName <- "Ecdat"
PkgRegExpr <- paste0('^', PkgName, '$')
(Pkg <- dir(pattern=PkgRegExpr))

devtools::check_win_devel(Pkg)
devtools::check_win_release(Pkg)
devtools::check_win_oldrelease(Pkg)

# devtools::check_rhub(Pkg)
#Error in match_platform(platform) :
#   Unknown R-hub platform, see rhub::platforms() for a list
# on 2022-07-04.

# https://r-pkgs.org/release.html
# now recommends:

rhub::check(Pkg)

# Select
# 3.  Apple Silicon (M1), macOS 11.6 Big Sur, R-release 
(macos-m1-bigsur-release)

# This may not be correct:  I have mac)S 11.6.7 running an Intel core i7.


#20.3.3.  Reverse dependencies

# install.packages("revdepcheck")
#devtools::install_github('r-lib/revdepcheck')

# revdepcheck::revdep_reset(Pkg)

# revdepcheck::revdep_check(Pkg, num_workers = 4)

#20.4.  Update README.md and NEWS.md

#20.5.  Submit to CRAN

library(devtools)
# spell_check(Pkg)

release(Pkg)

#20.6.  Update the version number for the future
#20.7.  Publicise

#20.1.  Pick a version number:  in DESCRIPTION > what's on CRAN

#20.2.  Run & document R CMD check
# 2.1-0 because this is to match the move of
# the database maintenance to wu.ut.at

#20.3.  Check CRAN policies
#20.4.  Update README.md and NEWS.md
#20.5.  Submit to CRAN
#20.6.  Update the version number for the future
#20.7.  Publicise


On 8/9/22 3:38 PM, Edward Wei wrote:

Hello. Here is my "NOTE" message.

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Edward Wei ’

New submission

Possibly misspelled words in DESCRIPTION:
   alphavantager (8:3, 9:7)
   Alphavantager (7:32)
   api (7:58, 8:36)
   Avfintools (10:18)
   Vantager (3:55, 10:46, 11:56)

* checking top-level files ... NOTE
Non-standard file/directory found at top level:
   ‘avfintools.tar.gz’

My questions are:

1. My misspelled words are just referencing names of packages and
programming terms etc. Is there a way to get around this or should I omit
them from my description and put them somewhere else.

2. I wanted to confirm this, but the tar.gz for CRAN submission SHOULD NOT
be in the folder of the directory for my package.

Thanks for your time,

[[alternative HTML version deleted]]

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[R-pkg-devel] Current recommendations re. GitHub Action?

[Spencer Graves]

Hello, All:


  What are current recommendations for GitHub Action?


	  My most recent change to "sos" generated "Failed to get R" for 
ubuntu-latest (release, devel, and oldrel-1).



https://github.com/sbgraves237/sos/actions/runs/3820307473/jobs/6498527786


  I would happily rtfm if I only knew which fmtr.


  Thanks,
  Spencer Graves

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Re: [R-pkg-devel] Current recommendations re. GitHub Action?

[Spencer Graves]

On 1/2/23 12:38 PM, Dirk Eddelbuettel wrote:


As the error is common against your _all three_ of your Ubuntu runs, you
could consider the possibility that the events are correlated.  Most often it
simply means a (temporary, usually) network or server outage.  I would wait,
and then relaunch (which these days you can do just for the failed jobs).

It is also worth paying attention to warnings such as

Warning: r-lib/actions/setup-r@v1 is deprecated. Please update your
workflow to use the 'v2' version. Also look at the examples at
https://github.com/r-lib/actions/tree/v2/examples because '@v2' workflows
are much simpler than 'v1' workflows.



	  Thanks to Zhian Kamvar and Dirk Eddelbuettel for encouraging me to 
look at the warning.



	  I replaced a few lined of my "R-CMD-check.yaml" file with the the 
"v3" and "v2" versions in the example in 
"https://github.com/r-lib/actions/tree/v2/examples; and deleted 
subsequent lines that I didn't understand, and I got an instant failure: 
 It didn't run even one of the 5 tests.  Then I did "git revert" with 
the version number from GitHub and changed several lines to match the 
example with the succeeding yaml code.  GitHub Action ran and failed on 
all 5 platforms.  I did "git revert" with that and changed 
"r-lib/actions/setup-r@v1" to "r-lib/actions/setup-r@v2".  With that, 
R-release ran successfully on Unbuntu as well as Windows and macOS.



	  However, Ubuntu failed with devel and oldrel1, complaining, "there is 
no package called ‘rcmdcheck’".



  See:


https://github.com/sbgraves237/sos


  Suggestions?
  Thanks,
  Spencer Graves



Hth,  Dirk



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Re: [R-pkg-devel] Mysterious "invalid z limit"

[Spencer Graves]

On 1/8/23 11:36 AM, Kevin Coombes wrote:
I have been using R-Forge for many years for package development. And I 
have been using GitLab for other projects almost as long.


However, over the past few months, the R-Forge support seems to be 
decaying, and I now have several projects that won't currently build 
there because of various items that appear to need fixing at their end. 
So, I am actively exploring what it will take to move packages and 
projects to git.



	  R-Forge was wonderful for me when I started using it.  Then several 
years ago, I started having problems like you described.  A few years 
ago I migrated from R-Forge to GitHub.



	  One problem I encountered in the transition:  On R-Forge, I had 
multiple packages in the same R-Forge project.  I had to split them 
apart for GitHub.




I already know how to use a git client to clone a Subversion repository 
from R-Forge (using "git svn"). And how to change the remote origin to 
push it to a new git location. (And I  may also be willing to lose the 
revision history if it is going to make the transition easier.)


I am now at the step of understanding the recent changes at GitLab with 
respect to support for "Educational" or "Open Source" status, especially 
in terms of how many monthly minutes of CI/CD time I can use for free. 
When working on a new package, I tend to make lots of small 
commit-pushes, and it sounds like each one of those will eat up minutes. 
So, any advice on how to manage that issue would be greatly appreciated.



	  When I first got into Subversion, I remember Doug Bates saying, 
"Commit early and often."  The word "Commit" doesn't mean the same in 
Git as in Subversion, so I would encourage you to "Git push early and 
often."



	  There may be limits on free use of GitHub, but I'm not aware of them: 
 If you want a private account, you need to pay for that, but the 
charges for that are not much.



	  If anyone knows anything different from what I've just said, I hope 
they will disabuse my of this part of my ignorance.



      Spencer



Best,
   Kevin

On Sun, Jan 8, 2023, 11:30 AM Spencer Graves 
<mailto:spencer.gra...@effectivedefense.org>> wrote:


           If you use GitHub, I highly recommend using "GitHub
Action" as
described by Wickham and Bryan, R Packages:


https://r-pkgs.org/code.html#code-style
<https://r-pkgs.org/code.html#code-style>


           I'm not sure the best way to get it set up, but I have
all my
packages on GitHub configured so each "push" that changes anything has
"R CMD Check" run on 5 different platforms:  The release version of
R on
the latest Windows, macOS, and Ubuntu plus the development version and
the most recent old release on Ubuntu.  I rarely run R CMD check on my
local machine anymore:  I just "git commit" and "git push".  Then
GitHub
Action manages testing on those 5 platforms.


           To be precise, I do "git status" before "git push" to
make sure I
have "committed" everything I want to commit before I "git push". 
And I

do "git pull" to make sure a collaborator hasn't "pushed" something new
I should look at before I "git push".


           Finally, I want to thank again Gábor Csárdi who helped me
greatly get
past problems I hand with "GitHub Action" for my "sos" package.  He
provided example workflows in:


https://github.com/r-lib/actions/blob/v2-branch/examples/check-standard.yaml 
<https://github.com/r-lib/actions/blob/v2-branch/examples/check-standard.yaml>


           I also needed LaTeX support, for which Gábor suggested
the following:


https://github.com/r-lib/actions/tree/v2/setup-tinytex#ctan-packages
<https://github.com/r-lib/actions/tree/v2/setup-tinytex#ctan-packages>


           Spencer Graves


On 1/8/23 9:11 AM, Kevin R. Coombes wrote:
 > A very helpful answer. For some reason (probably because I have an
 > ancient perl script that automates the steps i take when building
and
 > checking packages), I keep forgetting that the "tools" package
let's me
 > do these things from within R.
 >
 > I had already isolated the offending line ("plot(obj)") inside
the chunk
 > where the error occurred, and removed any additional arguments. I
 > wrapped that line in a "try" command followed by a conditional
 > "traceback()" to find the problem.  This allowed the package
build to
 > knit the vignette and provide some feedback about what was going
on. It
 > turned out that I had copied and pasted an assignment line of the
form
 >
 > main