Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

2018-04-20 Thread Martin Maechler
> Thierry Onkelinx 
> on Fri, 20 Apr 2018 09:14:44 +0200 writes:

> Dear Alex, Another idea is to use pkgdown
> (http://pkgdown.r-lib.org) to convert all the
> documentation of your package (include the vignettes) into
> a website. Then you make that available to your students,
> e.g. through github pages.

Hmm, sounds nice .. at first:  In teaching (and research!) I particularly
emphasize people use CRAN (or Bioconductor) packages.

Why on earth is pkgdown not on CRAN ?

Martin Maechler
ETH Zurich

> Best regards,

> ir. Thierry Onkelinx Statisticus / Statistician

> Vlaamse Overheid / Government of Flanders INSTITUUT VOOR
> NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND FOREST Team Biometrie & Kwaliteitszorg / Team
> Biometrics & Quality Assurance thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel www.inbo.be

> 
///
> To call in the statistician after the experiment is done
> may be no more than asking him to perform a post-mortem
> examination: he may be able to say what the experiment
> died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote
> is not data. ~ Roger Brinner The combination of some data
> and an aching desire for an answer does not ensure that a
> reasonable answer can be extracted from a given body of
> data. ~ John Tukey
> 
///




> 2018-04-19 18:33 GMT+02:00 Alexandre Courtiol
> :
>> Thanks a lot Thierry, I was happy to discover and
>> implement a "drat" installation workflow.  Unfortunately
>> it did not solve the issue (but I will stick to drat).
>> Also, I checked the sessionInfo() and could not find any
>> package version discriminating accurately between
>> computers that shows vignettes from those who do not.
>> Only Windows computer have the issue but this proves
>> nothing (and other computers with the same OS version are
>> fine).  Goergi, I did not yet retried outside RStudio (I
>> am trying not to waste too much time at the beginning of
>> each course...  I wish I could hijack a problematic
>> laptop but they don't let me do it as they need them).
>> ++ Alex
>> 
>> 
>> On 17 April 2018 at 10:42, Thierry Onkelinx
>>  wrote:
>>> 
>>> Dear Alex,
>>> 
>>> Have a look at drat
>>> (http://eddelbuettel.github.io/drat/DratForPackageAuthors.html). This
>>> makes it easier to distribute prepackaged R packages
>>> (including When you uploaded a new version, then the
>>> student would only have to do drat::addRepo("your_repo")
>>> and then install.pakages("LM2GLMM") or update.packages()
>>> 
>>> Best regards,
>>> 
>>> ir. Thierry Onkelinx Statisticus / Statistician
>>> 
>>> Vlaamse Overheid / Government of Flanders INSTITUUT VOOR
>>> NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>>> AND FOREST Team Biometrie & Kwaliteitszorg / Team
>>> Biometrics & Quality Assurance thierry.onkel...@inbo.be
>>> Havenlaan 88 bus 73, 1000 Brussel www.inbo.be
>>> 
>>> 
>>> 
///
>>> To call in the statistician after the experiment is done
>>> may be no more than asking him to perform a post-mortem
>>> examination: he may be able to say what the experiment
>>> died of. ~ Sir Ronald Aylmer Fisher The plural of
>>> anecdote is not data. ~ Roger Brinner The combination of
>>> some data and an aching desire for an answer does not
>>> ensure that a reasonable answer can be extracted from a
>>> given body of data. ~ John Tukey
>>> 
>>> 
///
>>> 
>>> 
>>> 
>>> 
>>> 2018-04-16 19:38 GMT+02:00 Alexandre Courtiol
>>> : > Re,
>>> >
>>> > On 16 April 2018 at 17:35, Georgi Boshnakov < >
>>> georgi.boshna...@manchester.ac.uk> wrote:
>>> >
>>> >> Hi,
>>> >>
>>> >> The problem is indeed difficult to debug but there
>>> are things that can >> be >> done to narrow it down.
>>> >>
>>> >> 1. Are there 1/3 unlucky computers fixed? (I.e does
>>> the problem occur >> always on the same computers) Also,
>>> do you really mean computer or >> user?
>>> >>
>>> >
>>> > Yes, I mean computer, not user.
>>> >
>>> >>
>>> >> 2. Are the students working under R studio? If so,
>>> does the same >> problem >> appear if the same procedure
>>> is run outside R studio.
>>> >>
>>> >
>>> > I will try tomorrow (but from memory I think the
>>> answer will be yes).
>>> >
>>> >>
>>> >> 3. Further to 2., You mention development mode - do
   

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

2018-04-20 Thread Thierry Onkelinx
Dear Alex,

Another idea is to use pkgdown (http://pkgdown.r-lib.org) to convert
all the documentation of your package (include the vignettes) into a
website. Then you make that available to your students, e.g. through
github pages.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///




2018-04-19 18:33 GMT+02:00 Alexandre Courtiol :
> Thanks a lot Thierry, I was happy to discover and implement a "drat"
> installation workflow.
> Unfortunately it did not solve the issue (but I will stick to drat).
> Also, I checked the sessionInfo() and could not find any package version
> discriminating accurately between computers that shows vignettes from those
> who do not.
> Only Windows computer have the issue but this proves nothing (and other
> computers with the same OS version are fine).
> Goergi, I did not yet retried outside RStudio (I am trying not to waste too
> much time at the beginning of each course...
> I wish I could hijack a problematic laptop but they don't let me do it as
> they need them).
> ++
> Alex
>
>
> On 17 April 2018 at 10:42, Thierry Onkelinx 
> wrote:
>>
>> Dear Alex,
>>
>> Have a look at drat
>> (http://eddelbuettel.github.io/drat/DratForPackageAuthors.html). This
>> makes it easier to distribute prepackaged R packages (including When
>> you uploaded a new version, then the student would only have to do
>> drat::addRepo("your_repo") and then install.pakages("LM2GLMM") or
>> update.packages()
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkel...@inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be
>>
>>
>> ///
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data. ~ John Tukey
>>
>> ///
>>
>>
>>
>>
>> 2018-04-16 19:38 GMT+02:00 Alexandre Courtiol
>> :
>> > Re,
>> >
>> > On 16 April 2018 at 17:35, Georgi Boshnakov <
>> > georgi.boshna...@manchester.ac.uk> wrote:
>> >
>> >> Hi,
>> >>
>> >> The problem is indeed difficult to debug but there are things that can
>> >> be
>> >> done to narrow it down.
>> >>
>> >> 1. Are there 1/3 unlucky computers fixed? (I.e does the problem occur
>> >> always on the same computers) Also, do you really mean computer or
>> >> user?
>> >>
>> >
>> > Yes, I mean computer, not user.
>> >
>> >>
>> >> 2. Are the students working under R studio? If so, does the same
>> >> problem
>> >> appear if the same procedure is run outside R studio.
>> >>
>> >
>> > I will try tomorrow (but from memory I think the answer will be yes).
>> >
>> >>
>> >> 3. Further to 2.,  You mention development mode - do (some) students
>> >> also
>> >> have a copy of your repository? This may be aproblem if they don't
>> >> update
>> >> it too.
>> >>
>> >
>> > No, only me has the devel version.
>> >
>> >>
>> >> 4. What happens if R is restarted?
>> >
>> >
>> > I will try tomorrow (but I think the answer will be nothing).
>> >
>> >
>> >> 5. It may be worth checking .Rprofle and similar for the concerned
>> >> computers (or users, see 1.)
>> >>
>> >
>> > I will try as well but most had a fresh install and did not mess with
>> > settings.
>> >
>> >>
>> >> Hope this is of some help.
>> >>
>> >
>> > I will look at all this and also gather the session infos as Ben
>> > suggested.
>> > I think I know how to proceed to get to the bottom of that, but I was
>> > just
>> > hoping that the problem was already well known and the answer as well...
>> > If i