[R-pkg-devel] line justification for long \code{} in .pdf manual

2020-06-04 Thread Fernando Roa 
I notice the CRAN pdf didn't justify correctly long texts inside \code{}
even having "," or spaces irrespective of the status of the argument
(oneliner or multiliner)
in source (.R / .Rd)
https://imgur.com/RvjzMDh

I noticed also that it is not a problem in a pkgdown doc:
https://imgur.com/LsmuPE1

I ended up splitting the \code{} into several \codes{} with
file.R with \code{...} in one line as input.
example
from:
  \code{unique(c(dfMarkPos$markName,dfCenMarks$markName) ) }
to:
  \code{unique(c(dfMarkPos$markName,} \code{dfCenMarks$markName) ) }
https://imgur.com/Pwhfu0j

I used roxygen formatted .R, but could work with .Rd
after .R script (below) I produced .Rd with devtools:document(), then,
pdf:  devtools::build_manual(path=getwd())

gblines<-readLines(file)
for (i in 1:length(gblines) ) {
  if(grepl("^#\'",gblines[i]) & grepl("\\code",gblines[i] ) ) {
co <- regmatches(gblines[i], gregexpr('code\\{.*?\\}', gblines[i],
perl=T) )
if(length(co[[1]])>0){
  co2 <- strsplit(co[[1]],",")
  withCode <-unlist(lapply(co2, function(x) unlist(regmatches(x,
gregexpr('code\\{.*', x, perl=T) ) ) ) )
  notWithCode <- (lapply(co2, function(x) unlist(regmatches(x,
gregexpr('^(?:(?!code\\{.*).)*$', x, perl=T) ) ) ) )
  names(notWithCode)<-1:length(notWithCode)
  names(withCode)<-1:length(withCode)
  l_tmp <- c(withCode, notWithCode)
  keys = unique(names(l_tmp))
  l = sapply(keys, function(name) {unlist(l_tmp[grep(name,
names(l_tmp))])}, simplify = F)
  repwith<-list(unlist(lapply(l, function(x) paste(x, collapse=",}
\\code{"))
   ) )
  regmatches(gblines[i], gregexpr('code\\{.*?\\}', gblines[i], perl=T)
) <-repwith
}
  }
}
writeLines(gblines, file)

best,


-- 
Fernando Roa

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Re: [R-pkg-devel] irrecoverable exception occurred during CRAN submission checks

2020-06-04 Thread Daniel Lüdecke 
Hi Dirk,

ok, I think I got what you meant. The error for insight-checks came from
panelr, which is a suggested package. I contacted the maintainer, who said
that he won't be able to fix panelr in time, so I removed the test for the
panelr-package from insight. So, for this submission, no matter what
problems the panelr-package has, this should not be related to the NOTE I
get from the CRAN checks during submission.

Best
Daniel

-Ursprüngliche Nachricht-
Von: Dirk Eddelbuettel  
Gesendet: Donnerstag, 4. Juni 2020 14:20
An: Daniel Lüdecke 
Cc: 'Dirk Eddelbuettel' ; r-package-devel@r-project.org
Betreff: Re: AW: [R-pkg-devel] irrecoverable exception occurred during CRAN
submission checks


Hi Daniel,

On 4 June 2020 at 08:19, Daniel Lüdecke wrote:
| the package in question is "insight"
| (https://cran.r-project.org/package=insight). Since a few days, the test
for
| the panelr-package fails, because panelr itself fails on many systems
| (https://cran.r-project.org/web/checks/check_results_panelr.html). I
*think*
| this is due to an update of dpylr that causes trouble with panelr, because
| both insight and panelr checks were OK the last weeks.

You could possibly confirm that hypothesis by working in a 'clean' test
environment -- Docker containers are an option -- via a simple comparison of
installing identical versions of all packages apart from the suspected one.
 
Dirk 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

--

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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
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[R-pkg-devel] Additional issues for the last version released on CRAN

2020-06-04 Thread Tiago Olivoto 
Dear all,

I have submitted a patch release (1.6.0) of my package metan
(https://cran.r-project.org/web/packages/metan/) to fix an additional issue
and implement some improvements. All local checks had no errors or warnings,
but after the submission process, I received the following message.

 

<<>>

 

Dear maintainer,

package metan_1.6.1.tar.gz has been auto-processed.

The auto-check found additional issues for the *last* version released on
CRAN:

  donttest < 
https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>

CRAN incoming checks do not test for these additional issues and you will
need an appropriately instrumented build of R to reproduce these.

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

Log dir:


The files will be removed after roughly 7 days.

Installation time in seconds: 52

Check time in seconds: 407 

R Under development (unstable) (2020-05-29 r78617)

Pretests results:

Windows: <

https://win-builder.r-project.org/incoming_pretest/metan_1.6.1_20200603_0626
35/Windows/00check.log>

Status: OK

Debian: <

https://win-builder.r-project.org/incoming_pretest/metan_1.6.1_20200603_0626
35/Debian/00check.log>

Status: OK

Last released version's CRAN status: OK: 12

See: < 
https://CRAN.R-project.org/web/checks/check_results_metan.html>

Last released version's additional issues:

  donttest < 
https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>

CRAN Web: < 
https://cran.r-project.org/package=metan>

No strong reverse dependencies to be checked.

 

<<>>

 

I replied to mailto:cran-submissi...@r-project.org> >  explaining how the error was
fixed, but since this is my first experience with an issue like that, I'm
not sure if I need to do anything more or simply await a response from the
CRAN team.

Thanks in advance for any comments or suggestion,

Tiago

 


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Re: [R-pkg-devel] irrecoverable exception occurred during CRAN submission checks

2020-06-04 Thread Daniel Lüdecke 
Hi Dirk,

I'm not sure I got what you mean? Locally, I used RStudio with R4.0 to check
the package. The checks I mentioned below were the official CRAN check
pages. I have now tried to run the checks on rhub, however, I'm not sure how
to access the logs:

https://builder.r-hub.io/status/insight_0.8.5.tar.gz-6f814b95949368dcdd83d8f
b9cee075b

Best
Daniel

-Ursprüngliche Nachricht-
Von: Dirk Eddelbuettel  
Gesendet: Donnerstag, 4. Juni 2020 14:20
An: Daniel Lüdecke 
Cc: 'Dirk Eddelbuettel' ; r-package-devel@r-project.org
Betreff: Re: AW: [R-pkg-devel] irrecoverable exception occurred during CRAN
submission checks


Hi Daniel,

On 4 June 2020 at 08:19, Daniel Lüdecke wrote:
| the package in question is "insight"
| (https://cran.r-project.org/package=insight). Since a few days, the test
for
| the panelr-package fails, because panelr itself fails on many systems
| (https://cran.r-project.org/web/checks/check_results_panelr.html). I
*think*
| this is due to an update of dpylr that causes trouble with panelr, because
| both insight and panelr checks were OK the last weeks.

You could possibly confirm that hypothesis by working in a 'clean' test
environment -- Docker containers are an option -- via a simple comparison of
installing identical versions of all packages apart from the suspected one.
 
Dirk 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

--

_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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Re: [R-pkg-devel] irrecoverable exception occurred during CRAN submission checks

2020-06-04 Thread Dirk Eddelbuettel 


Hi Daniel,

On 4 June 2020 at 08:19, Daniel Lüdecke wrote:
| the package in question is "insight"
| (https://cran.r-project.org/package=insight). Since a few days, the test for
| the panelr-package fails, because panelr itself fails on many systems
| (https://cran.r-project.org/web/checks/check_results_panelr.html). I *think*
| this is due to an update of dpylr that causes trouble with panelr, because
| both insight and panelr checks were OK the last weeks.

You could possibly confirm that hypothesis by working in a 'clean' test
environment -- Docker containers are an option -- via a simple comparison of
installing identical versions of all packages apart from the suspected one.
 
Dirk 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] irrecoverable exception occurred during CRAN submission checks

2020-06-04 Thread Daniel Lüdecke 
Hi Dirk,

the package in question is "insight"
(https://cran.r-project.org/package=insight). Since a few days, the test for
the panelr-package fails, because panelr itself fails on many systems
(https://cran.r-project.org/web/checks/check_results_panelr.html). I *think*
this is due to an update of dpylr that causes trouble with panelr, because
both insight and panelr checks were OK the last weeks.

Now win-builder checks for insight are OK, local checks (Win) are OK and
GitHub CI is ok (https://github.com/easystats/insight). 

If you need, I uploaded the source version of insight here:
https://drive.google.com/file/d/1sZ2n3utc27U0DrcFlAsH6NQpKMssIiEg/view?usp=s
haring

The GitHub version only differs in the package version number in the
DESCRIPTION file (which is 0.8.4.1 on GitHub and will be updated once the
update is accepted on CRAN).

I can't imagine any special revisions that might lead to that NOTE in the
incoming checks on Linux.

Hope that helps...

Best
Daniel

-Ursprüngliche Nachricht-
Von: Dirk Eddelbuettel  
Gesendet: Donnerstag, 4. Juni 2020 02:01
An: Daniel Lüdecke 
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] irrecoverable exception occurred during CRAN
submission checks


Daniel,

On 3 June 2020 at 10:18, Daniel Lüdecke wrote:
| I just submitted an update of my package to CRAN and it does not pass
| incoming checks. While local checks, win-builder and GitHub CI
| (Mac/Win/Linux) all pass, I get the Note you see below for the checks
during
| submission process. I have no idea why this happens and see this message
for
| the first time. I *assume* it's a temporary issue / false positive, but
want
| to be sure before I reply to the CRAN team.
| 
| Can anyone help how I can address this issue, or if it indeed might be a
| false positive?

What package? A package / repo name would have helped here. Did I miss it?

One of my golden rules for debugging is the old "doctor, doctor, I hurt when
I do this" joke. There is no shame in disabling a test that bites: "if it
hurts, don't do it". The next step then is is to reproduce locally---which
is
still an uphill battle because CRAN, resource contrained as they are, have
not provided their setups in ways that are easily reproducible by us
mortals.

Hth,  Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

--

_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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