date:20200826

Re: [R-pkg-devel] url checks not working for me

2020-08-26 Thread Dirk Eddelbuettel



On 26 August 2020 at 08:46, Dirk Eddelbuettel wrote:
| One way to ensure the last point is to have a file
| 
|   ~/.R/check.Renviron-Rdevel
| 
| which I had (but where I had commented out 'incoming' as it can take a
| moment).  Current values below, with thanks to Uwe for the reminder.

And I forgot to add them.  This time.  One of the values is local to my
R-devel build.  I am sure Henrik will follow-up soon with an extended list :)

| I reiterate that this really should be part of R CMD check --as-cran.  Maybe
| one day it will be.


edd@rob:~$ cat ~/.R/check.Renviron-Rdevel 
# See R Internals manual -- there is now --as-cran too
_R_CHECK_CRAN_INCOMING_=FALSE
_R_CHECK_FORCE_SUGGESTS_=FALSE
_R_CHECK_VC_DIRS_=TRUE
_R_CHECK_UNSAFE_CALLS_=TRUE
_R_CHECK_TIMINGS_=10
_R_CHECK_INSTALL_DEPENDS_=TRUE
_R_CHECK_SUGGESTS_ONLY_=TRUE
_R_CHECK_NO_RECOMMENDED_=TRUE
_R_CHECK_SUBDIRS_NOCASE_=TRUE
_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
_R_CHECK_LICENSE_=TRUE
_R_CHECK_DOC_SIZES2_=TRUE
_R_CHECK_CODETOOLS_PROFILE_='suppressPartialMatchArgs=false'
#
_R_CHECK_VIGNETTES_NLINES_=50
_R_CHECK_DOT_INTERNAL_=TRUE
#
# edd Apr 2015
_R_CHECK_CRAN_INCOMING_USE_ASPELL_=TRUE

# edd Jan 2018  for RD 
R_LIBS="/usr/local/lib/R-devel/site-library"

# edd Aug 2020
_R_CHECK_CRAN_INCOMING_=TRUE
edd@rob:~$


Dirk

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Re: [R-pkg-devel] url checks not working for me

2020-08-26 Thread Dirk Eddelbuettel



Ok, Uwe was kind enough to take me to task off-list and I can now confirm
that I _can_ replicate the URL issue locally by ensuring all three of

 - recent enough r-devel build (that was true, I may add that the
   rocker/r-devel and rocker/drd containers I look after can help)

 - built with libcurl support so check capabilities()[["libcurl"]] (that was
   also true for me)

 - CRAN incoming checks turned on (and that was my issue)

One way to ensure the last point is to have a file

  ~/.R/check.Renviron-Rdevel

which I had (but where I had commented out 'incoming' as it can take a
moment).  Current values below, with thanks to Uwe for the reminder.

I reiterate that this really should be part of R CMD check --as-cran.  Maybe
one day it will be.

Dirk

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Re: [R-pkg-devel] Error in winbuilder

2020-08-26 Thread Uwe Ligges


Pls try agaibn, if it fails again, pls let me know privately.

Best,
Uwe Ligges



On 26.08.2020 15:13, Nicholas Tierney wrote:

Hi Uwe,

OK thank you for that, good to know! I imagine it might be a bit tricky 
to know when, but do you have an idea of when submissions might return 
to normal? Or should I be good to submit again soon?


Thanks again,

Nick

On Wed, 26 Aug 2020 at 23:06, Uwe Ligges 
> wrote:


Friends, thias looks like a hang in the CRAN incoming feasibility
checks, hence may well be some web related issue as it seems it ran
into
the timeout there.

Best,
Uwe Ligges

On 26.08.2020 14:57, Nicholas Tierney wrote:
 > Hi Michael,
 >
 > I do indeed have quite a few examples in the package, this hasn't
been a
 > problem in the past, but I guess I could try reducing them down.
Have you
 > had this problem before?
 >
 > Cheers,
 >
 > Nick
 >
 > On Wed, 26 Aug 2020 at 22:49, Michael Dewey
mailto:li...@dewey.myzen.co.uk>> wrote:
 >
 >> Dear Nicholas
 >>
 >> Do you in fact have many examples in the package? Perhaps for some
 >> mysterious reason they take longer there than when you check at
home.
 >>
 >> Michael
 >>
 >> On 25/08/2020 14:54, Nicholas Tierney wrote:
 >>> Hi Everyone,
 >>>
 >>> I have an error when submitting to Winbuilder for my R package,
naniar
 >>> .
 >>>
 >>> When using `devtools::check_win_devel()` or
 >> `devtools::check_win_release()`
 >>> on naniar, I get the following logfile from winbuilder:
 >>>
 >>> ```
 >>> * using log directory
'd:/RCompile/CRANguest/R-release/naniar.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 'naniar/DESCRIPTION' ... OK
 >>> * checking extension type ... Package
 >>> * this is package 'naniar' version '0.5.3'
 >>> * package encoding: UTF-8
 >>> * checking CRAN incoming feasibility ... ERROR
 >>> Check process probably crashed or hung up for 20 minutes ... killed
 >>> Most likely this happened in the example checks (?),
 >>> if not, ignore the following last lines of example output:
 >>>
 >>>  End of example output (where/before crash/hang up
occured ?)
 >>> 
 >>> ```
 >>>
 >>> (submission URL here:
https://win-builder.r-project.org/77PYyM2kMri1/)
 >>>
 >>> I had previously thought this was a problem to do with CRAN
being closed
 >>> last week, but apparently this is not the case, and it should
have been
 >>> working. I cannot find any details on CRAN for this, but it
passes build
 >> on
 >>> R HUB for windows, and it passes build with no warnings,
errors, or notes
 >>> for me on Mac OSX, as well as on github actions (windows,
macOS, and
 >>> ubuntu).
 >>>
 >>> Just wondering if anyone has thoughts on this? I have also cross
 >>> posted on Rstudio
 >>> community
 >>> <
 >>>
 >>

https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492
  ,
 >>> in case that is of interest.
 >>>
 >>> Thanks for your time, and apologies if I have missed something
obvious.
 >>>
 >>> All the best,
 >>>
 >>> Nick
 >>>
 >>>        [[alternative HTML version deleted]]
 >>>
 >>> __
 >>> R-package-devel@r-project.org
 mailing list
 >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
 >>>
 >>
 >> --
 >> Michael
 >> http://www.dewey.myzen.co.uk/home.html
 >>
 >
 >       [[alternative HTML version deleted]]
 >
 > __
 > 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] Error in winbuilder

2020-08-26 Thread Nicholas Tierney

Hi Uwe,

OK thank you for that, good to know! I imagine it might be a bit tricky to
know when, but do you have an idea of when submissions might return to
normal? Or should I be good to submit again soon?

Thanks again,

Nick

On Wed, 26 Aug 2020 at 23:06, Uwe Ligges 
wrote:

> Friends, thias looks like a hang in the CRAN incoming feasibility
> checks, hence may well be some web related issue as it seems it ran into
> the timeout there.
>
> Best,
> Uwe Ligges
>
> On 26.08.2020 14:57, Nicholas Tierney wrote:
> > Hi Michael,
> >
> > I do indeed have quite a few examples in the package, this hasn't been a
> > problem in the past, but I guess I could try reducing them down. Have you
> > had this problem before?
> >
> > Cheers,
> >
> > Nick
> >
> > On Wed, 26 Aug 2020 at 22:49, Michael Dewey 
> wrote:
> >
> >> Dear Nicholas
> >>
> >> Do you in fact have many examples in the package? Perhaps for some
> >> mysterious reason they take longer there than when you check at home.
> >>
> >> Michael
> >>
> >> On 25/08/2020 14:54, Nicholas Tierney wrote:
> >>> Hi Everyone,
> >>>
> >>> I have an error when submitting to Winbuilder for my R package, naniar
> >>> .
> >>>
> >>> When using `devtools::check_win_devel()` or
> >> `devtools::check_win_release()`
> >>> on naniar, I get the following logfile from winbuilder:
> >>>
> >>> ```
> >>> * using log directory 'd:/RCompile/CRANguest/R-release/naniar.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 'naniar/DESCRIPTION' ... OK
> >>> * checking extension type ... Package
> >>> * this is package 'naniar' version '0.5.3'
> >>> * package encoding: UTF-8
> >>> * checking CRAN incoming feasibility ... ERROR
> >>> Check process probably crashed or hung up for 20 minutes ... killed
> >>> Most likely this happened in the example checks (?),
> >>> if not, ignore the following last lines of example output:
> >>>
> >>>  End of example output (where/before crash/hang up occured ?)
> >>> 
> >>> ```
> >>>
> >>> (submission URL here: https://win-builder.r-project.org/77PYyM2kMri1/)
> >>>
> >>> I had previously thought this was a problem to do with CRAN being
> closed
> >>> last week, but apparently this is not the case, and it should have been
> >>> working. I cannot find any details on CRAN for this, but it passes
> build
> >> on
> >>> R HUB for windows, and it passes build with no warnings, errors, or
> notes
> >>> for me on Mac OSX, as well as on github actions (windows, macOS, and
> >>> ubuntu).
> >>>
> >>> Just wondering if anyone has thoughts on this? I have also cross
> >>> posted on Rstudio
> >>> community
> >>> <
> >>>
> >>
> https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492
>  ,
> >>> in case that is of interest.
> >>>
> >>> Thanks for your time, and apologies if I have missed something obvious.
> >>>
> >>> All the best,
> >>>
> >>> Nick
> >>>
> >>>[[alternative HTML version deleted]]
> >>>
> >>> __
> >>> R-package-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>>
> >>
> >> --
> >> Michael
> >> http://www.dewey.myzen.co.uk/home.html
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > 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] Error in winbuilder

2020-08-26 Thread Uwe Ligges

Friends, thias looks like a hang in the CRAN incoming feasibility
checks, hence may well be some web related issue as it seems it ran into
the timeout there.

Best,
Uwe Ligges

On 26.08.2020 14:57, Nicholas Tierney wrote:

Hi Michael,

I do indeed have quite a few examples in the package, this hasn't been a
problem in the past, but I guess I could try reducing them down. Have you
had this problem before?

Cheers,

Nick

On Wed, 26 Aug 2020 at 22:49, Michael Dewey wrote:

Dear Nicholas

Do you in fact have many examples in the package? Perhaps for some
mysterious reason they take longer there than when you check at home.

Michael

On 25/08/2020 14:54, Nicholas Tierney wrote:

Hi Everyone,

I have an error when submitting to Winbuilder for my R package, naniar
.

When using `devtools::check_win_devel()` or

`devtools::check_win_release()`

on naniar, I get the following logfile from winbuilder:

```
* using log directory 'd:/RCompile/CRANguest/R-release/naniar.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 'naniar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'naniar' version '0.5.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... ERROR
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

End of example output (where/before crash/hang up occured ?)

```

(submission URL here: https://win-builder.r-project.org/77PYyM2kMri1/)

R HUB for windows, and it passes build with no warnings, errors, or notes
for me on Mac OSX, as well as on github actions (windows, macOS, and
ubuntu).

Just wondering if anyone has thoughts on this? I have also cross
posted on Rstudio
community
<

https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492

in case that is of interest.

Thanks for your time, and apologies if I have missed something obvious.

All the best,

Nick

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Re: [R-pkg-devel] url checks not working for me

2020-08-26 Thread Dirk Eddelbuettel



On 26 August 2020 at 14:34, Vincent van Hees wrote:
| Addressing the errors is not the problem. I want to be able to detect these
| problems when I do: R CMD check --as-cran.

You cannot :-/. I pointed that out to CRAN maintainers a few times myself.

| At the moment, I can only detect the errors by submitting the package to
| CRAN, because only their package check triggers these errors.

Apparently we are supposed to find that in the generated ${package}.Rcheck
directory even when no warning was issued. Supposedly one has to live in
Auckland, Dortmund, Oxford or Vienna to find that normal.

Dirk

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Re: [R-pkg-devel] Error in winbuilder

2020-08-26 Thread Nicholas Tierney

Hi Michael,

I do indeed have quite a few examples in the package, this hasn't been a
problem in the past, but I guess I could try reducing them down. Have you
had this problem before?

Cheers,

Nick

On Wed, 26 Aug 2020 at 22:49, Michael Dewey  wrote:

> Dear Nicholas
>
> Do you in fact have many examples in the package? Perhaps for some
> mysterious reason they take longer there than when you check at home.
>
> Michael
>
> On 25/08/2020 14:54, Nicholas Tierney wrote:
> > Hi Everyone,
> >
> > I have an error when submitting to Winbuilder for my R package, naniar
> > .
> >
> > When using `devtools::check_win_devel()` or
> `devtools::check_win_release()`
> > on naniar, I get the following logfile from winbuilder:
> >
> > ```
> > * using log directory 'd:/RCompile/CRANguest/R-release/naniar.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 'naniar/DESCRIPTION' ... OK
> > * checking extension type ... Package
> > * this is package 'naniar' version '0.5.3'
> > * package encoding: UTF-8
> > * checking CRAN incoming feasibility ... ERROR
> > Check process probably crashed or hung up for 20 minutes ... killed
> > Most likely this happened in the example checks (?),
> > if not, ignore the following last lines of example output:
> >
> >  End of example output (where/before crash/hang up occured ?)
> > 
> > ```
> >
> > (submission URL here: https://win-builder.r-project.org/77PYyM2kMri1/)
> >
> > I had previously thought this was a problem to do with CRAN being closed
> > last week, but apparently this is not the case, and it should have been
> > working. I cannot find any details on CRAN for this, but it passes build
> on
> > R HUB for windows, and it passes build with no warnings, errors, or notes
> > for me on Mac OSX, as well as on github actions (windows, macOS, and
> > ubuntu).
> >
> > Just wondering if anyone has thoughts on this? I have also cross
> > posted on Rstudio
> > community
> > <
> >
> https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492
> >> ,
> > in case that is of interest.
> >
> > Thanks for your time, and apologies if I have missed something obvious.
> >
> > All the best,
> >
> > Nick
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html
>

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Re: [R-pkg-devel] url checks not working for me

2020-08-26 Thread Bryan Hanson

Sorry, I was reading too fast.  One possibility is your R version is wee bit 
old.  Try a more recently daily build.

I recently saw such errors when submitting to Win-Builder, but was fine locally 
(per your situation).

Bryan

> On Aug 26, 2020, at 8:34 AM, Vincent van Hees  
> wrote:
> 
> Addressing the errors is not the problem. I want to be able to detect these 
> problems when I do: R CMD check --as-cran.
> At the moment, I can only detect the errors by submitting the package to 
> CRAN, because only their package check triggers these errors.
> 
> On Wed, 26 Aug 2020 at 14:30, Bryan Hanson  > wrote:
> At the minimum you should look at the “moved to” URLs and change your links 
> to those (some are outright changes in URLs that were redirected and some are 
> http to https changes).
> 
> Bryan
> 
> > On Aug 26, 2020, at 8:22 AM, Vincent van Hees  > > wrote:
> > 
> > Hello,
> > URL errors in my DESCRIPTION file and package vignette are not picked up
> > when I do R CMD check --as-cran or devtools::check(). I only know about
> > these errors because CRAN has rejected my package submission and instructed
> > me to fix the urls (example at end of this message).
> > 
> > I am trying to figure out how I can get R CMD check --as-cran to detect
> > these URL mistakes. From
> > https://cran.r-project.org/web/packages/URL_checks.html 
> >  I understand that 
> > I
> > need libcurl installed, which I have.
> > 
> > Can anyone tell me whether I am using the wrong combination of libcurl
> > version, R version, and Ubuntu version? (see versions below). If not, what
> > else can I do to get the URL checks to work?
> > 
> > Thanks, Vincent
> > 
> > vincent@vincent-VB:~$ curl-config --version
> > *libcurl 7.58.0*
> > 
> > vincent@vincent-VB:~$ curl -V
> > *curl 7.58.0* (x86_64-pc-linux-gnu) libcurl/7.58.0 OpenSSL/1.1.1
> > zlib/1.2.11 libidn2/2.0.4 libpsl/0.19.1 (+libidn2/2.0.4) nghttp2/1.30.0
> > librtmp/2.3
> > Release-Date: 2018-01-24
> > Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3
> > pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
> > Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB
> > SSL libz TLS-SRP HTTP2 UnixSockets HTTPS-proxy PSL
> > 
> > vincent@vincent-VB:~$ R --version
> > *R version 4.0.2* (2020-06-22) -- "Taking Off Again"
> > Copyright (C) 2020 The R Foundation for Statistical Computing
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > 
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under the terms of the
> > GNU General Public License versions 2 or 3.
> > For more information about these matters see
> > https://www.gnu.org/licenses/ .
> > 
> > vincent@vincent-VB:~$ lsb_release -a
> > No LSB modules are available.
> > Distributor ID: Ubuntu
> > Description: *Ubuntu 18.04.5 LTS*
> > Release: 18.04
> > Codename: bionic
> > 
> > Example of most recent URL mistakes in my package detected by CRAN package
> > submission process which I could not detect locally:
> > Found the following (possibly) invalid URLs: URL:
> > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533 
> > 
> > (moved to
> > https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533 
> > )
> > From: inst/CITATION Status: 200 Message: OK URL: https://geneactiv.org/ 
> > 
> > (moved to https://www.activinsights.com/ ) 
> > From: inst/doc/GGIR.html Status:
> > 200 Message: OK URL: https://www.accelting.com/ 
> >  (moved to
> > https://accelting.com/ ) From: inst/doc/GGIR.html 
> > Status: 200 Message: OK
> > URL: https://www.physiology.org/doi/10.1152/japplphysiol.00421.2014 
> >  (moved
> > to https://journals.physiology.org/doi/10.1152/japplphysiol.00421.2014 
> > )
> > From: inst/CITATION Status: 200 Message: OK
> > 
> >   [[alternative HTML version deleted]]
> > 
> > __
> > 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] url checks not working for me

2020-08-26 Thread Joshua Ulrich

On Wed, Aug 26, 2020 at 7:43 AM Vincent van Hees
 wrote:
>
> Addressing the errors is not the problem. I want to be able to detect these
> problems when I do: R CMD check --as-cran.
> At the moment, I can only detect the errors by submitting the package to
> CRAN, because only their package check triggers these errors.
>
The win-builder system will also detect them.

These checks trigger for me on your package.

> R CMD check GGIR_2.1-0.tar.gz --as-cran
* using log directory '/home/josh/git/GGIR.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'GGIR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GGIR' version '2.1-0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Vincent T van Hees '

New maintainer:
  Vincent T van Hees 
Old maintainer(s):
  Vincent T van Hees 

Found the following (possibly) invalid URLs:
  URL: https://cran.r-project.org/web/packages/activityCounts/index.html
From: inst/doc/ExternalFunction.html
Status: 200
Message: OK
CRAN URL not in canonical form
  URL: https://europepmc.org/article/med/22770768
From: inst/doc/GGIR.html
Status: Error
Message: libcurl error code 35:
  error:14094410:SSL routines:ssl3_read_bytes:sslv3 alert
handshake failure
  The canonical URL of the CRAN page for a package is
https://CRAN.R-project.org/package=pkgname
* checking package namespace information ... OK
* checking package dependencies ... OK
...

Make sure you have incoming checks enabled, by setting the environment
variable _R_CHECK_CRAN_INCOMING_=TRUE.

Best,
Josh

> On Wed, 26 Aug 2020 at 14:30, Bryan Hanson  wrote:
>
> > At the minimum you should look at the “moved to” URLs and change your
> > links to those (some are outright changes in URLs that were redirected and
> > some are http to https changes).
> >
> > Bryan
> >
> > > On Aug 26, 2020, at 8:22 AM, Vincent van Hees 
> > wrote:
> > >
> > > Hello,
> > > URL errors in my DESCRIPTION file and package vignette are not picked up
> > > when I do R CMD check --as-cran or devtools::check(). I only know about
> > > these errors because CRAN has rejected my package submission and
> > instructed
> > > me to fix the urls (example at end of this message).
> > >
> > > I am trying to figure out how I can get R CMD check --as-cran to detect
> > > these URL mistakes. From
> > > https://cran.r-project.org/web/packages/URL_checks.html I understand
> > that I
> > > need libcurl installed, which I have.
> > >
> > > Can anyone tell me whether I am using the wrong combination of libcurl
> > > version, R version, and Ubuntu version? (see versions below). If not,
> > what
> > > else can I do to get the URL checks to work?
> > >
> > > Thanks, Vincent
> > >
> > > vincent@vincent-VB:~$ curl-config --version
> > > *libcurl 7.58.0*
> > >
> > > vincent@vincent-VB:~$ curl -V
> > > *curl 7.58.0* (x86_64-pc-linux-gnu) libcurl/7.58.0 OpenSSL/1.1.1
> > > zlib/1.2.11 libidn2/2.0.4 libpsl/0.19.1 (+libidn2/2.0.4) nghttp2/1.30.0
> > > librtmp/2.3
> > > Release-Date: 2018-01-24
> > > Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps
> > pop3
> > > pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
> > > Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM
> > NTLM_WB
> > > SSL libz TLS-SRP HTTP2 UnixSockets HTTPS-proxy PSL
> > >
> > > vincent@vincent-VB:~$ R --version
> > > *R version 4.0.2* (2020-06-22) -- "Taking Off Again"
> > > Copyright (C) 2020 The R Foundation for Statistical Computing
> > > Platform: x86_64-pc-linux-gnu (64-bit)
> > >
> > > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > > You are welcome to redistribute it under the terms of the
> > > GNU General Public License versions 2 or 3.
> > > For more information about these matters see
> > > https://www.gnu.org/licenses/.
> > >
> > > vincent@vincent-VB:~$ lsb_release -a
> > > No LSB modules are available.
> > > Distributor ID: Ubuntu
> > > Description: *Ubuntu 18.04.5 LTS*
> > > Release: 18.04
> > > Codename: bionic
> > >
> > > Example of most recent URL mistakes in my package detected by CRAN
> > package
> > > submission process which I could not detect locally:
> > > Found the following (possibly) invalid URLs: URL:
> > > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533
> > > (moved to
> > >
> > https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533)
> > > From: inst/CITATION Status: 200 Message: OK URL: https://geneactiv.org/
> > > (moved to https://www.activinsights.com/) From: inst/doc/GGIR.html
> > Status:
> > > 200 Message: OK URL: https://www.accelting.com/ (moved to
> > > https://accelting.com/) From: inst/doc/GGIR.html Status: 200 Message: OK
> > > URL: https://www.physiology.org/doi/10.1152/japplphysiol.00421.2014
> > (moved
> > > to https://journals.physiology.org/doi/10.1152/japplphysiol.00421.2014)
> > > From:

Re: [R-pkg-devel] Error in winbuilder

2020-08-26 Thread Michael Dewey

Dear Nicholas

Do you in fact have many examples in the package? Perhaps for some
mysterious reason they take longer there than when you check at home.

Michael

On 25/08/2020 14:54, Nicholas Tierney wrote:

Hi Everyone,

I have an error when submitting to Winbuilder for my R package, naniar
.

When using `devtools::check_win_devel()` or `devtools::check_win_release()`
on naniar, I get the following logfile from winbuilder:

End of example output (where/before crash/hang up occured ?)

```

(submission URL here: https://win-builder.r-project.org/77PYyM2kMri1/)

I had previously thought this was a problem to do with CRAN being closed
last week, but apparently this is not the case, and it should have been
working. I cannot find any details on CRAN for this, but it passes build on
R HUB for windows, and it passes build with no warnings, errors, or notes
for me on Mac OSX, as well as on github actions (windows, macOS, and
ubuntu).

Just wondering if anyone has thoughts on this? I have also cross
posted on Rstudio
community
<
https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492

in case that is of interest.

Thanks for your time, and apologies if I have missed something obvious.

All the best,

Nick

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http://www.dewey.myzen.co.uk/home.html

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Re: [R-pkg-devel] url checks not working for me

2020-08-26 Thread Vincent van Hees

Addressing the errors is not the problem. I want to be able to detect these
problems when I do: R CMD check --as-cran.
At the moment, I can only detect the errors by submitting the package to
CRAN, because only their package check triggers these errors.

On Wed, 26 Aug 2020 at 14:30, Bryan Hanson  wrote:

> At the minimum you should look at the “moved to” URLs and change your
> links to those (some are outright changes in URLs that were redirected and
> some are http to https changes).
>
> Bryan
>
> > On Aug 26, 2020, at 8:22 AM, Vincent van Hees 
> wrote:
> >
> > Hello,
> > URL errors in my DESCRIPTION file and package vignette are not picked up
> > when I do R CMD check --as-cran or devtools::check(). I only know about
> > these errors because CRAN has rejected my package submission and
> instructed
> > me to fix the urls (example at end of this message).
> >
> > I am trying to figure out how I can get R CMD check --as-cran to detect
> > these URL mistakes. From
> > https://cran.r-project.org/web/packages/URL_checks.html I understand
> that I
> > need libcurl installed, which I have.
> >
> > Can anyone tell me whether I am using the wrong combination of libcurl
> > version, R version, and Ubuntu version? (see versions below). If not,
> what
> > else can I do to get the URL checks to work?
> >
> > Thanks, Vincent
> >
> > vincent@vincent-VB:~$ curl-config --version
> > *libcurl 7.58.0*
> >
> > vincent@vincent-VB:~$ curl -V
> > *curl 7.58.0* (x86_64-pc-linux-gnu) libcurl/7.58.0 OpenSSL/1.1.1
> > zlib/1.2.11 libidn2/2.0.4 libpsl/0.19.1 (+libidn2/2.0.4) nghttp2/1.30.0
> > librtmp/2.3
> > Release-Date: 2018-01-24
> > Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps
> pop3
> > pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
> > Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM
> NTLM_WB
> > SSL libz TLS-SRP HTTP2 UnixSockets HTTPS-proxy PSL
> >
> > vincent@vincent-VB:~$ R --version
> > *R version 4.0.2* (2020-06-22) -- "Taking Off Again"
> > Copyright (C) 2020 The R Foundation for Statistical Computing
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under the terms of the
> > GNU General Public License versions 2 or 3.
> > For more information about these matters see
> > https://www.gnu.org/licenses/.
> >
> > vincent@vincent-VB:~$ lsb_release -a
> > No LSB modules are available.
> > Distributor ID: Ubuntu
> > Description: *Ubuntu 18.04.5 LTS*
> > Release: 18.04
> > Codename: bionic
> >
> > Example of most recent URL mistakes in my package detected by CRAN
> package
> > submission process which I could not detect locally:
> > Found the following (possibly) invalid URLs: URL:
> > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533
> > (moved to
> >
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533)
> > From: inst/CITATION Status: 200 Message: OK URL: https://geneactiv.org/
> > (moved to https://www.activinsights.com/) From: inst/doc/GGIR.html
> Status:
> > 200 Message: OK URL: https://www.accelting.com/ (moved to
> > https://accelting.com/) From: inst/doc/GGIR.html Status: 200 Message: OK
> > URL: https://www.physiology.org/doi/10.1152/japplphysiol.00421.2014
> (moved
> > to https://journals.physiology.org/doi/10.1152/japplphysiol.00421.2014)
> > From: inst/CITATION Status: 200 Message: OK
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > 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] url checks not working for me

2020-08-26 Thread Bryan Hanson

At the minimum you should look at the “moved to” URLs and change your links to 
those (some are outright changes in URLs that were redirected and some are http 
to https changes).

Bryan

> On Aug 26, 2020, at 8:22 AM, Vincent van Hees  
> wrote:
> 
> Hello,
> URL errors in my DESCRIPTION file and package vignette are not picked up
> when I do R CMD check --as-cran or devtools::check(). I only know about
> these errors because CRAN has rejected my package submission and instructed
> me to fix the urls (example at end of this message).
> 
> I am trying to figure out how I can get R CMD check --as-cran to detect
> these URL mistakes. From
> https://cran.r-project.org/web/packages/URL_checks.html I understand that I
> need libcurl installed, which I have.
> 
> Can anyone tell me whether I am using the wrong combination of libcurl
> version, R version, and Ubuntu version? (see versions below). If not, what
> else can I do to get the URL checks to work?
> 
> Thanks, Vincent
> 
> vincent@vincent-VB:~$ curl-config --version
> *libcurl 7.58.0*
> 
> vincent@vincent-VB:~$ curl -V
> *curl 7.58.0* (x86_64-pc-linux-gnu) libcurl/7.58.0 OpenSSL/1.1.1
> zlib/1.2.11 libidn2/2.0.4 libpsl/0.19.1 (+libidn2/2.0.4) nghttp2/1.30.0
> librtmp/2.3
> Release-Date: 2018-01-24
> Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3
> pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
> Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB
> SSL libz TLS-SRP HTTP2 UnixSockets HTTPS-proxy PSL
> 
> vincent@vincent-VB:~$ R --version
> *R version 4.0.2* (2020-06-22) -- "Taking Off Again"
> Copyright (C) 2020 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under the terms of the
> GNU General Public License versions 2 or 3.
> For more information about these matters see
> https://www.gnu.org/licenses/.
> 
> vincent@vincent-VB:~$ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: *Ubuntu 18.04.5 LTS*
> Release: 18.04
> Codename: bionic
> 
> Example of most recent URL mistakes in my package detected by CRAN package
> submission process which I could not detect locally:
> Found the following (possibly) invalid URLs: URL:
> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533
> (moved to
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533)
> From: inst/CITATION Status: 200 Message: OK URL: https://geneactiv.org/
> (moved to https://www.activinsights.com/) From: inst/doc/GGIR.html Status:
> 200 Message: OK URL: https://www.accelting.com/ (moved to
> https://accelting.com/) From: inst/doc/GGIR.html Status: 200 Message: OK
> URL: https://www.physiology.org/doi/10.1152/japplphysiol.00421.2014 (moved
> to https://journals.physiology.org/doi/10.1152/japplphysiol.00421.2014)
> From: inst/CITATION Status: 200 Message: OK
> 
>   [[alternative HTML version deleted]]
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] url checks not working for me

2020-08-26 Thread Vincent van Hees

Hello,
URL errors in my DESCRIPTION file and package vignette are not picked up
when I do R CMD check --as-cran or devtools::check(). I only know about
these errors because CRAN has rejected my package submission and instructed
me to fix the urls (example at end of this message).

I am trying to figure out how I can get R CMD check --as-cran to detect
these URL mistakes. From
https://cran.r-project.org/web/packages/URL_checks.html I understand that I
need libcurl installed, which I have.

Can anyone tell me whether I am using the wrong combination of libcurl
version, R version, and Ubuntu version? (see versions below). If not, what
else can I do to get the URL checks to work?

Thanks, Vincent

vincent@vincent-VB:~$ curl-config --version
*libcurl 7.58.0*

vincent@vincent-VB:~$ curl -V
*curl 7.58.0* (x86_64-pc-linux-gnu) libcurl/7.58.0 OpenSSL/1.1.1
zlib/1.2.11 libidn2/2.0.4 libpsl/0.19.1 (+libidn2/2.0.4) nghttp2/1.30.0
librtmp/2.3
Release-Date: 2018-01-24
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3
pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB
SSL libz TLS-SRP HTTP2 UnixSockets HTTPS-proxy PSL

vincent@vincent-VB:~$ R --version
*R version 4.0.2* (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

vincent@vincent-VB:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: *Ubuntu 18.04.5 LTS*
Release: 18.04
Codename: bionic

Example of most recent URL mistakes in my package detected by CRAN package
submission process which I could not detect locally:
Found the following (possibly) invalid URLs: URL:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533
(moved to
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142533)
From: inst/CITATION Status: 200 Message: OK URL: https://geneactiv.org/
(moved to https://www.activinsights.com/) From: inst/doc/GGIR.html Status:
200 Message: OK URL: https://www.accelting.com/ (moved to
https://accelting.com/) From: inst/doc/GGIR.html Status: 200 Message: OK
URL: https://www.physiology.org/doi/10.1152/japplphysiol.00421.2014 (moved
to https://journals.physiology.org/doi/10.1152/japplphysiol.00421.2014)
From: inst/CITATION Status: 200 Message: OK

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Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] Error in winbuilder

Re: [R-pkg-devel] Error in winbuilder

Re: [R-pkg-devel] Error in winbuilder

Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] Error in winbuilder

Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] Error in winbuilder

Re: [R-pkg-devel] url checks not working for me

Re: [R-pkg-devel] url checks not working for me

[R-pkg-devel] url checks not working for me

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