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

Wed Aug 26 14:52:34 CEST 2020

On Wed, Aug 26, 2020 at 7:43 AM Vincent van Hees
<vincentvanhees using gmail.com> 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 <v.vanhees using accelting.com>'

New maintainer:
  Vincent T van Hees <v.vanhees using accelting.com>
Old maintainer(s):
  Vincent T van Hees <vincentvanhees using gmail.com>

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 <hanson using depauw.edu> 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 <vincentvanhees using gmail.com>
> > 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 using vincent-VB:~$ curl-config --version
> > > *libcurl 7.58.0*
> > >
> > > vincent using 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 using 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 using 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 using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com