Dear all,
we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic
is there any other solution to removing all links to external packages?
thanks, jo
[Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>
8 messages · Mike Smith, Shepherd, Lori, Håkon Tjeldnes +2 more
Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html I think you should be able to get round it by including the name of Rd file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I haven't actually tested this though). Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote:
Dear all,
we're experiencing WARNINGS in xcms on Tokay2 that are all related to
links in Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd
that links to the method in MSnbase, that works nicely on Linux and macOS
build machines, but on tokay2 we get:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
a topic
is there any other solution to removing all links to external packages?
thanks, jo
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that works on Linux and macOS should also work on Windows - otherwise what's the matter of the alias? Interestingly, on my Windows test machine (Windows 7) I don't get these warnings (R-devel from 2018-01-07 r74091). jo
On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html I think you should be able to get round it by including the name of Rd file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I haven't actually tested this though). Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages. Example: we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic is there any other solution to removing all links to external packages? thanks, jo
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote:
Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that works on Linux and macOS should also work on Windows - otherwise what's the matter of the alias? Interestingly, on my Windows test machine (Windows 7) I don't get these warnings (R-devel from 2018-01-07 r74091). jo
On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in
I think you should be able to get round it by including the name of Rd
file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).
Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu>
wrote:
Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to
links in Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in
XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic
is there any other solution to removing all links to external packages? thanks, jo
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This was also discussed in this thread a few weeks ago https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Mike Smith <grimbough at gmail.com>
Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>
Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>
Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: > Thanks Mike, > > I somehow missed the discussion you mentioned. I would really not like to > include the name of the Rd file I want to link to. The *default* way that > works on Linux and macOS should also work on Windows - otherwise what's the > matter of the alias? Interestingly, on my Windows test machine (Windows 7) > I don't get these warnings (R-devel from 2018-01-07 r74091). > > jo > > > On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: > > > > Hi Johannes, > > > > xcms is certainly not alone with the warning, and it was discussed in > https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html > > > > I think you should be able to get round it by including the name of Rd > file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} > (I haven't actually tested this though). > > > > Mike > > > > On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu> > wrote: > > Dear all, > > > > we're experiencing WARNINGS in xcms on Tokay2 that are all related to > links in Rd files to functions and methods in other packages. > > Example: > > we have \code{\link[MSnbase]{pickPeaks}} in > XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that > works nicely on Linux and macOS build machines, but on tokay2 we get: > > > > Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R. > INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link > 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as > a topic > > > > is there any other solution to removing all links to external packages? > > > > thanks, jo > > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
Two ways works for me, either link to the Rd file or only use tokens.
Don't know what is best, but I use tokens, that is :
\code{\link[MSnbase:pickpeaks-method]{pickPeaks}} ----becomes---> \code{\link{pickPeaks}}
On Windows, when you install, it will automatically find the correct links.
Someone from BioC should confirm that what I am saying is correct and a safe way of doing it.
________________________________
Fra: Bioc-devel <bioc-devel-bounces at r-project.org> p? vegne av Mike Smith <grimbough at gmail.com>
Sendt: 16. april 2018 12:13
Til: Rainer Johannes; bioc-devel
Tokay2>
Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.
Mike
On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu>
wrote:
Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that
he
I don't get these warnings (R-devel from 2018-01-07 r74091). jo
On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in
I think you should be able to get round it by including the name of Rd
file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).
Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu>
wrote:
Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to
links in Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in
XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic
is there any other solution to removing all links to external packages? thanks, jo
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
And I have now asked this in R-pkg-devel (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as suggested by Martin Maechler (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the thread linked by Lori. But if you can use \link{foo} (instead of \link[pkg]{foo} and \link[pkg:bar]{foo}), as also suggested by H?kon Tjeldnes, then you should have no problems. Best, R.
On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori <Lori.Shepherd at RoswellPark.org> wrote:
This was also discussed in this thread a few weeks ago https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Mike Smith <grimbough at gmail.com> Sent: Monday, April 16, 2018 6:13:38 AM To: Rainer Johannes; bioc-devel Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2> Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that works on Linux and macOS should also work on Windows - otherwise what's the matter of the alias? Interestingly, on my Windows test machine (Windows 7) I don't get these warnings (R-devel from 2018-01-07 r74091). jo On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html I think you should be able to get round it by including the name of Rd file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I haven't actually tested this though). Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages. Example: we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R. INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic is there any other solution to removing all links to external packages? thanks, jo _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz
Thanks for the update Ramon,
I believe that in my case \link{foo} will not work, because e.g. the pickPeaks method is defined in ProtGenerics, but I want to link to the implementation in MSnbase.
I'm with Martin proposing this should be a NOTE rather than a WARNING (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002622.html)
jo
On 16 Apr 2018, at 17:41, Ramon Diaz-Uriarte <rdiaz02 at gmail.com> wrote: And I have now asked this in R-pkg-devel (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as suggested by Martin Maechler (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the thread linked by Lori. But if you can use \link{foo} (instead of \link[pkg]{foo} and \link[pkg:bar]{foo}), as also suggested by H?kon Tjeldnes, then you should have no problems. Best, R. On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori <Lori.Shepherd at RoswellPark.org> wrote:
This was also discussed in this thread a few weeks ago https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Mike Smith <grimbough at gmail.com> Sent: Monday, April 16, 2018 6:13:38 AM To: Rainer Johannes; bioc-devel Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2> Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: Thanks Mike, I somehow missed the discussion you mentioned. I would really not like to include the name of the Rd file I want to link to. The *default* way that works on Linux and macOS should also work on Windows - otherwise what's the matter of the alias? Interestingly, on my Windows test machine (Windows 7) I don't get these warnings (R-devel from 2018-01-07 r74091). jo On 16 Apr 2018, at 10:49, Mike Smith <grimbough at gmail.com> wrote: Hi Johannes, xcms is certainly not alone with the warning, and it was discussed in https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html I think you should be able to get round it by including the name of Rd file you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I haven't actually tested this though). Mike On 16 April 2018 at 09:06, Rainer Johannes <Johannes.Rainer at eurac.edu> wrote: Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages. Example: we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and macOS build machines, but on tokay2 we get: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R. INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as a topic is there any other solution to removing all links to external packages? thanks, jo _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz