Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-26 Thread Rahmatallah, Yasir 
Lori,

Thank you for the clarification. I will try it.

Yasir

From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, April 26, 2018 6:14 AM
To: Rahmatallah, Yasir; joris.m...@ugent.be
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in 
package yy does not exist "


The packages will not be rejected for this WARNING, but please see the 
suggestion in the previous response that also might help clear them up.

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dexts.html-23Cross-5F002dreferences=DwQFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4=>





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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Joris Meys <joris.m...@ugent.be<mailto:joris.m...@ugent.be>>
Sent: Thursday, April 26, 2018 4:30:08 AM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in 
package yy does not exist "

On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir 
<yrahmatal...@uams.edu<mailto:yrahmatal...@uams.edu>>
wrote:

> Dear all,
>
> Build report show that many packages still have check warnings due to
> missing file links (cross referencing pages from other packages) under
> windows. The issue happens because there are different man pages for
> different operating systems. My package (GSAR) shows the same warning under
> Windows in the build report, although it locally passes R CMD build and R
> CMD check without warnings. Although not a perfect solution, substituting
> the linking in the .Rd file \code{\link[pkg:bar]{foo}} with
> \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent
> discussion
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013315.html=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=Mv-R1qX6544OBh7KthjZO_bsy4Vi1k7I8cQ4lcxDVN4=>


Actually, that is the correct solution. As per "Writing R Extensions",
\link[pkg]{name} searches for a html file with the name name.html in
package pkg. In a number of cases the name of the html help file is not the
same as the function you want to point to. For example, ppois and qpois etc
are discussed in a page called Poisson. Also in "Writing R Extensions" they
mention that if you want to use another name as a link, you should do
\link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dexts.html-23Cross-5F002dreferences=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4=>

>
> I understood that although a check warning is produced (under Windows
> only), it will be accepted (considered as advice) and packages that
> currently show it will proceed to Bioc release. Is that correct? There are
> still many packages showing this warning in yesterday's report
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.7_bioc-2DLATEST_-23show-3Dwarnings=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=loZl-moADbYBJHjxIwCU5MzqJc2uYVLPa0i7psS3eg0=>
>

As this is the case for even recommended packages like the survival
package, I don't see how this would be a reason to reject a package. But it
still makes sense to adapt your links in the way it is specified in the
official R manual.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3DCoupure-2Blinks-2B653-2C-25C2-25A0B-2D9000-2BGent-2C-25C2-25A0Belgium-26entry-3Dgmail-26source-3Dg=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWd

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-26 Thread Shepherd, Lori 
The packages will not be rejected for this WARNING, but please see the 
suggestion in the previous response that also might help clear them up.

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences




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-boun...@r-project.org> on behalf of Joris Meys 
<joris.m...@ugent.be>
Sent: Thursday, April 26, 2018 4:30:08 AM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in 
package yy does not exist "

On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir <yrahmatal...@uams.edu>
wrote:

> Dear all,
>
> Build report show that many packages still have check warnings due to
> missing file links (cross referencing pages from other packages) under
> windows. The issue happens because there are different man pages for
> different operating systems. My package (GSAR) shows the same warning under
> Windows in the build report, although it locally passes R CMD build and R
> CMD check without warnings. Although not a perfect solution, substituting
> the linking in the .Rd file \code{\link[pkg:bar]{foo}} with
> \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent
> discussion
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html


Actually, that is the correct solution. As per "Writing R Extensions",
\link[pkg]{name} searches for a html file with the name name.html in
package pkg. In a number of cases the name of the html help file is not the
same as the function you want to point to. For example, ppois and qpois etc
are discussed in a page called Poisson. Also in "Writing R Extensions" they
mention that if you want to use another name as a link, you should do
\link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences

>
> I understood that although a check warning is produced (under Windows
> only), it will be accepted (considered as advice) and packages that
> currently show it will proceed to Bioc release. Is that correct? There are
> still many packages showing this warning in yesterday's report
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings
>

As this is the case for even recommended packages like the survival
package, I don't see how this would be a reason to reject a package. But it
still makes sense to adapt your links in the way it is specified in the
official R manual.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-26 Thread Joris Meys 
On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir 
wrote:

> Dear all,
>
> Build report show that many packages still have check warnings due to
> missing file links (cross referencing pages from other packages) under
> windows. The issue happens because there are different man pages for
> different operating systems. My package (GSAR) shows the same warning under
> Windows in the build report, although it locally passes R CMD build and R
> CMD check without warnings. Although not a perfect solution, substituting
> the linking in the .Rd file \code{\link[pkg:bar]{foo}} with
> \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent
> discussion
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html


Actually, that is the correct solution. As per "Writing R Extensions",
\link[pkg]{name} searches for a html file with the name name.html in
package pkg. In a number of cases the name of the html help file is not the
same as the function you want to point to. For example, ppois and qpois etc
are discussed in a page called Poisson. Also in "Writing R Extensions" they
mention that if you want to use another name as a link, you should do
\link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences

>
> I understood that although a check warning is produced (under Windows
> only), it will be accepted (considered as advice) and packages that
> currently show it will proceed to Bioc release. Is that correct? There are
> still many packages showing this warning in yesterday's report
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings
>

As this is the case for even recommended packages like the survival
package, I don't see how this would be a reason to reject a package. But it
still makes sense to adapt your links in the way it is specified in the
official R manual.

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-25 Thread Rahmatallah, Yasir 
Dear all,

Build report show that many packages still have check warnings due to missing 
file links (cross referencing pages from other packages) under windows. The 
issue happens because there are different man pages for different operating 
systems. My package (GSAR) shows the same warning under Windows in the build 
report, although it locally passes R CMD build and R CMD check without 
warnings. Although not a perfect solution, substituting the linking in the .Rd 
file \code{\link[pkg:bar]{foo}} with \code{\link{foo}} or 
\code{\link[pkg]{foo}} was suggested in a recent discussion
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html
I understood that although a check warning is produced (under Windows only), it 
will be accepted (considered as advice) and packages that currently show it 
will proceed to Bioc release. Is that correct? There are still many packages 
showing this warning in yesterday's report
http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings

Thank you,
Yasir

Yasir Rahmatallah, PhD
Assistant Professor
Department of Biomedical Informatics
University of Arkansas for Medical Sciences (UAMS)
4301 W. Markham St., slot 782, office 476, Little Rock, AR 72205

-Original Message-
From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Vincent 
Carey
Sent: Wednesday, April 18, 2018 2:14 PM
To: Martin Morgan
Cc: bioc-devel; ramon.d...@iib.uam.es
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in 
package yy does not exist "

yes, the [] is a habit i need to break.  ok, we'll get by.

On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan < martin.mor...@roswellpark.org> 
wrote:

>
>
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan < 
>> martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
>> wrote:
>>
>>
>>
>> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>>
>>
>> Dear Martin,
>>
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan
>> <martin.mor...@roswellpark.org
>> <mailto:martin.mor...@roswellpark.org>> wrote:
>>
>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>>
>> I have recently faced a similar warning.
>> This is when a link to a help page of another package is
>> broken (there is
>> not such help page). Although those could be false
>> positives:
>> mclapply help page does exists in parallel package.
>> as.MAList does exists in devel limma
>>
>>
>> when \link-ing to another package, from RShowDoc("R-exts")
>> section 2.5
>> the [] has to name the html help page, not the name of the
>> function. For
>> instance, `mclapply` is documented on a man page called
>> mcdummies.Rd
>> (!), so '\link[parallel:mcdummies]{nearest} would 
>> presumably not
>>
>>
>> I am confused here: as far as I can tell, there is an
>> mclapply.html file:
>>
>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__stat.ethz.ch_R-2D
>> manual_R-2Ddevel_library_parallel_html_m=DwIFaQ=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=pdAHJUFvmcwWmj0ex
>> F6lMOOuP8Dv-l3xeaCJK8C7VCI=
>> clapply.html
>> 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__stat.ethz.ch_R-2
>> Dmanual_R-2Ddevel_library_parallel_html_=DwIFaQ=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=ZmZcWjEF0mMhZfp_F
>> fBLbP0o7TSjRcTe-C5vLFDMxt8=
>> mclapply.html>
>>
>> In addition, when I use the \link[parallel:mcdummies] I get a
>> warning when
>> testing under Linux.
>>
>>
>> yeah, this is a pretty good one. If you look at
>>
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r-2Dsource_tree_trunk_src_library_parallel_man=DwIFaQ=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=9d8xOxiij058sxHT_J9Nqk3e-z0Hwh4CoSXVNelJqu4=
>> 
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_
>> r-2Dsource_tree_trunk_src_library_parallel_man=DwIFaQ=27AKQ-AFTMv
>> LXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaD

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-19 Thread Ramon Diaz-Uriarte 
On Wed, 18-April-2018, at 21:09:32, Martin Morgan 
 wrote:
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>> 
>> 
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan 
>> > 
>> wrote:
>> 
>> 
>> 
>> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>> 
>> 
>> Dear Martin,
>> 
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan
>> > > wrote:
>> 
>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>> 
>> I have recently faced a similar warning.
>> This is when a link to a help page of another package is
>> broken (there is
>> not such help page). Although those could be false
>> positives:
>> mclapply help page does exists in parallel package.
>> as.MAList does exists in devel limma
>> 
>> 
>> when \link-ing to another package, from RShowDoc("R-exts")
>> section 2.5
>> the [] has to name the html help page, not the name of the
>> function. For
>> instance, `mclapply` is documented on a man page called
>> mcdummies.Rd
>> (!), so '\link[parallel:mcdummies]{nearest} would presumably not
>> 
>> 
>> I am confused here: as far as I can tell, there is an
>> mclapply.html file:
>> 
>> 
>> http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html
>> 
>> 
>> 
>> In addition, when I use the \link[parallel:mcdummies] I get a
>> warning when
>> testing under Linux.
>> 
>> 
>> yeah, this is a pretty good one. If you look at
>> 
>> https://github.com/wch/r-source/tree/trunk/src/library/parallel/man
>> 
>> 
>> you'll see that there are different man pages for different
>> operating systems. On windows there is mcdummies, on unix mclapply &
>> friends. This seems like a bad idea (users comparing notes to work
>> through a problem get different help pages!). I don't really know
>> how to link explicitly to these in a conditional manner.
>> 
>> 
>> Does this mean that to cross-reference to MArrayLM-class, I need to find 
>> limma source and
>> determine that the topic is covered in marraylm.Rd and use 
>> \link[limma:marraylm]{MArrayLM-class} for
>> the cross-reference? I don't see how this is good -- are the page names 
>> programmatically accessible
>> to developers who want to cross-reference? here's the grep result:
>> 
>> marraylm.Rd:\alias{MArrayLM-class}
>
> I agree that this is a bad idea.
>
> I think the first solution is not to use \link[pkg]{foo} when it is not 
> needed, which Writing R Extensions 
> (https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences)
>  
> says
>
>"These are rarely needed, perhaps to refer to not-yet-installed 
> packages (but there the HTML help system will resolve the link at run 
> time) or in the normally undesirable event that more than one package 
> offers help on a topic"
>
> Packages you depend / import and even suggest will be installed by the 
> build system, so the only need is when two or more packages define the 
> same topic.
>
> But even then, when faced with a WARNING, and even Bioc core team 
> members or reviewers for new packages hassling you about correcting 
> WARNINGs, I personally would trade off sanity for perfection and stick 
> with \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning 
> says that it's going to treat MArrayLM-class as a topic (alias) and 
> it'll get resolved correctly.
>

Martin, thanks for the detailed explanation (and the choice of sanity over
perfection :-) ). 


Best,

R.


> Also, for what it's worth, the opinion expressed in 
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences
>  
> is that the fact that these WARNINGs are often Windows-specific is more 
> likely that the linux check is wrong (i.e., the WARNING should also be 
> generated there). I will try to investigate that further.
>
> Martin
>
>
>> 
>> 
>> And in general it seems highly fragile to link to the name of the
>> help page, rather than to the alias. I'd treat the 'warning' as
>> (maybe bad) advice, rather than a requirement.
>> 
>> On rereading section 2.5, I think \link[pkg]{foo} should work
>> too (if there
>> is a foo.html file.)
>> 
>> 
>> it does (but on windows there is no mclapply.html). But also on
>> windows the '...treated as a topic' part of the warning actually
>> indicates that R has figured out where it should link, so you get
>> the warning but also a working link.
>> 
>>

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-18 Thread Martin Morgan 



On 04/18/2018 02:45 PM, Vincent Carey wrote:



On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan 
> 
wrote:




On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:


Dear Martin,

On Fri, 06-April-2018, at 18:59:00, Martin Morgan
> wrote:

On 04/06/2018 10:44 AM, Lluís Revilla wrote:

I have recently faced a similar warning.
This is when a link to a help page of another package is
broken (there is
not such help page). Although those could be false
positives:
mclapply help page does exists in parallel package.
as.MAList does exists in devel limma


when \link-ing to another package, from RShowDoc("R-exts")
section 2.5
the [] has to name the html help page, not the name of the
function. For
instance, `mclapply` is documented on a man page called
mcdummies.Rd
(!), so '\link[parallel:mcdummies]{nearest} would presumably not


I am confused here: as far as I can tell, there is an
mclapply.html file:

http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html



In addition, when I use the \link[parallel:mcdummies] I get a
warning when
testing under Linux.


yeah, this is a pretty good one. If you look at

https://github.com/wch/r-source/tree/trunk/src/library/parallel/man


you'll see that there are different man pages for different
operating systems. On windows there is mcdummies, on unix mclapply &
friends. This seems like a bad idea (users comparing notes to work
through a problem get different help pages!). I don't really know
how to link explicitly to these in a conditional manner.


Does this mean that to cross-reference to MArrayLM-class, I need to find 
limma source and
determine that the topic is covered in marraylm.Rd and use 
\link[limma:marraylm]{MArrayLM-class} for
the cross-reference?  I don't see how this is good -- are the page names 
programmatically accessible

to developers who want to cross-reference?  here's the grep result:

marraylm.Rd:\alias{MArrayLM-class}


I agree that this is a bad idea.

I think the first solution is not to use \link[pkg]{foo} when it is not 
needed, which Writing R Extensions 
(https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences) 
says


  "These are rarely needed, perhaps to refer to not-yet-installed 
packages (but there the HTML help system will resolve the link at run 
time) or in the normally undesirable event that more than one package 
offers help on a topic"


Packages you depend / import and even suggest will be installed by the 
build system, so the only need is when two or more packages define the 
same topic.


But even then, when faced with a WARNING, and even Bioc core team 
members or reviewers for new packages hassling you about correcting 
WARNINGs, I personally would trade off sanity for perfection and stick 
with \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning 
says that it's going to treat MArrayLM-class as a topic (alias) and 
it'll get resolved correctly.


Also, for what it's worth, the opinion expressed in 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences 
is that the fact that these WARNINGs are often Windows-specific is more 
likely that the linux check is wrong (i.e., the WARNING should also be 
generated there). I will try to investigate that further.


Martin





And in general it seems highly fragile to link to the name of the
help page, rather than to the alias. I'd treat the 'warning' as
(maybe bad) advice, rather than a requirement.

On rereading section 2.5, I think \link[pkg]{foo} should work
too (if there
is a foo.html file.)


it does (but on windows there is no mclapply.html). But also on
windows the '...treated as a topic' part of the warning actually
indicates that R has figured out where it should link, so you get
the warning but also a working link.

Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
\link[pkg:bar]{foo} are rarely needed, so I'll try to remove
them (except
in those cases, covered in section 2.5, where "more than one
package offers
help on a topic")


yes the first pass should also be the simplest -- no fancy markup
unless necessary.

Martin




generate the warning. Similarly
\link[limma:asmalist]{as.MAList}.

There are several things that still need

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-18 Thread Vincent Carey 
yes, the [] is a habit i need to break.  ok, we'll get by.

On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

>
>
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
>> martin.mor...@roswellpark.org >
>> wrote:
>>
>>
>>
>> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>>
>>
>> Dear Martin,
>>
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan
>> > > wrote:
>>
>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>>
>> I have recently faced a similar warning.
>> This is when a link to a help page of another package is
>> broken (there is
>> not such help page). Although those could be false
>> positives:
>> mclapply help page does exists in parallel package.
>> as.MAList does exists in devel limma
>>
>>
>> when \link-ing to another package, from RShowDoc("R-exts")
>> section 2.5
>> the [] has to name the html help page, not the name of the
>> function. For
>> instance, `mclapply` is documented on a man page called
>> mcdummies.Rd
>> (!), so '\link[parallel:mcdummies]{nearest} would presumably
>> not
>>
>>
>> I am confused here: as far as I can tell, there is an
>> mclapply.html file:
>>
>> http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/m
>> clapply.html
>> > mclapply.html>
>>
>> In addition, when I use the \link[parallel:mcdummies] I get a
>> warning when
>> testing under Linux.
>>
>>
>> yeah, this is a pretty good one. If you look at
>>
>> https://github.com/wch/r-source/tree/trunk/src/library/parallel/man
>> 
>>
>> you'll see that there are different man pages for different
>> operating systems. On windows there is mcdummies, on unix mclapply &
>> friends. This seems like a bad idea (users comparing notes to work
>> through a problem get different help pages!). I don't really know
>> how to link explicitly to these in a conditional manner.
>>
>>
>> Does this mean that to cross-reference to MArrayLM-class, I need to find
>> limma source and
>> determine that the topic is covered in marraylm.Rd and use
>> \link[limma:marraylm]{MArrayLM-class} for
>> the cross-reference?  I don't see how this is good -- are the page names
>> programmatically accessible
>> to developers who want to cross-reference?  here's the grep result:
>>
>> marraylm.Rd:\alias{MArrayLM-class}
>>
>
> I agree that this is a bad idea.
>
> I think the first solution is not to use \link[pkg]{foo} when it is not
> needed, which Writing R Extensions (https://cran.r-project.org/do
> c/manuals/r-release/R-exts.html#Cross_002dreferences) says
>
>   "These are rarely needed, perhaps to refer to not-yet-installed packages
> (but there the HTML help system will resolve the link at run time) or in
> the normally undesirable event that more than one package offers help on a
> topic"
>
> Packages you depend / import and even suggest will be installed by the
> build system, so the only need is when two or more packages define the same
> topic.
>
> But even then, when faced with a WARNING, and even Bioc core team members
> or reviewers for new packages hassling you about correcting WARNINGs, I
> personally would trade off sanity for perfection and stick with
> \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning says
> that it's going to treat MArrayLM-class as a topic (alias) and it'll get
> resolved correctly.
>
> Also, for what it's worth, the opinion expressed in
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html
> #Cross_002dreferences is that the fact that these WARNINGs are often
> Windows-specific is more likely that the linux check is wrong (i.e., the
> WARNING should also be generated there). I will try to investigate that
> further.
>
> Martin
>
>
>
>>
>> And in general it seems highly fragile to link to the name of the
>> help page, rather than to the alias. I'd treat the 'warning' as
>> (maybe bad) advice, rather than a requirement.
>>
>> On rereading section 2.5, I think \link[pkg]{foo} should work
>> too (if there
>> is a foo.html file.)
>>
>>
>> it does (but on windows there is no mclapply.html). But also on
>> windows the '...treated as a topic' part of the warning actually
>> indicates that R has figured out where it should link, so you get
>> the warning but also a working link.
>>
>> Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
>> \link[pkg:bar]{foo} are rarely

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-18 Thread Vincent Carey 
On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

>
>
> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>
>>
>> Dear Martin,
>>
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>>
>>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>>>
 I have recently faced a similar warning.
 This is when a link to a help page of another package is broken (there
 is
 not such help page). Although those could be false positives:
 mclapply help page does exists in parallel package.
 as.MAList does exists in devel limma

>>>
>>> when \link-ing to another package, from RShowDoc("R-exts") section 2.5
>>> the [] has to name the html help page, not the name of the function. For
>>> instance, `mclapply` is documented on a man page called mcdummies.Rd
>>> (!), so '\link[parallel:mcdummies]{nearest} would presumably not
>>>
>>
>> I am confused here: as far as I can tell, there is an mclapply.html file:
>>
>> http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html
>>
>> In addition, when I use the \link[parallel:mcdummies] I get a warning when
>> testing under Linux.
>>
>
> yeah, this is a pretty good one. If you look at
>
>   https://github.com/wch/r-source/tree/trunk/src/library/parallel/man
>
> you'll see that there are different man pages for different operating
> systems. On windows there is mcdummies, on unix mclapply & friends. This
> seems like a bad idea (users comparing notes to work through a problem get
> different help pages!). I don't really know how to link explicitly to these
> in a conditional manner.
>

Does this mean that to cross-reference to MArrayLM-class, I need to find
limma source and
determine that the topic is covered in marraylm.Rd and use
\link[limma:marraylm]{MArrayLM-class} for
the cross-reference?  I don't see how this is good -- are the page names
programmatically accessible
to developers who want to cross-reference?  here's the grep result:

marraylm.Rd:\alias{MArrayLM-class}


>
> And in general it seems highly fragile to link to the name of the help
> page, rather than to the alias. I'd treat the 'warning' as (maybe bad)
> advice, rather than a requirement.
>
> On rereading section 2.5, I think \link[pkg]{foo} should work too (if there
>> is a foo.html file.)
>>
>
> it does (but on windows there is no mclapply.html). But also on windows
> the '...treated as a topic' part of the warning actually indicates that R
> has figured out where it should link, so you get the warning but also a
> working link.
>
> Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
>> \link[pkg:bar]{foo} are rarely needed, so I'll try to remove them (except
>> in those cases, covered in section 2.5, where "more than one package
>> offers
>> help on a topic")
>>
>
> yes the first pass should also be the simplest -- no fancy markup unless
> necessary.
>
> Martin
>
>
>
>>
>> generate the warning. Similarly \link[limma:asmalist]{as.MAList}.
>>>
>>> There are several things that still need exploration.
>>>
>>> - platform-specific (I have a vague understanding that Windows is
>>> special, but that might be outdated... [at least in this context...])
>>>
>>>
>> I am only getting the warnings under Windows (which lead me to think it
>> was
>> windows misbehaving).
>>
>>
>> - recent. I have to admit to changing the text of the warning with this
>>> commit
>>>
>>>
>>> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11e
>>> e2440fbde891cba524e
>>>
>>> but what I was intending to do was to change what it says, from the
>>> warning in release ('missing file link') to what it says, correctly, in
>>> devel 'file link ... does not exist and so has been treated as a topic'.
>>> The old text appears in release, and the new in devel, as anticipated.
>>> If I messed up somehow please let me know...
>>>
>>> - even with the warning, the link isn't broken in the dynamic help
>>> system (it might have been broken prior to my commit...).
>>>
>>
>> OK, thanks.
>>
>> Best,
>>
>>
>> R.
>>
>>
>>
>>> Martin
>>>
>>>
 HTH

 On 6 April 2018 at 16:35, Vincent Carey 
 wrote:

 ive seen this too apropos bigrquery on windows
>
> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
> wrote:
>
>
>> Dear All,
>>
>> Two packages I maintain are showing, in Windows, a warning during
>> check
>> with messages like
>>
>> Rd warning:
>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL2
>> 3343f935731/
>>
> OncoSimulR/man/oncoSimulIndiv.Rd:570:
>
>> file link 'mclapply' in package 'parallel' does not exist and so has
>> been
>> treated as a topic
>>
>> or
>>
>> Rd warning:
>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>>
> INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
>
>> file link 'as.MAList' in package

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-16 Thread Ramon Diaz-Uriarte 

Dear Martin,


On Mon, 09-April-2018, at 17:35:47, Martin Maechler 
 wrote:
>> Ramon Diaz-Uriarte 
>> on Mon, 9 Apr 2018 16:51:38 +0200 writes:
>
> > Dear Martin,
>
> > On Fri, 06-April-2018, at 18:59:00, Martin Morgan
> >  wrote:
> >> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
> >>> I have recently faced a similar warning.  This is when a
> >>> link to a help page of another package is broken (there
> >>> is not such help page). Although those could be false
> >>> positives: mclapply help page does exists in parallel
> >>> package.  as.MAList does exists in devel limma
> >> 
> >> when \link-ing to another package, from
> >> RShowDoc("R-exts") section 2.5 the [] has to name the
> >> html help page, not the name of the function. For
> >> instance, `mclapply` is documented on a man page called
> >> mcdummies.Rd (!), so '\link[parallel:mcdummies]{nearest}
> >> would presumably not
>
> > I am confused here: as far as I can tell, there is an
> > mclapply.html file:
>
> > http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html
>
> > In addition, when I use the \link[parallel:mcdummies] I
> > get a warning when testing under Linux.
>
>
> > On rereading section 2.5, I think \link[pkg]{foo} should
> > work too (if there is a foo.html file.)
>
> > Nevertheless, section 2.5 indicates that \link[pkg]{foo}
> > and \link[pkg:bar]{foo} are rarely needed, so I'll try to
> > remove them (except in those cases, covered in section
> > 2.5, where "more than one package offers help on a topic")
>
> Only on Windows, indeed,
> mclapply() is just a dummy function, calling lapply() IIRC.
>
> It is unfortunate that given the above you would be lead to use
> different \link{}s if you are on Windows than on non-Win...
>
> This would be a good question on the   R-package-devel   mailing
> list.
>

Done (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html).

Thanks,

R.


> Martin
>
>
> >> generate the warning. Similarly
> >> \link[limma:asmalist]{as.MAList}.
> >> 
> >> There are several things that still need exploration.
> >> 
> >> - platform-specific (I have a vague understanding that
> >> Windows is special, but that might be outdated... [at
> >> least in this context...])
> >> 
>
> > I am only getting the warnings under Windows (which lead
> > me to think it was windows misbehaving).
>
>
> >> - recent. I have to admit to changing the text of the
> >> warning with this commit
> >> 
> >> 
> >> 
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> >> 
> >> but what I was intending to do was to change what it
> >> says, from the warning in release ('missing file link')
> >> to what it says, correctly, in devel 'file link ... does
> >> not exist and so has been treated as a topic'.  The old
> >> text appears in release, and the new in devel, as
> >> anticipated.  If I messed up somehow please let me
> >> know...
> >> 
> >> - even with the warning, the link isn't broken in the
> >> dynamic help system (it might have been broken prior to
> >> my commit...).
>
> > OK, thanks.
>
> > Best,
>
>
> > R.
>
>
> >> 
> >> Martin
> >> 
> >>> 
> >>> HTH
> >>> 
> >>> On 6 April 2018 at 16:35, Vincent Carey
> >>>  wrote:
> >>> 
>  ive seen this too apropos bigrquery on windows
>  
>  On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
>   wrote:
>  
> > 
> > Dear All,
> > 
> > Two packages I maintain are showing, in Windows, a
> > warning during check with messages like
> > 
> > Rd warning:
> > 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>  OncoSimulR/man/oncoSimulIndiv.Rd:570:
> > file link 'mclapply' in package 'parallel' does not
> > exist and so has been treated as a topic
> > 
> > or
> > 
> > Rd warning:
> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>  INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> > file link 'as.MAList' in package 'limma' does not
> > exist and so has been treated as a topic
> > 
> > 
> > 
> > that I cannot reproduce under Linux and that I think
> > are false positives. Is there a way to avoid this
> > warning? As far as I can tell, those links really
> > exist.
> > 
> > Best,
> > 
> > 
> > R.
> > 
> > --
> > Ramon Diaz-Uriarte Department of Biochemistry, Lab
> > B-25 Facultad de Medicina Universidad

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-09 Thread Martin Morgan 



On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:


Dear Martin,

On Fri, 06-April-2018, at 18:59:00, Martin Morgan 
 wrote:

On 04/06/2018 10:44 AM, Lluís Revilla wrote:

I have recently faced a similar warning.
This is when a link to a help page of another package is broken (there is
not such help page). Although those could be false positives:
mclapply help page does exists in parallel package.
as.MAList does exists in devel limma


when \link-ing to another package, from RShowDoc("R-exts") section 2.5
the [] has to name the html help page, not the name of the function. For
instance, `mclapply` is documented on a man page called mcdummies.Rd
(!), so '\link[parallel:mcdummies]{nearest} would presumably not


I am confused here: as far as I can tell, there is an mclapply.html file:

http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html

In addition, when I use the \link[parallel:mcdummies] I get a warning when
testing under Linux.


yeah, this is a pretty good one. If you look at

  https://github.com/wch/r-source/tree/trunk/src/library/parallel/man

you'll see that there are different man pages for different operating 
systems. On windows there is mcdummies, on unix mclapply & friends. This 
seems like a bad idea (users comparing notes to work through a problem 
get different help pages!). I don't really know how to link explicitly 
to these in a conditional manner.


And in general it seems highly fragile to link to the name of the help 
page, rather than to the alias. I'd treat the 'warning' as (maybe bad) 
advice, rather than a requirement.



On rereading section 2.5, I think \link[pkg]{foo} should work too (if there
is a foo.html file.)


it does (but on windows there is no mclapply.html). But also on windows 
the '...treated as a topic' part of the warning actually indicates that 
R has figured out where it should link, so you get the warning but also 
a working link.



Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
\link[pkg:bar]{foo} are rarely needed, so I'll try to remove them (except
in those cases, covered in section 2.5, where "more than one package offers
help on a topic")


yes the first pass should also be the simplest -- no fancy markup unless 
necessary.


Martin





generate the warning. Similarly \link[limma:asmalist]{as.MAList}.

There are several things that still need exploration.

- platform-specific (I have a vague understanding that Windows is
special, but that might be outdated... [at least in this context...])



I am only getting the warnings under Windows (which lead me to think it was
windows misbehaving).



- recent. I have to admit to changing the text of the warning with this
commit


https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e

but what I was intending to do was to change what it says, from the
warning in release ('missing file link') to what it says, correctly, in
devel 'file link ... does not exist and so has been treated as a topic'.
The old text appears in release, and the new in devel, as anticipated.
If I messed up somehow please let me know...

- even with the warning, the link isn't broken in the dynamic help
system (it might have been broken prior to my commit...).


OK, thanks.

Best,


R.




Martin



HTH

On 6 April 2018 at 16:35, Vincent Carey  wrote:


ive seen this too apropos bigrquery on windows

On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
wrote:



Dear All,

Two packages I maintain are showing, in Windows, a warning during check
with messages like

Rd warning:
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/

OncoSimulR/man/oncoSimulIndiv.Rd:570:

file link 'mclapply' in package 'parallel' does not exist and so has been
treated as a topic

or

Rd warning:
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.

INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:

file link 'as.MAList' in package 'limma' does not exist and so has been
treated as a topic



that I cannot reproduce under Linux and that I think are false
positives. Is there a way to avoid this warning? As far as I can tell,
those links really exist.

Best,


R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
 ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



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___
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-09 Thread Martin Maechler 
> Ramon Diaz-Uriarte 
> on Mon, 9 Apr 2018 16:51:38 +0200 writes:

> Dear Martin,

> On Fri, 06-April-2018, at 18:59:00, Martin Morgan
>  wrote:
>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>>> I have recently faced a similar warning.  This is when a
>>> link to a help page of another package is broken (there
>>> is not such help page). Although those could be false
>>> positives: mclapply help page does exists in parallel
>>> package.  as.MAList does exists in devel limma
>> 
>> when \link-ing to another package, from
>> RShowDoc("R-exts") section 2.5 the [] has to name the
>> html help page, not the name of the function. For
>> instance, `mclapply` is documented on a man page called
>> mcdummies.Rd (!), so '\link[parallel:mcdummies]{nearest}
>> would presumably not

> I am confused here: as far as I can tell, there is an
> mclapply.html file:

> http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html

> In addition, when I use the \link[parallel:mcdummies] I
> get a warning when testing under Linux.


> On rereading section 2.5, I think \link[pkg]{foo} should
> work too (if there is a foo.html file.)

> Nevertheless, section 2.5 indicates that \link[pkg]{foo}
> and \link[pkg:bar]{foo} are rarely needed, so I'll try to
> remove them (except in those cases, covered in section
> 2.5, where "more than one package offers help on a topic")

Only on Windows, indeed,
mclapply() is just a dummy function, calling lapply() IIRC.

It is unfortunate that given the above you would be lead to use
different \link{}s if you are on Windows than on non-Win...

This would be a good question on the   R-package-devel   mailing
list.

Martin


>> generate the warning. Similarly
>> \link[limma:asmalist]{as.MAList}.
>> 
>> There are several things that still need exploration.
>> 
>> - platform-specific (I have a vague understanding that
>> Windows is special, but that might be outdated... [at
>> least in this context...])
>> 

> I am only getting the warnings under Windows (which lead
> me to think it was windows misbehaving).


>> - recent. I have to admit to changing the text of the
>> warning with this commit
>> 
>> 
>> 
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
>> 
>> but what I was intending to do was to change what it
>> says, from the warning in release ('missing file link')
>> to what it says, correctly, in devel 'file link ... does
>> not exist and so has been treated as a topic'.  The old
>> text appears in release, and the new in devel, as
>> anticipated.  If I messed up somehow please let me
>> know...
>> 
>> - even with the warning, the link isn't broken in the
>> dynamic help system (it might have been broken prior to
>> my commit...).

> OK, thanks.

> Best,


> R.


>> 
>> Martin
>> 
>>> 
>>> HTH
>>> 
>>> On 6 April 2018 at 16:35, Vincent Carey
>>>  wrote:
>>> 
 ive seen this too apropos bigrquery on windows
 
 On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
  wrote:
 
> 
> Dear All,
> 
> Two packages I maintain are showing, in Windows, a
> warning during check with messages like
> 
> Rd warning:
> 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
 OncoSimulR/man/oncoSimulIndiv.Rd:570:
> file link 'mclapply' in package 'parallel' does not
> exist and so has been treated as a topic
> 
> or
> 
> Rd warning:
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
 INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> file link 'as.MAList' in package 'limma' does not
> exist and so has been treated as a topic
> 
> 
> 
> that I cannot reproduce under Linux and that I think
> are false positives. Is there a way to avoid this
> warning? As far as I can tell, those links really
> exist.
> 
> Best,
> 
> 
> R.
> 
> --
> Ramon Diaz-Uriarte Department of Biochemistry, Lab
> B-25 Facultad de Medicina Universidad Autónoma de
> Madrid Arzobispo Morcillo, 4 28029 Madrid Spain
> 
> Phone: +34-91-497-2412
> 
> Email: rdia...@gmail.com ramon.d...@iib.uam.es
> 
> http://ligarto.org/rdiaz
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
 
 [[alternative HTML

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-09 Thread Ramon Diaz-Uriarte 

Dear Martin,

On Fri, 06-April-2018, at 18:59:00, Martin Morgan 
 wrote:
> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>> I have recently faced a similar warning.
>> This is when a link to a help page of another package is broken (there is
>> not such help page). Although those could be false positives:
>> mclapply help page does exists in parallel package.
>> as.MAList does exists in devel limma
>
> when \link-ing to another package, from RShowDoc("R-exts") section 2.5
> the [] has to name the html help page, not the name of the function. For
> instance, `mclapply` is documented on a man page called mcdummies.Rd
> (!), so '\link[parallel:mcdummies]{nearest} would presumably not

I am confused here: as far as I can tell, there is an mclapply.html file:

http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html

In addition, when I use the \link[parallel:mcdummies] I get a warning when
testing under Linux.

On rereading section 2.5, I think \link[pkg]{foo} should work too (if there
is a foo.html file.)

Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
\link[pkg:bar]{foo} are rarely needed, so I'll try to remove them (except
in those cases, covered in section 2.5, where "more than one package offers
help on a topic")



> generate the warning. Similarly \link[limma:asmalist]{as.MAList}.
>
> There are several things that still need exploration.
>
> - platform-specific (I have a vague understanding that Windows is
> special, but that might be outdated... [at least in this context...])
>

I am only getting the warnings under Windows (which lead me to think it was
windows misbehaving).


> - recent. I have to admit to changing the text of the warning with this
> commit
>
>
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
>
>but what I was intending to do was to change what it says, from the
> warning in release ('missing file link') to what it says, correctly, in
> devel 'file link ... does not exist and so has been treated as a topic'.
> The old text appears in release, and the new in devel, as anticipated.
> If I messed up somehow please let me know...
>
> - even with the warning, the link isn't broken in the dynamic help
> system (it might have been broken prior to my commit...).

OK, thanks.

Best,


R.


>
> Martin
>
>>
>> HTH
>>
>> On 6 April 2018 at 16:35, Vincent Carey  wrote:
>>
>>> ive seen this too apropos bigrquery on windows
>>>
>>> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
>>> wrote:
>>>

 Dear All,

 Two packages I maintain are showing, in Windows, a warning during check
 with messages like

 Rd warning:
 C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>>> OncoSimulR/man/oncoSimulIndiv.Rd:570:
 file link 'mclapply' in package 'parallel' does not exist and so has been
 treated as a topic

 or

 Rd warning:
 C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>>> INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
 file link 'as.MAList' in package 'limma' does not exist and so has been
 treated as a topic



 that I cannot reproduce under Linux and that I think are false
 positives. Is there a way to avoid this warning? As far as I can tell,
 those links really exist.

 Best,


 R.

 --
 Ramon Diaz-Uriarte
 Department of Biochemistry, Lab B-25
 Facultad de Medicina
 Universidad Autónoma de Madrid
 Arzobispo Morcillo, 4
 28029 Madrid
 Spain

 Phone: +34-91-497-2412

 Email: rdia...@gmail.com
 ramon.d...@iib.uam.es

 http://ligarto.org/rdiaz

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel

>>>
>>>  [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
> ___
> Bioc-devel@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 Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-06 Thread Martin Morgan 



On 04/06/2018 10:44 AM, Lluís Revilla wrote:

I have recently faced a similar warning.
This is when a link to a help page of another package is broken (there is
not such help page). Although those could be false positives:
mclapply help page does exists in parallel package.
as.MAList does exists in devel limma


when \link-ing to another package, from RShowDoc("R-exts") section 2.5 
the [] has to name the html help page, not the name of the function. For 
instance, `mclapply` is documented on a man page called mcdummies.Rd 
(!), so '\link[parallel:mcdummies]{nearest} would presumably not 
generate the warning. Similarly \link[limma:asmalist]{as.MAList}.


There are several things that still need exploration.

- platform-specific (I have a vague understanding that Windows is 
special, but that might be outdated... [at least in this context...])


- recent. I have to admit to changing the text of the warning with this 
commit



https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e

  but what I was intending to do was to change what it says, from the 
warning in release ('missing file link') to what it says, correctly, in 
devel 'file link ... does not exist and so has been treated as a topic'. 
The old text appears in release, and the new in devel, as anticipated. 
If I messed up somehow please let me know...


- even with the warning, the link isn't broken in the dynamic help 
system (it might have been broken prior to my commit...).


Martin



HTH

On 6 April 2018 at 16:35, Vincent Carey  wrote:


ive seen this too apropos bigrquery on windows

On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
wrote:



Dear All,

Two packages I maintain are showing, in Windows, a warning during check
with messages like

Rd warning:
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/

OncoSimulR/man/oncoSimulIndiv.Rd:570:

file link 'mclapply' in package 'parallel' does not exist and so has been
treated as a topic

or

Rd warning:
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.

INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:

file link 'as.MAList' in package 'limma' does not exist and so has been
treated as a topic



that I cannot reproduce under Linux and that I think are false
positives. Is there a way to avoid this warning? As far as I can tell,
those links really exist.

Best,


R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___
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 [[alternative HTML version deleted]]

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This email message may contain legally privileged and/or...{{dropped:2}}

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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-06 Thread Ramon Diaz-Uriarte 
Dear Lluis and Vincent,

Thanks for confirming this in other packages.

In the two examples shown, these must be false positives, as the links
exist. But also the fact that the warnings only appear in Windows suggests
a false positive: I do not understand how this warning would not be
triggered in Linux and Mac if the links did not exist.

Best,


R.


On Fri, 06-April-2018, at 16:44:42, Lluís Revilla  
wrote:
> I have recently faced a similar warning.
> This is when a link to a help page of another package is broken (there is
> not such help page). Although those could be false positives:
> mclapply help page does exists in parallel package.
> as.MAList does exists in devel limma
>
> HTH
>
> On 6 April 2018 at 16:35, Vincent Carey  wrote:
>
>> ive seen this too apropos bigrquery on windows
>>
>> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
>> wrote:
>>
>> >
>> > Dear All,
>> >
>> > Two packages I maintain are showing, in Windows, a warning during check
>> > with messages like
>> >
>> > Rd warning:
>> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>> OncoSimulR/man/oncoSimulIndiv.Rd:570:
>> > file link 'mclapply' in package 'parallel' does not exist and so has been
>> > treated as a topic
>> >
>> > or
>> >
>> > Rd warning:
>> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>> INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
>> > file link 'as.MAList' in package 'limma' does not exist and so has been
>> > treated as a topic
>> >
>> >
>> >
>> > that I cannot reproduce under Linux and that I think are false
>> > positives. Is there a way to avoid this warning? As far as I can tell,
>> > those links really exist.
>> >
>> > Best,
>> >
>> >
>> > R.
>> >
>> > --
>> > Ramon Diaz-Uriarte
>> > Department of Biochemistry, Lab B-25
>> > Facultad de Medicina
>> > Universidad Autónoma de Madrid
>> > Arzobispo Morcillo, 4
>> > 28029 Madrid
>> > Spain
>> >
>> > Phone: +34-91-497-2412
>> >
>> > Email: rdia...@gmail.com
>> >ramon.d...@iib.uam.es
>> >
>> > http://ligarto.org/rdiaz
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@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 Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-06 Thread Lluís Revilla 
I have recently faced a similar warning.
This is when a link to a help page of another package is broken (there is
not such help page). Although those could be false positives:
mclapply help page does exists in parallel package.
as.MAList does exists in devel limma

HTH

On 6 April 2018 at 16:35, Vincent Carey  wrote:

> ive seen this too apropos bigrquery on windows
>
> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
> wrote:
>
> >
> > Dear All,
> >
> > Two packages I maintain are showing, in Windows, a warning during check
> > with messages like
> >
> > Rd warning:
> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
> OncoSimulR/man/oncoSimulIndiv.Rd:570:
> > file link 'mclapply' in package 'parallel' does not exist and so has been
> > treated as a topic
> >
> > or
> >
> > Rd warning:
> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
> INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> > file link 'as.MAList' in package 'limma' does not exist and so has been
> > treated as a topic
> >
> >
> >
> > that I cannot reproduce under Linux and that I think are false
> > positives. Is there a way to avoid this warning? As far as I can tell,
> > those links really exist.
> >
> > Best,
> >
> >
> > R.
> >
> > --
> > Ramon Diaz-Uriarte
> > Department of Biochemistry, Lab B-25
> > Facultad de Medicina
> > Universidad Autónoma de Madrid
> > Arzobispo Morcillo, 4
> > 28029 Madrid
> > Spain
> >
> > Phone: +34-91-497-2412
> >
> > Email: rdia...@gmail.com
> >ramon.d...@iib.uam.es
> >
> > http://ligarto.org/rdiaz
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-06 Thread Vincent Carey 
ive seen this too apropos bigrquery on windows

On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte 
wrote:

>
> Dear All,
>
> Two packages I maintain are showing, in Windows, a warning during check
> with messages like
>
> Rd warning:
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/OncoSimulR/man/oncoSimulIndiv.Rd:570:
> file link 'mclapply' in package 'parallel' does not exist and so has been
> treated as a topic
>
> or
>
> Rd warning:
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> file link 'as.MAList' in package 'limma' does not exist and so has been
> treated as a topic
>
>
>
> that I cannot reproduce under Linux and that I think are false
> positives. Is there a way to avoid this warning? As far as I can tell,
> those links really exist.
>
> Best,
>
>
> R.
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email: rdia...@gmail.com
>ramon.d...@iib.uam.es
>
> http://ligarto.org/rdiaz
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-06 Thread Ramon Diaz-Uriarte 

Dear All,

Two packages I maintain are showing, in Windows, a warning during check
with messages like

Rd warning:  
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/OncoSimulR/man/oncoSimulIndiv.Rd:570:
  file link 'mclapply' in package 'parallel' does not exist and so has been  
treated as a topic

or

Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
 file link 'as.MAList' in package 'limma' does not exist and so has been 
treated as a topic
  


that I cannot reproduce under Linux and that I think are false
positives. Is there a way to avoid this warning? As far as I can tell,
those links really exist.

Best,


R.

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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