[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Rahmatallah, Yasir
YRahmatallah at uams.edu
Wed Apr 25 23:52:35 CEST 2018
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-bounces at r-project.org] On Behalf Of Vincent Carey
Sent: Wednesday, April 18, 2018 2:14 PM
To: Martin Morgan
Cc: bioc-devel; ramon.diaz at 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.morgan at 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.morgan at roswellpark.org <mailto:martin.morgan at 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.morgan at roswellpark.org
>> <mailto:martin.morgan at 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&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=pdAHJUFvmcwWmj0ex
>> F6lMOOuP8Dv-l3xeaCJK8C7VCI&e=
>> clapply.html
>>
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__stat.ethz.ch_R-2
>> Dmanual_R-2Ddevel_library_parallel_html_&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=ZmZcWjEF0mMhZfp_F
>> fBLbP0o7TSjRcTe-C5vLFDMxt8&e=
>> 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&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=9d8xOxiij058sxHT_J9Nqk3e-z0Hwh4CoSXVNelJqu4&e=
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_
>> r-2Dsource_tree_trunk_src_library_parallel_man&d=DwIFaQ&c=27AKQ-AFTMv
>> LXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR
>> 5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=9d8xOxiij05
>> 8sxHT_J9Nqk3e-z0Hwh4CoSXVNelJqu4&e=>
>>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject
> .org_do&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft6
> 2y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7
> UZ2iMg6_7bpavI&s=VA_wL4Vla3uvCAXHqiNZWEXCYEKT-OgcBPMsjRtzTfk&e=
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.
> org_doc_manuals_r-2Drelease_R-2Dexts.html&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7
> shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFM
> uI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=xlivJQpLips7VDTJrYd
> g4HYtSco26wTCR8eblRiJUew&e= #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 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r
>> -2Dsource_commit_cbd7ca1b1aedf0405e11e&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7sh
>> ZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMu
>> I&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=J9oO8s3E5x0RS6sVrhX
>> vPqbvnamFfCDmXjLfypfWOYM&e=
>> e2440fbde891cba524e
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_
>> r-2Dsource_commit_cbd7ca1b1aedf0405e11&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7sh
>> ZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMu
>> I&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=PCaCRkhgD4O1B5IGY56
>> fWnm25LOpXkSknXvSeh3s83E&e=
>> ee2440fbde891cba524e>
>>
>> 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
>> <stvjc at channing.harvard.edu
>> <mailto:stvjc at channing.harvard.edu>> wrote:
>>
>> ive seen this too apropos bigrquery on windows
>>
>> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
>> <rdiaz02 at gmail.com <mailto:rdiaz02 at gmail.com>>
>>
>> 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-bio
>> c/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-bio
>> c/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: rdiaz02 at gmail.com <mailto:
>> rdiaz02 at gmail.com>
>> ramon.diaz at iib.uam.es <mailto:
>> ramon.diaz at iib.uam.es>
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz
>> &d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZ
>> B9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iM
>> g6_7bpavI&s=NAeHWqOlztiTN7M9MjSk28mg64btcyx318ekluTLdWY&e=
>>
>> _______________________________________________
>> Bioc-devel at r-project.org
>> <mailto:Bioc-devel at r-project.org> mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbtdKYIRX2An5eZ8&e=
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
>> ilman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwz
>> pqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgf
>> VoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbt
>> dKYIRX2An5eZ8&e=
>> >
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org
>> <mailto:Bioc-devel at r-project.org> mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbtdKYIRX2An5eZ8&e=
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
>> ilman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwz
>> pqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgf
>> VoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbt
>> dKYIRX2An5eZ8&e=>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org
>> <mailto:Bioc-devel at r-project.org> mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbtdKYIRX2An5eZ8&e=
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
>> ilman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwz
>> pqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgf
>> VoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbt
>> dKYIRX2An5eZ8&e=>
>>
>>
>>
>> This email message may contain legally privileged
>> and/or...{{dropped:2}}
>>
>> _______________________________________________
>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>> mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbtdKYIRX2An5eZ8&e=
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
>> ilman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwz
>> pqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgf
>> VoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbt
>> dKYIRX2An5eZ8&e=>
>>
>>
>>
>> --
>> 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: rdiaz02 at gmail.com <mailto:rdiaz02 at gmail.com>
>> ramon.diaz at iib.uam.es <mailto:ramon.diaz at iib.uam.es>
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz
>> &d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZ
>> B9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iM
>> g6_7bpavI&s=NAeHWqOlztiTN7M9MjSk28mg64btcyx318ekluTLdWY&e=
>>
>>
>>
>> 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.
>>
>>
>>
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI&s=K5bHOEMx3GaGqD_aUDyecbN2VumCbtdKYIRX2An5eZ8&e=
----------------------------------------------------------------------
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
More information about the Bioc-devel
mailing list