Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
On 3/11/21 7:45 AM, Oluwafemi OLUSOJI wrote:
Hello Herves,
I finally solved this. It had more to do with my commits than the
package itself.
There is this error message when the package is built on a Windows
server. What am I to do about this?
The flowCore package cannot currently be installed because it requires
cytolib >= 2.3.4 which doesn't compile on Windows at the moment. The
cytolib maintainers are aware of the situation and working on it.
Not much we can do so let's ignore for now.
Thanks,
H.
Regards,
Daniel
===
R CMD BUILD
===
* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
---
ERROR: dependency 'flowCore' is not available for package 'cyanoFilter'
* removing
'C:/Users/pkgbuild/AppData/Local/Temp/RtmpYhB4xB/Rinst1ce0655031d2/cyanoFilter'
---
ERROR: package installation failed
Op do 11 mrt. 2021 om 15:54 schreef Oluwafemi OLUSOJI
mailto:oluwafemi.olus...@uhasselt.be>>:
Hello Herve,
Thank you for the insight, but after rewriting the man pages by
hand. I still get the same error after the latest commit. I am
really at a loss here because this builds perfectly on my system.
Regards,
Daniel
Op do 11 mrt. 2021 om 03:11 schreef Hervé Pagès
mailto:hpages.on.git...@gmail.com>>:
Hi,
I don't see that you have aliases for these symbols, hence the
warning:
hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
hpages@spectre:~/cyanoFilter/man$ grep
'alias{clusterExtract}' *.Rd
etc...
Note that even though you have aliases for some PhytoFilter
**methods**:
hpages@spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd |
grep
alias | grep method
fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}
here 'R CMD check' is complaining about the lack of an alias for
the
PhytoFilter **object** (which turns out to be a function). Since
you
export this symbol (via the export(PhytoFilter) directive in your
NAMESPACE file), you need to provide an alias for it in one of
your man
pages.
Hope this helps,
H.
On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
> Dear All,
>
> I get this warning on the latest update of my package. The
warning occurs
> only with Mac and Linux. I am a bit at loss here. These
errors don't
> actually exist because these functions and methods are
properly documented.
> The missing link doesn't even exist anymore.
>
> I have rebuilt both the documentation and rebuilt the source.
R CMD check
> and R CMS check --as.cran doesn't report either on my system
as well. I
> will appreciate any heads-up here.
>
> Regards,
> Daniel
>
>
> Missing link or links in documentation object 'oneDgate.Rd':
> getChannel
>
> See section 'Cross-references' in the 'Writing R Extensions'
manual.
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
> PhytoFilter clusterExtract clusterExtractp debrisNc
> getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
> reducedFlowframe rowNumbers summaries
> Undocumented S4 methods:
> generic 'summaries' and siglist 'DebrisFilter'
> generic 'summaries' and siglist 'MarginEvents'
> generic 'summaries' and siglist 'PhytoFilter'
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org
mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hello Herves,
I finally solved this. It had more to do with my commits than the package
itself.
There is this error message when the package is built on a Windows server.
What am I to do about this?
Regards,
Daniel
===
R CMD BUILD
===
* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
---
ERROR: dependency 'flowCore' is not available for package 'cyanoFilter'
* removing
'C:/Users/pkgbuild/AppData/Local/Temp/RtmpYhB4xB/Rinst1ce0655031d2/cyanoFilter'
---
ERROR: package installation failed
Op do 11 mrt. 2021 om 15:54 schreef Oluwafemi OLUSOJI <
oluwafemi.olus...@uhasselt.be>:
> Hello Herve,
>
> Thank you for the insight, but after rewriting the man pages by hand. I
> still get the same error after the latest commit. I am really at a loss
> here because this builds perfectly on my system.
>
> Regards,
> Daniel
>
> Op do 11 mrt. 2021 om 03:11 schreef Hervé Pagès <
> hpages.on.git...@gmail.com>:
>
>> Hi,
>>
>> I don't see that you have aliases for these symbols, hence the warning:
>>
>>hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
>>hpages@spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
>>etc...
>>
>> Note that even though you have aliases for some PhytoFilter **methods**:
>>
>>hpages@spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep
>> alias | grep method
>>
>>
>> fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
>>plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
>>
>>
>> reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}
>>
>>
>> here 'R CMD check' is complaining about the lack of an alias for the
>> PhytoFilter **object** (which turns out to be a function). Since you
>> export this symbol (via the export(PhytoFilter) directive in your
>> NAMESPACE file), you need to provide an alias for it in one of your man
>> pages.
>>
>> Hope this helps,
>>
>> H.
>>
>>
>> On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
>> > Dear All,
>> >
>> > I get this warning on the latest update of my package. The warning
>> occurs
>> > only with Mac and Linux. I am a bit at loss here. These errors don't
>> > actually exist because these functions and methods are properly
>> documented.
>> > The missing link doesn't even exist anymore.
>> >
>> > I have rebuilt both the documentation and rebuilt the source. R CMD
>> check
>> > and R CMS check --as.cran doesn't report either on my system as well. I
>> > will appreciate any heads-up here.
>> >
>> > Regards,
>> > Daniel
>> >
>> >
>> > Missing link or links in documentation object 'oneDgate.Rd':
>> >getChannel
>> >
>> > See section 'Cross-references' in the 'Writing R Extensions' manual.
>> > * checking for missing documentation entries ... WARNING
>> > Undocumented code objects:
>> >PhytoFilter clusterExtract clusterExtractp debrisNc
>> >getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
>> >reducedFlowframe rowNumbers summaries
>> > Undocumented S4 methods:
>> >generic 'summaries' and siglist 'DebrisFilter'
>> >generic 'summaries' and siglist 'MarginEvents'
>> >generic 'summaries' and siglist 'PhytoFilter'
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> --
>> Hervé Pagès
>>
>> Bioconductor Core Team
>> hpages.on.git...@gmail.com
>>
>
[[alternative HTML version deleted]]
___
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Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hello Herve,
Thank you for the insight, but after rewriting the man pages by hand. I
still get the same error after the latest commit. I am really at a loss
here because this builds perfectly on my system.
Regards,
Daniel
Op do 11 mrt. 2021 om 03:11 schreef Hervé Pagès :
> Hi,
>
> I don't see that you have aliases for these symbols, hence the warning:
>
>hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
>hpages@spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
>etc...
>
> Note that even though you have aliases for some PhytoFilter **methods**:
>
>hpages@spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep
> alias | grep method
>
>
> fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
>plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
>
>
> reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}
>
>
> here 'R CMD check' is complaining about the lack of an alias for the
> PhytoFilter **object** (which turns out to be a function). Since you
> export this symbol (via the export(PhytoFilter) directive in your
> NAMESPACE file), you need to provide an alias for it in one of your man
> pages.
>
> Hope this helps,
>
> H.
>
>
> On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
> > Dear All,
> >
> > I get this warning on the latest update of my package. The warning occurs
> > only with Mac and Linux. I am a bit at loss here. These errors don't
> > actually exist because these functions and methods are properly
> documented.
> > The missing link doesn't even exist anymore.
> >
> > I have rebuilt both the documentation and rebuilt the source. R CMD check
> > and R CMS check --as.cran doesn't report either on my system as well. I
> > will appreciate any heads-up here.
> >
> > Regards,
> > Daniel
> >
> >
> > Missing link or links in documentation object 'oneDgate.Rd':
> >getChannel
> >
> > See section 'Cross-references' in the 'Writing R Extensions' manual.
> > * checking for missing documentation entries ... WARNING
> > Undocumented code objects:
> >PhytoFilter clusterExtract clusterExtractp debrisNc
> >getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
> >reducedFlowframe rowNumbers summaries
> > Undocumented S4 methods:
> >generic 'summaries' and siglist 'DebrisFilter'
> >generic 'summaries' and siglist 'MarginEvents'
> >generic 'summaries' and siglist 'PhytoFilter'
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
[[alternative HTML version deleted]]
___
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Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hi,
I don't see that you have aliases for these symbols, hence the warning:
hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
hpages@spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
etc...
Note that even though you have aliases for some PhytoFilter **methods**:
hpages@spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep
alias | grep method
fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}
here 'R CMD check' is complaining about the lack of an alias for the
PhytoFilter **object** (which turns out to be a function). Since you
export this symbol (via the export(PhytoFilter) directive in your
NAMESPACE file), you need to provide an alias for it in one of your man
pages.
Hope this helps,
H.
On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
Dear All,
I get this warning on the latest update of my package. The warning occurs
only with Mac and Linux. I am a bit at loss here. These errors don't
actually exist because these functions and methods are properly documented.
The missing link doesn't even exist anymore.
I have rebuilt both the documentation and rebuilt the source. R CMD check
and R CMS check --as.cran doesn't report either on my system as well. I
will appreciate any heads-up here.
Regards,
Daniel
Missing link or links in documentation object 'oneDgate.Rd':
getChannel
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
PhytoFilter clusterExtract clusterExtractp debrisNc
getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
reducedFlowframe rowNumbers summaries
Undocumented S4 methods:
generic 'summaries' and siglist 'DebrisFilter'
generic 'summaries' and siglist 'MarginEvents'
generic 'summaries' and siglist 'PhytoFilter'
[[alternative HTML version deleted]]
___
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
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Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hello, It is a package I recently submitted, cyaniFilter. Thank you for the prompt response. Regards, Daniel On Tue, Mar 9, 2021, 00:09 Nitesh Turaga wrote: > Hi > > We can help you better if you tell us which package you are talking about ? > > Best, > > Nitesh > > On 3/8/21, 5:46 PM, "Bioc-devel on behalf of Oluwafemi OLUSOJI via > Bioc-devel" bioc-devel@r-project.org> wrote: > > Dear All, > > I get this warning on the latest update of my package. The warning > occurs > only with Mac and Linux. I am a bit at loss here. These errors don't > actually exist because these functions and methods are properly > documented. > The missing link doesn't even exist anymore. > > I have rebuilt both the documentation and rebuilt the source. R CMD > check > and R CMS check --as.cran doesn't report either on my system as well. I > will appreciate any heads-up here. > > Regards, > Daniel > > > Missing link or links in documentation object 'oneDgate.Rd': > getChannel > > See section 'Cross-references' in the 'Writing R Extensions' manual. > * checking for missing documentation entries ... WARNING > Undocumented code objects: > PhytoFilter clusterExtract clusterExtractp debrisNc > getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate > reducedFlowframe rowNumbers summaries > Undocumented S4 methods: > generic 'summaries' and siglist 'DebrisFilter' > generic 'summaries' and siglist 'MarginEvents' > generic 'summaries' and siglist 'PhytoFilter' > > [[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
Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hi We can help you better if you tell us which package you are talking about ? Best, Nitesh On 3/8/21, 5:46 PM, "Bioc-devel on behalf of Oluwafemi OLUSOJI via Bioc-devel" wrote: Dear All, I get this warning on the latest update of my package. The warning occurs only with Mac and Linux. I am a bit at loss here. These errors don't actually exist because these functions and methods are properly documented. The missing link doesn't even exist anymore. I have rebuilt both the documentation and rebuilt the source. R CMD check and R CMS check --as.cran doesn't report either on my system as well. I will appreciate any heads-up here. Regards, Daniel Missing link or links in documentation object 'oneDgate.Rd': getChannel See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: PhytoFilter clusterExtract clusterExtractp debrisNc getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate reducedFlowframe rowNumbers summaries Undocumented S4 methods: generic 'summaries' and siglist 'DebrisFilter' generic 'summaries' and siglist 'MarginEvents' generic 'summaries' and siglist 'PhytoFilter' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Dear All, I get this warning on the latest update of my package. The warning occurs only with Mac and Linux. I am a bit at loss here. These errors don't actually exist because these functions and methods are properly documented. The missing link doesn't even exist anymore. I have rebuilt both the documentation and rebuilt the source. R CMD check and R CMS check --as.cran doesn't report either on my system as well. I will appreciate any heads-up here. Regards, Daniel Missing link or links in documentation object 'oneDgate.Rd': getChannel See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: PhytoFilter clusterExtract clusterExtractp debrisNc getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate reducedFlowframe rowNumbers summaries Undocumented S4 methods: generic 'summaries' and siglist 'DebrisFilter' generic 'summaries' and siglist 'MarginEvents' generic 'summaries' and siglist 'PhytoFilter' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
