[Bioc-devel] No write permissions to push changes to my devel package
Hi, I have developed a package BPRMeth in Bioconductor and now I want to make changes however it seems that I *do not have write permissions* to my own package in g...@git.bioconductor.org I submitted my github ID (which contains my public SSH keys) to the google form (however I still have not received an email back). When running: > ssh -T g...@git.bioconductor.org hello andreaskapou, this is ... ... R packages/BPRMeth ... It shows I have only read permission and *not write permission* to my package BPRMeth. For completeness here is the output of *git clone -v* origin g...@github.com:andreaskapou/BPRMeth.git (fetch) origin g...@github.com:andreaskapou/BPRMeth.git (push) upstream g...@git.bioconductor.org:packages/BPRMeth.git (fetch) upstream g...@git.bioconductor.org:packages/BPRMeth.git (push) Thanks, CAK -- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh http://homepages.inf.ed.ac.uk/s1263191/ e-mail : C.A.Kapourani.ed.ac.uk : kapouranis.andr...@gmail.com [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitted package not available in Bioconductor 3.4
Dear Martin, Thanks for this! I was not aware that I should leave the issue open. Regards, Andreas -- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh http://homepages.inf.ed.ac.uk/s1263191/ e-mail : C.A.Kapourani.ed.ac.uk : kapouranis.andr...@gmail.com On Fri, Oct 21, 2016 at 11:14 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 10/21/2016 05:30 AM, Andreas Kapouranis wrote: > >> Hi, >> >> Recently I submitted a package named "BPRMeth" for Bioconductor and it was >> marked as accepted more than one month ago. Here is the link for my >> submission: >> >> https://github.com/Bioconductor/Contributions/issues/74 >> >> However, with the new release of Bioconductor 3.4, I still cannot search >> for my package online? >> >> Does anyone know what the issue might be? >> > > Our down-stream processing (where we add the package to our repository and > nightly builds) assumes that the issue has the '3a. accepted' label and is > open. It looks like you manually closed the issue after it was accepted, so > it was never processed. > > We will fix this error and add your package to the release as well as > devel builds; the package should be available by Monday. > > Martin > > > >> Thanks in advance! >> >> Regards, >> Andreas >> >> [[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 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Submitted package not available in Bioconductor 3.4
Hi, Recently I submitted a package named "BPRMeth" for Bioconductor and it was marked as accepted more than one month ago. Here is the link for my submission: https://github.com/Bioconductor/Contributions/issues/74 However, with the new release of Bioconductor 3.4, I still cannot search for my package online? Does anyone know what the issue might be? Thanks in advance! Regards, Andreas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Michael,
Thanks for the suggestion. When I depend my package on GenomicRanges the
warning is now gone.
Regards,
Andreas
--
Chantriolnt - Andreas Kapourani
PhD Candidate in Data Science,
School of Informatics,
University of Edinburgh
e-mail : c.a.kapour...@sms.ed.ac.uk
: kapouranis.andr...@gmail.com
On Tue, Feb 16, 2016 at 11:28 AM, Michael Lawrence <
lawrence.mich...@gene.com> wrote:
> If you are expecting the user to manipulate that granges then you should
> depend on GenomicRanges.
>
> I guess R is loading the data to check the docs. When the methods
> namespace is loaded, it conveniently attaches the package defining the
> class.
> On Feb 16, 2016 3:48 AM, "Andreas Kapouranis" <
> kapouranis.andr...@gmail.com> wrote:
>
>> Hi Michael,
>>
>> Thanks for the reply.
>>
>> I created a minimal reproducible package with the issue. As it seems the
>> warning comes because I have a 'data' folder where I have stored some
>> example data, and one of the data is stored in GRanges format.
>> If I delete the GRanges example data and keep any other data, I get no
>> warning.
>>
>> So the issue is only when I import the 'methods' package and I have data
>> locally stored as GRanges objects in the 'data' folder.
>>
>> You can download and install the simple example package by typing:
>>
>> devtools::install_github("andreaskapou/simplePackage")
>>
>>
>> Or you can see the code in the following link, which just contains a
>> simple function to call the methods::is() function and create a GRanges
>> object.
>> https://github.com/andreaskapou/simplePackage
>>
>> Thanks,
>> Andreas
>>
>> --
>> Chantriolnt - Andreas Kapourani
>> PhD Candidate in Data Science,
>> School of Informatics,
>> University of Edinburgh
>>
>> e-mail : c.a.kapour...@sms.ed.ac.uk
>>: kapouranis.andr...@gmail.com
>>
>> On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence <
>> lawrence.mich...@gene.com> wrote:
>>
>>> It would be helpful to have a reproducible example, i.e., your actual
>>> package or a skeleton of it that reproduces the issue. Btw, you might
>>> be able to debug this behavior by:
>>>
>>> debug(tools::undoc)
>>> tools::undoc(dir=yourPackageDir)
>>>
>>>
>>>
>>> On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis
>>> wrote:
>>> > Hi,
>>> >
>>> > I am developing a package for Bioconductor, and I have a weird issue
>>> when
>>> > importing the 'methods' package. Before I add the 'methods' package in
>>> > Imoprts in the DESCRIPTION file, I pass the CMD check without any
>>> warnings.
>>> >
>>> > However, when I add the 'methods' package in the Imports field, I get a
>>> > warning during CMD check. (I need the methods package since I use the
>>> > methods::is() function, and if I call it just as is(), when running the
>>> > package from Rscript will fail since by default it does not load the
>>> > 'methods' package.)
>>> >
>>> > I read a similar issue here:
>>> > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
>>> > and I updated all my packages from Bioconductor including IRanges and
>>> > GenomicRanges.
>>> >
>>> > This is the warning that I get, which is exactly the same as the
>>> previous
>>> > issue in Bioc-Devel, and I understand that for some reason the
>>> BiocGenerics
>>> > is attached only when the 'methods' package is imported.
>>> >
>>> > * checking for missing documentation entries ... WARNING
>>> >
>>> > Attaching package: ‘BiocGenerics’
>>> >
>>> > The following objects are masked from ‘package:parallel’:
>>> >
>>> > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>>> > clusterExport, clusterMap, parApply, parCapply, parLapply,
>>> > parLapplyLB, parRapply, parSapply, parSapplyLB
>>> >
>>> > The following objects are masked from ‘package:stats’:
>>> >
>>> > IQR, mad, xtabs
>>> >
>>> > The following objects are masked from ‘package:base’:
>>> >
>>> > Filter, Find, Map, Position, Reduce, any
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Michael,
Thanks for the reply.
I created a minimal reproducible package with the issue. As it seems the
warning comes because I have a 'data' folder where I have stored some
example data, and one of the data is stored in GRanges format.
If I delete the GRanges example data and keep any other data, I get no
warning.
So the issue is only when I import the 'methods' package and I have data
locally stored as GRanges objects in the 'data' folder.
You can download and install the simple example package by typing:
devtools::install_github("andreaskapou/simplePackage")
Or you can see the code in the following link, which just contains a simple
function to call the methods::is() function and create a GRanges object.
https://github.com/andreaskapou/simplePackage
Thanks,
Andreas
--
Chantriolnt - Andreas Kapourani
PhD Candidate in Data Science,
School of Informatics,
University of Edinburgh
e-mail : c.a.kapour...@sms.ed.ac.uk
: kapouranis.andr...@gmail.com
On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence wrote:
> It would be helpful to have a reproducible example, i.e., your actual
> package or a skeleton of it that reproduces the issue. Btw, you might
> be able to debug this behavior by:
>
> debug(tools::undoc)
> tools::undoc(dir=yourPackageDir)
>
>
>
> On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis
> wrote:
> > Hi,
> >
> > I am developing a package for Bioconductor, and I have a weird issue when
> > importing the 'methods' package. Before I add the 'methods' package in
> > Imoprts in the DESCRIPTION file, I pass the CMD check without any
> warnings.
> >
> > However, when I add the 'methods' package in the Imports field, I get a
> > warning during CMD check. (I need the methods package since I use the
> > methods::is() function, and if I call it just as is(), when running the
> > package from Rscript will fail since by default it does not load the
> > 'methods' package.)
> >
> > I read a similar issue here:
> > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
> > and I updated all my packages from Bioconductor including IRanges and
> > GenomicRanges.
> >
> > This is the warning that I get, which is exactly the same as the previous
> > issue in Bioc-Devel, and I understand that for some reason the
> BiocGenerics
> > is attached only when the 'methods' package is imported.
> >
> > * checking for missing documentation entries ... WARNING
> >
> > Attaching package: ‘BiocGenerics’
> >
> > The following objects are masked from ‘package:parallel’:
> >
> > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> > clusterExport, clusterMap, parApply, parCapply, parLapply,
> > parLapplyLB, parRapply, parSapply, parSapplyLB
> >
> > The following objects are masked from ‘package:stats’:
> >
> > IQR, mad, xtabs
> >
> > The following objects are masked from ‘package:base’:
> >
> > Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> > as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
> > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
> > tapply, union, unique, unlist, unsplit
> >
> > All user-level objects in a package should have documentation entries.
> > See chapter ‘Writing R documentation files’ in the ‘Writing R
> > Extensions’ manual.
> >
> >
> >
> > My DESCRIPTION file when I add the 'methods' package is the following:
> > ...
> > Depends: R (>= 3.2.0)
> > LazyData: TRUE
> > RoxygenNote: 5.0.1
> > Imports: GenomicRanges,
> > IRanges,
> > assertthat,
> > S4Vectors,
> > graphics,
> > data.table,
> > methods
> > Suggests: knitr,
> > rmarkdown,
> > testthat
> > VignetteBuilder: knitr
> >
> >
> >
> > Regards,
> > Andreas
> >
> > [[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] BiocGenerics attaches when methods package is imported
Hi Joris, Apologies for not including the NAMESPACE file, but I have included the methods package also there, although I have used: importFrom(methods,is) since I just need the is() function for the time being. Regards, Andreas -- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh e-mail : c.a.kapour...@sms.ed.ac.uk : kapouranis.andr...@gmail.com On Mon, Feb 15, 2016 at 4:16 PM, Joris Meys wrote: > Hi Andreas, > > for a good understanding: just mentioning the methods package in the > DESCRIPTION file isn't doing a thing if you don't also add > > import(methods) > > to the NAMESPACE file. > > So it looks like the warning occurs when the package indicates that the > methods package is imported when it actually isn't. Do you still get that > warning if you update the NAMESPACE file? > > Cheers > Joris > > On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis < > kapouranis.andr...@gmail.com> wrote: > >> Hi, >> >> I am developing a package for Bioconductor, and I have a weird issue when >> importing the 'methods' package. Before I add the 'methods' package in >> Imoprts in the DESCRIPTION file, I pass the CMD check without any >> warnings. >> >> However, when I add the 'methods' package in the Imports field, I get a >> warning during CMD check. (I need the methods package since I use the >> methods::is() function, and if I call it just as is(), when running the >> package from Rscript will fail since by default it does not load the >> 'methods' package.) >> >> I read a similar issue here: >> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html >> and I updated all my packages from Bioconductor including IRanges and >> GenomicRanges. >> >> This is the warning that I get, which is exactly the same as the previous >> issue in Bioc-Devel, and I understand that for some reason the >> BiocGenerics >> is attached only when the 'methods' package is imported. >> >> * checking for missing documentation entries ... WARNING >> >> Attaching package: ‘BiocGenerics’ >> >> The following objects are masked from ‘package:parallel’: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following objects are masked from ‘package:stats’: >> >> IQR, mad, xtabs >> >> The following objects are masked from ‘package:base’: >> >> Filter, Find, Map, Position, Reduce, anyDuplicated, append, >> as.data.frame, as.vector, cbind, colnames, do.call, duplicated, >> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, >> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, >> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist, unsplit >> >> All user-level objects in a package should have documentation entries. >> See chapter ‘Writing R documentation files’ in the ‘Writing R >> Extensions’ manual. >> >> >> >> My DESCRIPTION file when I add the 'methods' package is the following: >> ... >> Depends: R (>= 3.2.0) >> LazyData: TRUE >> RoxygenNote: 5.0.1 >> Imports: GenomicRanges, >> IRanges, >> assertthat, >> S4Vectors, >> graphics, >> data.table, >> methods >> Suggests: knitr, >> rmarkdown, >> testthat >> VignetteBuilder: knitr >> >> >> >> Regards, >> Andreas >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > Joris Meys > Statistical consultant > > Ghent University > Faculty of Bioscience Engineering > Department of Mathematical Modelling, Statistics and Bio-Informatics > > tel : +32 9 264 59 87 > joris.m...@ugent.be > --- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocGenerics attaches when methods package is imported
Hi, I am developing a package for Bioconductor, and I have a weird issue when importing the 'methods' package. Before I add the 'methods' package in Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings. However, when I add the 'methods' package in the Imports field, I get a warning during CMD check. (I need the methods package since I use the methods::is() function, and if I call it just as is(), when running the package from Rscript will fail since by default it does not load the 'methods' package.) I read a similar issue here: https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html and I updated all my packages from Bioconductor including IRanges and GenomicRanges. This is the warning that I get, which is exactly the same as the previous issue in Bioc-Devel, and I understand that for some reason the BiocGenerics is attached only when the 'methods' package is imported. * checking for missing documentation entries ... WARNING Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. My DESCRIPTION file when I add the 'methods' package is the following: ... Depends: R (>= 3.2.0) LazyData: TRUE RoxygenNote: 5.0.1 Imports: GenomicRanges, IRanges, assertthat, S4Vectors, graphics, data.table, methods Suggests: knitr, rmarkdown, testthat VignetteBuilder: knitr Regards, Andreas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
