Re: [Rd] Fields used by available.packages

[Lluís Revilla]

Yes, I think that would be enough.
Thank you, Kurt!

Lluís

On Wed, 12 Jun 2024 at 16:35, Kurt Hornik  wrote:

> >>>>> Lluís Revilla writes:
>
> Lluis,
>
> So in available.packages() I could replace
>
> if (is.null(fields))
> fields <- requiredFields
> else {
> stopifnot(is.character(fields))
> fields <- unique(c(requiredFields, fields))
> }
>
> by someting like
>
> if(is.null(fields))
> fields <- getOption("available_packages_fields")
> if(is.null(fields))
> fields <- requiredFields
> else {
> stopifnot(is.character(fields))
> fields <- unique(c(requiredFields, fields))
> }
>
> ?
>
> Best
> -k
>
>
>
> > Hi all,
> > I have recently been researching how available.packages and
> > install.packages filter packages from repositories with additional fields
> > in their PACKAGES file.
>
> > Currently there are some default filters, but users (and R admins) can
> set
> > up their own filters by passing a list to the fields argument or adding
> > them to the "available_packages_filters" option.
> > But if the fields used by the filters are not read by default, then users
> > must manually add the required fields to each call to available.packages.
>
> > This makes it difficult to use new fields and to control what is
> installed
> > in highly regulated systems which want to use more fields to select what
> is
> > installed.
>
> > Current workarounds considered are:
> >  1) The filtering function requiring new fields intercepts the call to
> > available.packages and adds the desired fields via eval in
> > parent.environment and then adds the filters again.
> >  2) Import new data (remote or local) when filtering packages, merge them
> > and filter accordingly.
> >  3) Suggestions?
>
> > The first solution is complicated, while the second doesn't use the R
> > machinery of tools::write_PACKAGES to set up the repository with all the
> > fields (although how to add more fields to the repository file is a
> > different issue).
>
> > Would it be possible to add a new option to add fields to be read by
> > available.packages, similar to filters?
> > The same approach for fields as for filters would avoid the two
> workarounds
> > mentioned. To match it, the new option could be named
> > "available_packages_fields".
>
> > I look forward to hearing from you,
>
> > Lluís
>
> >   [[alternative HTML version deleted]]
>
> > __
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> > https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] Fields used by available.packages

[Lluís Revilla]

Hi all,

I have recently been researching how available.packages and
install.packages filter packages from repositories with additional fields
in their PACKAGES file.

Currently there are some default filters, but users (and R admins) can set
up their own filters by passing a list to the fields argument or adding
them to the "available_packages_filters" option.
But if the fields used by the filters are not read by default, then users
must manually add the required fields to each call to available.packages.

This makes it difficult to use new fields and to control what is installed
in highly regulated systems which want to use more fields to select what is
installed.

Current workarounds considered are:
 1) The filtering function requiring new fields intercepts the call to
available.packages and adds the desired fields via eval in
parent.environment and then adds the filters again.
 2) Import new data (remote or local) when filtering packages, merge them
and filter accordingly.
 3) Suggestions?

The first solution is complicated, while the second doesn't use the R
machinery of tools::write_PACKAGES to set up the repository with all the
fields (although how to add more fields to the repository file is a
different issue).

Would it be possible to add a new option to add fields to be read by
available.packages, similar to filters?
The same approach for fields as for filters would avoid the two workarounds
mentioned. To match it, the new option could be named
"available_packages_fields".

I look forward to hearing from you,

Lluís

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

[Lluís Revilla]

Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with
knitr: In any case it seems that it would be a requirement (Imports, or
Depends).

However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown
if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  wrote:

> Hi everyone,
>
> I recently developed an R package called 'StepReg' and used the
> Bioconductor R package 'BiocStyle' in my vignettes, as shown below:
>
> output:
>   BiocStyle::html_document:
> toc_float: true
>   BiocStyle::pdf_document: default
>
> In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
> included a new line 'biocViews:', as follows:
>
> VignetteBuilder: knitr
> biocViews:
> Suggests:
> knitr,
> testthat,
> BiocStyle,
> kableExtra
>
> You may find all those information here:
> https://github.com/JunhuiLi1017/StepReg/tree/dev
>
> There were no error messages when checking with 'R CMD check' and on
> https://win-builder.r-project.org/upload.aspx. However, an error message
> occurred when I attempted to upload it to CRAN:
>
> * checking re-building of vignette outputs ... ERROR
> Error(s) in re-building vignettes:
> --- re-building 'StepReg.Rmd' using rmarkdown
> Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
> there is no package called 'BiocStyle'
> --- failed re-building 'StepReg.Rmd'
>
> SUMMARY: processing the following file failed:
>'StepReg.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
> For version 1.5.0 (
> https://cran.r-project.org/web/packages/StepReg/index.html), I
> successfully uploaded it to CRAN without including 'biocViews:' in the
> DESCRIPTION file two months ago. However, I'm encountering difficulties
> this time. Any insights or suggestions on resolving this issue would be
> greatly appreciated.
>
> Thanks,
> Junhui
>
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>
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Re: [Rd] RSS Feed of NEWS needs a hand

[Lluís Revilla]

Many thanks Duncan,
I tried to look into the code but didn't manage to advance much due to some
java configuration issues.

To prevent being flooded by content of old versions I added a filter to
only repost those that the release version of the branch is in the title of
the content.
Maybe this would be helpful to avoid publishing the full NEWS again.

Lluís

On Tue, 2 Apr 2024 at 14:50, Dirk Eddelbuettel  wrote:

>
> On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote:
> |
> | On 2 April 2024 at 08:21, Duncan Murdoch wrote:
> | | I have just added R-4-4-branch to the feeds.  I think I've also fixed
> | | the \I issue, so today's news includes a long list of old changes.
> |
> | These feeds can fussy: looks like you triggered many updates. Feedly
> | currently greets me with 569 new posts (!!) in that channel.
>
> Now 745 -- and the bigger issue seems to be that the 'posted at' timestamp
> is
> wrong and 'current' so all the old posts are now seen as 'fresh'. Hence the
> flood ... of unsorted post.
>
> blosxom, simple as it is, takes (IIRC) filesystem ctime as the posting
> timestamp so would be best if you had a backup with the old timestamps.
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [Bioc-devel] Package size issue

[Lluís Revilla]

Hi Gabriel,

You can find how to use BFG and other related recommendations at the R
devel book:
https://contributions.bioconductor.org/git-version-control.html?q=BFG#removing-large-files-from-history-with-bfg-repo-cleaner

I hope this helps with this and other questions,

Lluís

On Fri, 29 Mar 2024 at 01:05, Ali Sajid Imami 
wrote:

> Hi,
> I am not part of the core Bioconductor team, but I have been in this
> situation before. I would suggest you use the BFG Repo Cleaner (
> https://rtyley.github.io/bfg-repo-cleaner/) to remove the errant bam file
> from your repo's history. It's very likely that adding and removing the bam
> file means that that file is still part of the history. That should help
> you cut down on the size.
>
>
> Regards,
> Dr. Ali Sajid Imami
> LinkedIn 
>
>
> On Thu, Mar 28, 2024 at 7:17 PM gabriel.villa...@mdc-berlin.de <
> gabriel.villa...@mdc-berlin.de> wrote:
>
> > Hi!
> >
> > This is my first message to the mailing list so apologies if I am
> breaking
> > any guidelines.
> >
> > I am submitting a package called Ribostan and the build report gives an
> > error that the package tarball exceeds the size requirement. I am also
> > being warned that individual package files exceed the 5MB size limit.
> >
> > The total size of a fresh clone of my package is 5.9MB, but 3.9MB of that
> > is from the single packfile in .git/objects/pack. As I understand, the
> > packfile contains the history of all files that have ever been in the
> > repository, including files that have been deleted.
> >
> > I am wondering if this packfile is what is inflating my package size in
> > the build and whether there is a solution to reduce its size. In case it
> is
> > relevant: at some point a 1.38MB bam file was committed to the repo as
> toy
> > data for running examples, but has since been deleted. I am also
> wondering
> > why an individual file is reported to be exceeding 5MB when I don’t see
> any
> > such file in my repo.
> >
> > Any advice would be very welcome!
> >
> > Best regards,
> > Gabriel
> > ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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Re: [Rd] RSS Feed of NEWS needs a hand

[Lluís Revilla]

Hi!

Thanks for this service! It is very helpful to know what is being developed.

I distribute the content to other venues and I noticed some times that the
updates are duplicated.
For example, the sentence "‘is.R()’ is deprecated as no other S dialect is
known to be in use (and this could only identify historical dialects, not
future ones)." is duplicated in different days:
Day 1:
https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2024/03/07#n2024-03-07
Day 2:
https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2024/03/09#n2024-03-09

I tried to look up how to avoid duplications with Blosxom
 but I didn't find a way.
It would be great if this could be further improved to avoid this
duplication.

Thanks!

Lluís

On Fri, 15 Mar 2024 at 13:50, Dirk Eddelbuettel  wrote:

>
> Years ago Duncan set up a nightly job to feed RSS based off changes to
> NEWS,
> borrowing some setup parts from CRANberries as for example the RSS
> 'compiler'.
>
> That job is currently showing the new \I{...} curly protection in an
> unfavourable light. Copying from the RSS reader I had pointed at this since
> the start [1], for today I see (indented by four spaces)
>
> CHANGES IN R-devel INSTALLATION on WINDOWS
>
> The makefiles and installer scripts for Windows have been tailored to
> \IRtools44, an update of the \IRtools43 toolchain. It is based on GCC
> 13
> and newer versions of \IMinGW-W64, \Ibinutils and libraries (targeting
> 64-bit Intel CPUs). R-devel can no longer be built using \IRtools43
> without changes.
>
> \IRtools44 has experimental suport for 64-bit ARM (aarch64) CPUs via
> LLVM
> 17 toolchain using lld, clang/flang-new and libc++.
>
> Can some kind soul put a filter over it to remove the \I ?
>
> Thanks,  Dirk
>
> [1] Feedly. Unless we set this up so early that I once used Google
> Reader. It's been a while...
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
> __
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Re: [R-pkg-devel] Package failing reverse dependency checks

[Lluís Revilla]

Hi David,

Dependency checks cannot be run on win /Mac builders as far as I know.
Some packages have more than 2000 packages depending on them.
It would be too much for the heavily used CRAN's machines.

Best,

Lluís

On Thu, 8 Feb 2024 at 13:52, David Hugh-Jones 
wrote:

> Thanks for this tip. Out of interest, is there a way to make win/Mac
> builder run revdep checks?
>
> Writing: wyclif.substack.com
> Book: www.wyclifsdust.com
>
>
> On Thu, 8 Feb 2024 at 10:26, Lluís Revilla 
> wrote:
>
>> Hi David,
>>
>> If you didn't increase the version number it could happen that the old
>> version of the package was used (as CRAN might not be aware that there is a
>> new version).
>> The CRAN repository policy says: "Increasing the version number at each
>> submission reduces confusion so is preferred even when a previous
>> submission was not accepted".
>> In addition, it is easier to track how smooth the submission process is
>> for maintainers/developers.
>>
>> I would recommend submitting again, changing the version number of the
>> package.
>> Checking on  win builders and macos builders CRAN provides is the closest
>> one, other approaches include rhub2.
>>
>> Best,
>>
>> Lluís
>>
>>
>>
>> On Thu, 8 Feb 2024 at 10:24, David Hugh-Jones 
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm trying to upload a new version of my "huxtable" package. It is
>>> currently failing reverse dependency checks for two packages (homnormal
>>> and
>>> RSStest). The relevant failures are below.
>>>
>>> I got this failure one time, and fixed the problem, which relates to
>>> mistakenly relying on the Suggested: knitr package (see here for the
>>> commit: https://github.com/hughjonesd/huxtable/commit/5a3edc). After the
>>> commit, reverse dependency checks for homnormal and RSStest pass on my
>>> machine, when testing either with revdepcheck::revdep_check or
>>> tools::check_packages_in_dir, and even when knitr is not installed. But,
>>> after I uploaded the new package to CRAN, the same failure recurred.
>>>
>>> My new release candidate had the same version number as the previous one
>>> (which had failed the revdep check, and therefore not been published on
>>> CRAN). Is it possible that CRAN just tested the old version again?
>>>
>>> If not, then can anyone suggest the best way to debug a revdep check on
>>> as
>>> close a setup to the CRAN machines as possible?
>>>
>>> Cheers,
>>> David
>>>
>>> Git tag for the last CRAN submission:
>>> https://github.com/hughjonesd/huxtable/releases/tag/v5.5.4-rc3
>>>
>>> Info from the CRAN email:
>>> --
>>> Debian: <
>>>
>>> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/reverseDependencies/summary.txt
>>> >
>>> RSStest, homnormal
>>>
>>> Log dir: <
>>>
>>> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/
>>> >
>>> The files will be removed after roughly 7 days.
>>>
>>> Pretests:
>>> Windows: <
>>>
>>> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/Windows/00check.log
>>> >
>>> Debian: <
>>>
>>> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/Debian/00check.log
>>> >
>>> --
>>> Changes to worse in reverse depends:
>>>
>>> Package: homnormal
>>> Check: examples
>>> New result: ERROR
>>>   Running examples in ‘homnormal-Ex.R’ failed
>>>   The error most likely occurred in:
>>>
>>>   > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>>>   > ### Name: Brown_Forsythe
>>>   > ### Title: Brown-Forsythe Test for Homogeniety
>>>   > ### Aliases: Brown_Forsythe
>>>   >
>>>   > ### ** Examples
>>>   >
>>>   > data(FH_data)
>>>   >x1=FH_data$SurvivalTime
>>>   >x2=FH_data$HospitalNo
>>>   >Brown_Forsythe(x1,x2)
>>>   Error in loadNamespace(x) : there is no package called ‘knitr’
>>>   Calls: Brown_Forsythe ... loadNamespace -> withRestarts ->
>>> withOneRestart
>>> -> doWithOneRestart
>>>   Execution halted
>>>
>>> Package: RSStest
>>> Check: examples
>>>

Re: [R-pkg-devel] Package failing reverse dependency checks

[Lluís Revilla]

Hi David,

If you didn't increase the version number it could happen that the old
version of the package was used (as CRAN might not be aware that there is a
new version).
The CRAN repository policy says: "Increasing the version number at each
submission reduces confusion so is preferred even when a previous
submission was not accepted".
In addition, it is easier to track how smooth the submission process is for
maintainers/developers.

I would recommend submitting again, changing the version number of the
package.
Checking on  win builders and macos builders CRAN provides is the closest
one, other approaches include rhub2.

Best,

Lluís



On Thu, 8 Feb 2024 at 10:24, David Hugh-Jones 
wrote:

> Hi all,
>
> I'm trying to upload a new version of my "huxtable" package. It is
> currently failing reverse dependency checks for two packages (homnormal and
> RSStest). The relevant failures are below.
>
> I got this failure one time, and fixed the problem, which relates to
> mistakenly relying on the Suggested: knitr package (see here for the
> commit: https://github.com/hughjonesd/huxtable/commit/5a3edc). After the
> commit, reverse dependency checks for homnormal and RSStest pass on my
> machine, when testing either with revdepcheck::revdep_check or
> tools::check_packages_in_dir, and even when knitr is not installed. But,
> after I uploaded the new package to CRAN, the same failure recurred.
>
> My new release candidate had the same version number as the previous one
> (which had failed the revdep check, and therefore not been published on
> CRAN). Is it possible that CRAN just tested the old version again?
>
> If not, then can anyone suggest the best way to debug a revdep check on as
> close a setup to the CRAN machines as possible?
>
> Cheers,
> David
>
> Git tag for the last CRAN submission:
> https://github.com/hughjonesd/huxtable/releases/tag/v5.5.4-rc3
>
> Info from the CRAN email:
> --
> Debian: <
>
> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/reverseDependencies/summary.txt
> >
> RSStest, homnormal
>
> Log dir: <
>
> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/
> >
> The files will be removed after roughly 7 days.
>
> Pretests:
> Windows: <
>
> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/Windows/00check.log
> >
> Debian: <
>
> https://win-builder.r-project.org/incoming_pretest/huxtable_5.5.4_20240205_164815/Debian/00check.log
> >
> --
> Changes to worse in reverse depends:
>
> Package: homnormal
> Check: examples
> New result: ERROR
>   Running examples in ‘homnormal-Ex.R’ failed
>   The error most likely occurred in:
>
>   > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>   > ### Name: Brown_Forsythe
>   > ### Title: Brown-Forsythe Test for Homogeniety
>   > ### Aliases: Brown_Forsythe
>   >
>   > ### ** Examples
>   >
>   > data(FH_data)
>   >x1=FH_data$SurvivalTime
>   >x2=FH_data$HospitalNo
>   >Brown_Forsythe(x1,x2)
>   Error in loadNamespace(x) : there is no package called ‘knitr’
>   Calls: Brown_Forsythe ... loadNamespace -> withRestarts -> withOneRestart
> -> doWithOneRestart
>   Execution halted
>
> Package: RSStest
> Check: examples
> New result: ERROR
>   Running examples in ‘RSStest-Ex.R’ failed
>   The error most likely occurred in:
>
>   > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>   > ### Name: teststat_MRSS
>   > ### Title: Median Ranked Set Sampling Test
>   > ### Aliases: teststat_MRSS
>   >
>   > ### ** Examples
>   >
>   > x1=matrix(c(1,2.3, 3.4,4.5,5.6,4 ),nrow=3)
>   > x2=matrix(c(2,3.2, 4.2,6.5,4.6,6 ),nrow=3)
>   > teststat_MRSS(x1,x2,tn=1000)
>   Error in loadNamespace(x) : there is no package called ‘knitr’
>   Calls: teststat_MRSS ... loadNamespace -> withRestarts -> withOneRestart
> -> doWithOneRestart
>   Execution halted
>
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Re: [R-pkg-devel] new maintainer for CRAN package XML

[Lluís Revilla]

Dear Uwe and the CRAN team,

Many thanks for maintaining the package for so long (>10 years!).

I see the latest changes are in some internal C code related to
updating the libxml2 library.
In CRAN's experience, is this the highest time consuming task?

I have some questions about how the maintenance transfer will go:
Would someone from the CRAN team help/review the new maintainer for some time?
Or would there be a change in the "cre" role and that's all the
further involvement of the CRAN team with the package (besides the
excellent checks on CRAN)?

For anyone considering it, I analyzed a bit the situation of XML and
RCurl: https://llrs.dev/post/2023/05/03/cran-maintained-packages/
In short, with ~300 direct dependencies, and many highly used, across
CRAN and Bioconductor's packages.

Kind regards,

Lluís


On Mon, 22 Jan 2024 at 15:51, Uwe Ligges
 wrote:
>
> Dear package developers,
>
> the CRAN team (and Professor Ripley in particular) has been the defacto
> maintainer of CRAN package 'XML'.
> Our hope was that maintainers of packages depending on XML will migrate
> to other packages for reading XML structures. This has not happened and
> we still see dozens of strong dependencies on XML.
>
> So we are looking for a person volunteering to take over 'XML'.
> Please let us know if you are interested.
>
> For the CRAN team,
> Uwe Ligges
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Re: [R-pkg-devel] Assistance Needed for Resolving Submission Issues with openaistream Package

[Lluís Revilla]

Hi Li Gen,

This NOTE is part of the new checks on CRAN to comply with its policy.
The error message was introduced in c85587 (2023/11/22), when
incorporating this suggestion
https://bugs.r-project.org/show_bug.cgi?id=18611.
You can see the changes and checks in the browser here:
https://github.com/r-devel/r-svn/commit/c82305de4adc1a8ee01aaf3b4c84bd55721e77fc)
But the solution is what Ivan already wrote: simply provide a file
LICENSE that can be read with read.dcf with those two fields.

Best regards,

Lluís


On Mon, 22 Jan 2024 at 15:19, Ivan Krylov via R-package-devel
 wrote:
>
> Hello Li Gen and welcome to R-package-devel!
>
> В Mon, 22 Jan 2024 17:50:33 +0800
>  пишет:
>
> > The specific areas of concern are:License Information: There's a note
> > indicating that the license stub is an "invalid DCF". I've used 'MIT
> > + file LICENSE' as the licensing terms. I would appreciate guidance
> > on how to correctly format this section to meet the DCF standards.
>
> Leave just the following lines in the LICENSE file, as it currently is
> on CRAN [*]:
>
> YEAR: 2023
> COPYRIGHT HOLDER: openaistream authors
>
> Why would you like to change it? CRAN doesn't want packages to provide
> yet another copy of the MIT license inside the tarball. The text of the
> MIT license is always available in an R install at
> file.path(R.home('share'), 'licenses', 'MIT').
>
> If you need a copy of the MIT license inside your GitHub repository,
> store it elsewhere (e.g. LICENSE.md) and list it in .Rbuildignore [**].
>
> Since you composed your e-mail in HTML and left your mailer to generate
> a plain text equivalent, we only got the latter, somewhat mangled:
> https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010356.html
>
> Please compose your messages to R mailing lists in plain text.
>
> --
> Best regards,
> Ivan
>
> [*]
> https://cran.r-project.org/web/packages/openaistream/LICENSE
>
> [**]
> https://cran.r-project.org/doc/manuals/R-exts.html#Building-package-tarballs
>
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Re: [Rd] R test coverage

[Lluís Revilla]

Hi Jim,

Thanks for the info.
I disregarded covr in my search results as I thought it would only apply to
packages outside base and recommended.
The code is pure R code so it might work, but it reads a file so it might
involve some C code.

Thanks!

Lluís

On Mon, 27 Nov 2023 at 20:11, Jim Hester  wrote:

> It should be possible to use covr to do this, see this old issue
> (https://github.com/r-lib/covr/issues/59). However interpreting the
> results can prove challenging as naturally covr uses functions
> from the base internally. Unfortunately the base and many of the
> internal and recommended packages have somewhat bespoke installation,
> so it would likely take some additional work on your end to get
> reporting working. I had thought of doing this at one point, but
> wasn't sure there would be any audience for the results, so did not
> pursue it further.
>
> For measuring coverage of the C code in the R runtime alone you could
> use gcov and run the test suite, which depending on your contribution
> may be the most informative route.
>
> (replying for the list, accidentally replied only to Lluís the first time)
>
> On Mon, Nov 27, 2023 at 10:15 AM Lluís Revilla 
> wrote:
> >
> > Hi all,
> >
> > I recently proposed a change in R that has led to the addition of new
> code
> > to the R source code.
> >
> > The code added, as far as I know, has no tests and it might affect many
> > packages in CRAN.
> > I was wondering if adding a test would be helpful or it is already
> covered
> > by some other test.
> > Which brought me to the question: what is the coverage of R checks
> > (check-devel)?
> >
> > My searches in the mailing list or other places didn't return anything
> > close to it.
> > But I am curious if someone has already done this and how.
> >
> > Many thanks,
> >
> > Lluís
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] R test coverage

[Lluís Revilla]

Hi all,

I recently proposed a change in R that has led to the addition of new code
to the R source code.

The code added, as far as I know, has no tests and it might affect many
packages in CRAN.
I was wondering if adding a test would be helpful or it is already covered
by some other test.
Which brought me to the question: what is the coverage of R checks
(check-devel)?

My searches in the mailing list or other places didn't return anything
close to it.
But I am curious if someone has already done this and how.

Many thanks,

Lluís

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Re: [Bioc-devel] Is my package suitable for Bioconductor?

[Lluís Revilla]

Hi Tim,

I think there is a mentorship program for cases like this (I am not sure if
it still accepts mentees):
https://www.bioconductor.org/developers/new-developer-program/
I also recommend the book the Bioconductor community wrote to help with
submissions: https://contributions.bioconductor.org/index.html

Questions are usually posted here, which will not only help you but future
users/potential contributors with the same doubts/questions.
So I would recommend that if the previous resources do not help to just
list your questions here for anyone to chime in.

If you want more feedback, you  may address the question to someone you
know from the community or using the slack to ask some questions are also
good options.

Looking forward to seeing the package in Bioconductor.

I hope this helps,

Lluís

On Tue, 24 Oct 2023 at 12:46, Timothy Barry  wrote:

> Hello,
>
> My collaborators and I are considering submitting our R package for
> single-cell CRISPR screen data analysis to Bioconductor (package website <
> https://katsevich-lab.github.io/sceptre/> and e-book <
> https://timothy-barry.github.io/sceptre-book/>). We have several
> questions about the suitability of our package for Bioconductor and changes
> that we might need to implement to make our package more consistent with
> Bioconductor package guidelines. Would a member of the Bioconductor team be
> available for a brief (30-60 minute) Zoom call to discuss these issues? We
> would very much appreciate the help.
>
> Thank you greatly,
> Tim Barry
>
> Timothy Barry, PhD
> University of Pennsylvania
> Department of Statistics and Data Science
> Postdoctoral researcher
>
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] Status of adbcpostgresql

[Lluís Revilla]

Hi Dewey,

Currently there are several packages on a subfolder for human inspection.
I don't think you can do anything else: sending this email might help
drawing attention from your reviewer to your package.
There might be some issues in the package that you'll need to address, try
to find them in advance or prepare a reply for them.

Probably the reviewer is busy with other non-CRAN related things. Or maybe
the review fell between emails.
After a couple of weeks you could try again sending an email to the
reviewer.

Best,

Lluís

On Thu, 5 Oct 2023 at 03:39, Dewey Dunnington  wrote:

> Hi all,
>
> I submitted the first release of adbcpostgresql (an R repackaging of
> ADBC's Postgres driver) about a month ago and it has been pending human
> inspection (I think) since then. I did reply-all to the email once to
> inquire about status but haven't heard back. Where is the best place to
> direct communication about the status of the package? I am certainly
> happy to fix any problems that arise.
>
> Cheers,
>
> -dewey
>
> __
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Re: [Bioc-devel] Not receiving original posts for watched tags at bioconductor support

[Lluís Revilla]

Hi,

While checking this, I realized that
https://support.bioconductor.org/mytags/ doesn't show the tags I have in my
profile as "My Tags" and as "Watched Tags".
Not sure if it is related.

Best,

Lluís

On Thu, 28 Sept 2023 at 01:00, Alexey Sergushichev 
wrote:

> Hi,
>
> I have a problem that I only receive e-mail notifications from
> support.bioconductor.org for my watched tags (e.g. "fgsea") with the
> answers and comments but not for the post itself. So I never learn about
> the unanswered questions unless I go directly to
> https://support.bioconductor.org/mytags/ Does anyone else have this
> problem?
>
> Best,
> Alexey
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] What to do when a package is archived from CRAN

[Lluís Revilla]

The reasons that CRAN has for this (from:
https://cran.r-project.org/src/contrib/PACKAGES.in) are:

X-CRAN-History: Archived on 2023-08-19 for policy violation.
  Downloading on installation from github.
  Unarchived on 2023-08-30.
X-CRAN-Comment: Archived on 2023-08-31 for policy violation.
  .
  Downloading on installation from github.

I see your file src/rust/Cargo.lock has some references to github.com
which is probably what has triggered this.
I'm sorry I cannot help further.

Good luck!


On Thu, 31 Aug 2023 at 14:54, Dirk Eddelbuettel  wrote:

>
> On 31 August 2023 at 07:32, SHIMA Tatsuya wrote:
> | I submitted prqlr 0.5.1 yesterday, which is almost identical to prqlr
> | 0.5.0, and prqlr is now available again on CRAN.
> | Thanks to the CRAN reviewers for their quick reaction.
>
> And it is gone again (per CRANberries). Never a dull moment with CRAN.
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
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Re: [R-pkg-devel] package submissions no auto-processed message

[Lluís Revilla]

Hi,

Are you referring to your package formods?
I see it was released the same Friday 17 and it is already on CRAN.

If this is not the package, it might be on the backlog of packages
submitted to CRAN.
You can check the queue at:
https://r-hub.github.io/cransays/articles/dashboard.html

Best,

Lluís


On Sun, 27 Aug 2023 at 23:16, John Harrold  wrote:

> Howdy Folks,
>
> I submitted a package on Friday. I got the normal email where you have to
> click on the link to confirm. Then I got an email saying that the package
> was uploaded. Normally after that I get an email saying the package was
> auto-processed. That generally doesn't take very long (typically less than
> an hour). I wanted to know if there was something on the backend that was
> causing a delay, or if there was something wrong and I needed to resubmit
> it.
>
> Thank you,
> John
> :wq
>
> [[alternative HTML version deleted]]
>
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Re: [Rd] Vectorize library() to improve handling of versioned deps [sprint project proposal]

[Lluís Revilla]

Hi Gabriel,

Nice idea! I have encountered this problem several times, while probably a
better management of libraries could avoided the issue this is an elegant
solution.

How would this proposal handle arguments mask.ok, include.only and exclude?
For example, in the (edge) case two packages export a function with the
same name but we want to mask one of them (pkgA::fun, pkgC::fun).
How would that work for instance in library(c("pkgA", "pkgC"), mask.ok = c(
pkgC = "fun"))?
Would the name of the character be useful to decide which one is ok to
mask? (in the example I would expect the pkgC::fun be masked by pkgA::fun in
the inverse order or loading).

If this doesn't go ahead, perhaps a function could be implemented to check
these situations in the .libPaths (in a package if not in base) ?

Best,

Lluís

On Mon, 7 Aug 2023 at 22:34, Gabriel Becker  wrote:

> Hi All,
>
> This is a proposal for a project which could be worked on during the R
> development Sprint at the end of this month; it was requested that we start
> a discussion here to see what R-core's thoughts on it were before we
> officially add it to the docket.
>
>
> AFAIK, R officially supports both versioned dependencies (almost
> exclusively of the >=version variety) and library paths with more than one
> directory. Further, I believe if at least de facto supports the same
> package being installed in different directories along the lib path. The
> most common of these, I'd bet, would be different versions of the same
> library being installed in a site library and in a user's personal library,
> though that's not the only way this can happen.
>
> The combination of these two features, however can give rise to
> packages which are all correctly installed and all loadable individually,
> but which must be loaded in a particular order when used together or the
> loading of some of them will fail.
>
> Consider the following dependency structure between packages
>
> pkgA: pkgB (>= 0.5.0)
>
> pkgC: pkgB (>= 0.6.0)
>
> Consider the following multi-libpath setup:
>
> ~/pth1/: pkgA, pkg B [0.5.1]
> ~/pth2/: pkg C, pkg B [0.6.5]
>
> And consider that we have the libpath c("~/pth1/", "~/pth2").
>
> If we do
>
> library(pkgA)
>
> Things will work great.
>
> Same if we do
>
> library(pkgC)
>
> BUT, if we do
>
> library(pkgA)
> library(pkgC)
>
> pkgC will not be able to be loaded, because an insufficient version of
> pkgB will
> already be loaded.
>
> I propose that library be modified to be able to take a character vector of
> package names, when it does, it performs the dependency calculations to
> determine how all packages in the vector can be loaded (in the order they
> appear). In the example above, this would mean that if we did
>
> library(c("pkgA", "pkgC"))
>
> It would determine that pkgB version 0.6.5 was needed (or alternatively,
> that version 0.5.1 was insufficient) and use that *when loading the
> dependencies of pkgA*.
>
> The proposal issue for the sprint itself is here:
> https://github.com/r-devel/r-project-sprint-2023/discussions/15
>
> Thoughts?
>
> ~G
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] Missing ggPMX causing failure for nlmixr2rpt

[Lluís Revilla]

Dear John,

I think the problem is that the package ggPMX is suggested, but
nlmixr2rpt isn't prepared for when it isn't available.
In such cases, a package shouldn't fail the checks.

>From the CRAN policies https://cran.r-project.org/web/packages/policies.html :
"A package listed in ‘Suggests’ or ‘Enhances’ should be used
conditionally in examples or tests if it cannot straightforwardly be
installed on the major R platforms. (‘Writing R Extensions’ recommends
that they are always used conditionally.)"

Among other things in the file test-rptnlmixr.R you load several
suggested packages without checking if they are available.
You should only run those tests and examples that need those packages
if they are available.
Checking via:  if (requireNamespace("ggPMX", verbose = FALSE) could be enough

There's also an example that seems to be failing, I didn't understand
the reason behind it but it might be related.

Best,

Lluís


On Fri, 2 Jun 2023 at 02:49, John Harrold  wrote:
>
> Hello,
>
> I recently got a "Dear Maintainer" email from Brian Ripley. It was
> concerning the nlmixr2rpt package I maintain:
>
> https://cran.r-project.org/web/checks/check_results_nlmixr2rpt.html
>
> It looks like there is an error on r-release-linux-x86_64 that is causing
> it. If I'm reading that correctly there is a problem finding ggPMX on that
> flavor. If I look at the check results for ggPMX it seems to be building
> fine there:
>
> https://cran.r-project.org/web/checks/check_results_ggPMX.html
>
> Am I reading that correctly that ggPMX not being found is the cause of my
> issues? If that's the case and it seems to be present now, can I just wait
> and let CRAN machines find it? Or should I just resubmit with those pieces
> removed from the version I submit to CRAN?
>
> --
> Thank you,
> John
> :wq
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] Bioconductor packages released: archive

[Lluís Revilla]

Dear all,

I'm looking into the impact of two packages and I want to check
Bioconductor packages that depend on them (around 130).

There are some functions to retrieve information about CRAN with the
current packages and all the previous releases: tools:::CRAN_archive_db()
and tools::CRAN_package_db()

Those files provide information I want such as the release date and
(indirectly) the number of releases of those packages.

With BiocPkgTools::biocPkgList() I can retrieve the latest release date of
each package but not the number of previous releases. Is there something
similar for Bioconductor that returns all the release dates?

Best wishes,

Lluís

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Re: [Bioc-devel] Bioconductor 3.17 requires R 4.3?

[Lluís Revilla]

Dear Tag,

Congratulations for your successful submission of TDbasedUFE!

Your package was accepted and included in the devel branch of Bioconductor:
See this document about what to do now:
https://contributions.bioconductor.org/bioconductor-package-submissions.html#afteraccept
The devel version of Biocondutor will be 3.17 which will work with R 4.3
(The source code of R 4.3  is here: http://svn.r-project.org/R/trunk/) .
R 4.3 is in development. Once released, Bioconductor 3.17 will be released,
probably around April.
See this document about working with devel branch of Bioconductor and how
releases work:
https://contributions.bioconductor.org/use-devel.html?q=devel#which-version-of-r

The current release of Bioconductor is 3.16 which works with R-4.2.
You can see here all the information about past releases:
https://www.bioconductor.org/about/release-announcements/
Your package is not included in the 3.16 release because it was just
accepted.

I hope this helps.

Lluís




On Fri, 24 Feb 2023 at 10:56, Y-h. Taguchi  wrote:

> Hi, people,
>
> I have released TDbasedUFE
>
> https://doi.org/doi:10.18129/B9.bioc.TDbasedUFE
>
> for Bioc 3.17.
>
> In order to install this package, it says
>
> To install this package, start R (version "4.3") and enter:
>
> but the latest R is 4.2.2 and in
>
> Bioconductor - Install 
>
> "The development version of *Bioconductor* is version *3.17*; it works with
> *R* version 4.2.0."
>
> Bioc 3.17 works under R 4.2 or 4.3 ? The information is conflicting.
>
> If Bioc 3.17 requires  R 4.3, where is it?
>
> I am glad if you can help me on this issue.
>
> Yours, tag
>
> --
> Y-h. Taguchi, Dept. Phys., Chuo Univ., Kasuga, Bunkyo-ku, Tokyo
> 112-8551,Japan
> Tel./Fax.  +81-3-3817-1791/1792 https://researchmap.jp/Yh_Taguchi/
> 〒112-8551 中央大学理工学部 物理学科 田口善弘 電話/FAX 03-3817-1791/1792
>
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Re: [R-pkg-devel] CRAN Vignette pdfs garbled in Firefox pdf viewer

[Lluís Revilla]

Hi,

I can't read any vignettes of gcplyr in Firefox 109.0.1 from a Windows 10.
But sorry, I don't have any solution.

On Thu, 9 Feb 2023 at 21:18, Duncan Murdoch 
wrote:

> On 09/02/2023 10:27 a.m., Mike Blazanin wrote:
> > Hi all, my package gcplyr has several vignettes which, from CRAN, appear
> > garbled when opened with Firefox's pdf viewer (
> > https://cran.r-project.org/web/packages/gcplyr/index.html).
> Specifically,
> > instead of regular characters, there are numerous black-outlined white
> > boxes with text inside like "EO 88" or "EO 55". This doesn't occur with
> the
> > pdf vignettes on Github (https://github.com/mikeblazanin/gcplyr/). This
> > also doesn't occur when CRAN pdfs are opened with Chrome's pdf viewer or
> > Microsoft Edge's pdf viewer, nor when files are downloaded from CRAN and
> > opened with a local pdf viewer.
>
> I don't see a problem in Firefox 109.0.1 on a Mac.  Maybe the "0.1" is a
> bug fix?  Or maybe I looked in the wrong place.  Could you be very
> specific, i.e. URL, page, line.
>
>
> Duncan Murdoch
>
>
> >
> > The issue was documented here:
> > https://github.com/mikeblazanin/gcplyr/issues/112
> >
> > Anyone have any suggestions for what could be causing this?
> >
> > Thanks!
> > Mike Blazanin
> >
> >   [[alternative HTML version deleted]]
> >
> > __
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Re: [Bioc-devel] Large vignettes

[Lluís Revilla]

Hi all,

Perhaps instead of long vignettes, it would be better to use a book hosted
and in sync with the packages at Bioconductor.
There are already a few: https://www.bioconductor.org/books/release/
But I was not able to find how to submit such bookdowns to Bioconductor (I
briefly searched the website and the dev book at
https://contributions.bioconductor.org/docs.html?q=book).
I think the limits are less restrictive and there is no minimum size of
chapters or documentation, but I am not sure.

Some authors already have books outside bioconductor to have extensive
examples of their packages.
They will also benefit from having them with the Bioconductor framework and
in sync with the packages released to the users.

Best,

Lluís


On Wed, 4 Jan 2023 at 21:39, Vincent Carey 
wrote:

> I am glad you brought this up here, and I welcome further discussion on
> this mailing list.  It is important to understand the constraints on
> development
> that arise from Bioconductor's package guidelines.
>
> I don't think we want to change the limits on package payload size without
> understanding the consequences for users and our build system.  The split
> approach mentioned by Lambda seems sensible to me, and I hope it is
> not too burdensome.  Additional commentary and details from the community
> are welcome.
>
> On Wed, Jan 4, 2023 at 3:21 PM Lambda Moses  wrote:
>
> > Hi Adam,
> >
> > I also got this problem, and I would like some input from Bioc Core
> > Team. I worked around it by writing a minimal vignette in the main
> > branch. Then I made a documentation branch, where I have the same code
> > as in main branch, but with more elaborate vignettes used to build a
> > pkgdown website. I made a rule for myself that I can only merge from the
> > main or devel branch to the documentation branch but not the other way
> > round. I would switch branch when I find a bug or want a new feature
> > while writing the vignettes. You can see the main branch here:
> > https://github.com/pachterlab/voyager/tree/main The documentation branch
> > here: https://github.com/pachterlab/voyager/tree/documentation
> >
> > I kind of wonder if the 5 MB rule is outdated in the age of increasing
> > computer power and internet speed. A jpeg photo can easily exceed 5 MB.
> > I also wonder if this rule is deliberately kept for good reasons, like
> > to make R more inclusive to disadvantaged people with limited internet
> > services.
> >
> > Regards,
> >
> > Lambda
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:10}}

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Re: [Bioc-devel] Packages failing Development build due to LaTex problem in .Rnw vignette

[Lluís Revilla]

Hi Rory,

There was a recent change in R devel (
https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
 - sessionInfo() records (and by default prints) the system time zone as
part of the locale information.
It was reported a couple of days ago in the R-devel mailing list by Henrik
Bengtsson, that time zones with underscores caused problems which seems to
be your case with the New_York time zone.
This will probably be fixed at the R core level.

The other option would be to set the local time to another timezone (you or
the Bioconductor core team).

Best,

Lluís

On Fri, 9 Dec 2022 at 16:01, Rory Stark via Bioc-devel <
bioc-devel@r-project.org> wrote:

> My packages are failing in the Development build due to something going
> wrong processing the .Rnw vignettes. Looking around I see a number of other
> packages with similar errors.
>
> They mostly include this error:
>
> LaTeX errors:
> ! Missing $ inserted.
> 
> $
> l.4064   \item Time zone America/New_
>  York
> ! LaTeX Error: Command \item invalid in math mode.
>
>
> although the details differ on each platform.
>
> Something has changed in the environment (headers?) that I can't quite
> track down (the source documents have not changed). Is this a known issue?
> Any suggestions on resolving it?
>
> Rory
>
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] BiocManager::install() behavior with available updates

[Lluís Revilla]

Hi Matej,

Usually when I find this kind of message it indicates that the package
is installed in different libraries and you are updating in just one
library.

Have you checked that it is installed in multiple libraries? I usually
use something similar to this to identify those packages:

ip1 <- installed.packages(lib = .libPaths()[1])
ip2 <- installed.packages(lib = .libPaths()[2])
union(rownames(ip1), rownames(ip2))

I hope this helps.

Best,

Lluís

On Sat, 12 Nov 2022 at 17:37, Matej Lexa  wrote:
>
> Dear all,
>
> I encountered strange behavior of BiocManager::install(). When I ask it
> to install a package that is flagged as one with available updates, it
> gives me the option to upgrade immediately after I install the latest
> version. Not a big deal but thought it should not offer that
> possibility. See my latest test:
>
> ==
>
>  > BiocManager::install("VennDiagram")
> 'getOption("repos")' replaces Bioconductor standard repositories, see
> '?repositories' for details
>
> replacement repositories:
>  CRAN: https://cloud.r-project.org
>
> Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
> Installing package(s) 'VennDiagram'
> trying URL
> 'https://cloud.r-project.org/src/contrib/VennDiagram_1.7.3.tar.gz'
> Content type 'application/x-gzip' length 78508 bytes (76 KB)
> ==
> downloaded 76 KB
>
> * installing *source* package ‘VennDiagram’ ...
> ** package ‘VennDiagram’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** R
> ** data
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded from temporary location
> ** testing if installed package can be loaded from final location
> ** testing if installed package keeps a record of temporary installation
> path
> * DONE (VennDiagram)
>
> The downloaded source packages are in
>  ‘/tmp/RtmpaW1s0x/downloaded_packages’
> Old packages: 'VennDiagram'
> Update all/some/none? [a/s/n]: a
>
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Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

[Lluís Revilla]

Hi,

I would still submit the package:
First I agree with Ben that the note is worth fixing (and easily enough you
just need to remove rgdal from your Description if it is not used.)
Second, and more important, because perhaps in the 9 months since the last
check changes in r-devel or quality checks might currently cause the
package to fail the checks.

The idea behind CRAN, and packages repositories like it (Bioconductor), is
that packages in them should work together.
Sometimes this makes it easier for developers to write more complex
packages but dependencies have their own cost such as this situation.
You can share your package via other methods but usually users install
packages from repositories.

Cheers,

Lluís


On Thu, 22 Sept 2022 at 22:25, Ben Bolker  wrote:

>* Automatic unarchiving *might* happen because someone on the CRAN
> team happens to read this thread, but you will improve your odds greatly
> by e-mailing c...@r-project.org with as polite a request as you can
> manage ...
>
>   * My guess is that nothing will happen until you resubmit (FWIW the
> NOTE definitely seems like something CRAN would object to, so you should
> fix it before resubmitting ...)
>
>good luck,
> Ben Bolker
>
> On 9/22/22 4:15 PM, Carsten Croonenbroeck wrote:
> > Hi Lluís,
> >
> > thanks for the clarification. And kudos to your detective flair. I’m
> serious about that, as I would never have found out about this chain of
> events.
> >
> > Well, there are no error or warnings to fix, so I think it would be best
> if someone from the CRAN team could “unarchive” wflo since there is no
> problem there and none of the events that were set in motion were due to
> any of my doings. Actually, I don’t really agree to have to resubmit, and
> my time for doing so is very limited. Maybe in the next few weeks or so.
> >
> > Best
> >
> > Carsten
> >
> >
> > Von: Lluís Revilla [mailto:lluis.revi...@gmail.com]
> > Gesendet: Donnerstag, 22. September 2022 15:33
> > An: Carsten Croonenbroeck
> > Cc: r-package-devel@r-project.org
> > Betreff: Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN
> repository.
> >
> > Hi Carsten,
> >
> > This seems to be an unfortunate chain of events between different
> packages: RcppMLPACK -> emstreeR -> wflo
> >
> > Package RcppMLPACK was archived on 2021-12-20 as issues were not
> corrected despite reminders.
> > This resulted in the package emstreeR being archived on 2021-12-20 as
> requires archived package 'RcppMLPACK'.
> > Which also resulted in your package, wflo, being archived.
> > Later, emstreeR was unarchived on 2022-03-21 after a successful
> submission improving the dependencies (probably removing the dependency to
> RcppMLPACK).
> > You can see the source of this info on
> https://cran.r-project.org/src/contrib/PACKAGES.in
> >
> > About the emails, usually maintainers whose package depends on a package
> that is about to be removed receive an email with a date by which they
> should fix the problems.
> > But, as I am not part of the CRAN team I cannot check it.
> >
> > I would recommend preparing a new submission with all the errors and
> warnings fixed.
> > Note that I think the package will be checked as a new package.
> >
> > Best,
> >
> > Lluís
> >
> >
> >
> >
> >
> > On Thu, 22 Sept 2022 at 13:17, Carsten Croonenbroeck <
> carsten.croonenbro...@uni-rostock.de carsten.croonenbro...@uni-rostock.de>> wrote:
> > Hi,
> >
> > I was really, really, really surprised to learn today that my package
> “wflo” was removed from CRAN almost a year ago!
> >
> > Telling from the output at https://CRAN.R-project.org/package=wflo,
> this is due to my package being “Archived on 2021-12-20 as requires
> archived package 'emstreeR'.” However, emstreeR is in no way archived (see
> https://CRAN.R-project.org/package=emstreeR). Clicking “check results
> archive”, it says that there is only a note
> >
> > Result: NOTE
> >  Namespace in Imports field not imported from: ‘rgdal’
> >   All declared Imports should be used.
> >
> > which is indeed correct, I don’t use rgdal anymore. What now, remove the
> rgdal import and resubmit? How come I wasn’t informed, my E-Mail is running
> perfectly. Very puzzling…
> >
> > Best
> >
> > Carsten
> >
> >  [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org<mailto:R-package-devel@r-project.org>
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-de

Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

[Lluís Revilla]

Hi Carsten,

This seems to be an unfortunate chain of events between different packages:
RcppMLPACK -> emstreeR -> wflo

Package RcppMLPACK was archived on 2021-12-20 as issues were not corrected
despite reminders.
This resulted in the package emstreeR being archived on 2021-12-20 as
requires archived package 'RcppMLPACK'.
Which also resulted in your package, wflo, being archived.
Later, emstreeR was unarchived on 2022-03-21 after a successful submission
improving the dependencies (probably removing the dependency to RcppMLPACK).
You can see the source of this info on
https://cran.r-project.org/src/contrib/PACKAGES.in

About the emails, usually maintainers whose package depends on a package
that is about to be removed receive an email with a date by which they
should fix the problems.
But, as I am not part of the CRAN team I cannot check it.

I would recommend preparing a new submission with all the errors and
warnings fixed.
Note that I think the package will be checked as a new package.

Best,

Lluís





On Thu, 22 Sept 2022 at 13:17, Carsten Croonenbroeck <
carsten.croonenbro...@uni-rostock.de> wrote:

> Hi,
>
> I was really, really, really surprised to learn today that my package
> “wflo” was removed from CRAN almost a year ago!
>
> Telling from the output at https://CRAN.R-project.org/package=wflo, this
> is due to my package being “Archived on 2021-12-20 as requires archived
> package 'emstreeR'.” However, emstreeR is in no way archived (see
> https://CRAN.R-project.org/package=emstreeR). Clicking “check results
> archive”, it says that there is only a note
>
> Result: NOTE
> Namespace in Imports field not imported from: ‘rgdal’
>  All declared Imports should be used.
>
> which is indeed correct, I don’t use rgdal anymore. What now, remove the
> rgdal import and resubmit? How come I wasn’t informed, my E-Mail is running
> perfectly. Very puzzling…
>
> Best
>
> Carsten
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [Bioc-devel] Packages removing documentation

[Lluís Revilla]

Hi Lori,

Many thanks for your quick response.

I think the requirements for new packages are great but I'm not sure
all these standards can be applied to older packages:
The new requirements in BiocCheck might result in warnings and errors
to many packages.
For instance, new submitted packages are required to remove files such
as .Rproj or the .github folder [1, 2], which some older packages have
(including mine).
There was a discussion about these files a couple of years ago in the
community-bioc slack and more recently to allow the inclusion of these
files [3, 4, 5]
Older packages might not have vignettes with executed code, which
might be difficult for maintainers to now rewrite the vignettes.

I don't know enough about the resources of Bioconductor to propose a
good solution.
But I think lower BiocChecks frequency than current checks, such as
once every 3 months or at similar frequencies, would allow
Bioconductor to detect those issues while not imposing too much burden
on the Bioconductor resources.
However, a faster and lighter approach might be using static analysis
on the packages: grep or specific tools such as
https://github.com/ropensci-review-tools/pkgstats.

Cheers,

Lluís


[1]: 
https://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#bad-file-check
[2]: 
https://github.com/Bioconductor/Contributions/issues/2658#issuecomment-1121182390
[3]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1604600559030500
[4]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1649041312699229
[5]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1621466394001900
and subsequent messages




On Tue, 2 Aug 2022 at 13:22, Kern, Lori  wrote:
>
> Thank you.
>
> I agree packages should maintain the high integrity that they were accepted 
> with.  For now if you find these packages please let us know their name by 
> sending an email to maintai...@bioconductor.org and we will reach out to 
> notify them they are not in Bioconductor standards and will get a warning to 
> fix or  we will consider deprecating.
>
> We would like to run BiocCheck but our current resources do not allow for 
> that.  We will look into some other options for trying to run BiocCheck on 
> the current Bioconductor packages for at least status checks.  Hopefully we 
> can find a way to identify these types of packages without increasing the 
> build resource load.
>
> Cheers,
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Lluís 
> Revilla 
> Sent: Monday, August 1, 2022 5:36 PM
> To: bioc-devel 
> Subject: [Bioc-devel] Packages removing documentation
>
> Dear Bioconductor community,
>
> One of the oldest requirements of Bioconductor is a vignette with some
> executed code.
>
> Recently I found some packages that do not have examples for some
> functions and vignettes with executed code in the current release
> while they did some versions ago. The vignette was replaced with a
> link to resources outside the Bioconductor repository.
> These resources might not be in sync with the released code of the
> package or might not work. Users, as I did, might get confused if code
> linked from the vignette does not work or is not found in the package.
>
> This is possible because submitted packages need to pass all checks
> specified by R CMD check and by BioCheck() in the BiocCheck package.
> However, once accepted, checks are no longer done with BiocCheck() and
> just with R CMD check.
>
> I think it would be desirable to keep the initial high quality of the
> packages after the peer review and with the BiocCheck. If authors need
> to move their code to a book they can use the book infrastructure set
> up by Bioconductor too.
> Perhaps Bioconductor checks on existing packages could use the same
> version of BiocCheck that was initially used or some specific tests to
> ensure that documentation is not dismissed.
>
> I would appreciate your thoughts on this.
>
> Best,
>
> Lluís
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1Bp9IWsmviNqtOXHZ8gQHEN2itJq-bl9sZVS3MlFqyqvm1ZUu_ETpQJ8E-kMwnkpHMw1wQ1jvRfZtcX47aEKiC-NeK9LKh_EqowOHdf6xg9D6BusJI6T19FILEzgFk43YumLMXkNcCK_pr5WLn1gnw9SjAysgQccaW2L1r8wBp7DLdxH1vsMzx_-bpYzxze13pD8CC4BiH379f56RX07mkreVsMmm9HJZmUXllPZioNdw3vzkVRsGSk_bsYhq9VLMJUMbFJLI62oalZJlnTVibPl5_vqRx85wdrx1kxQNsUcXZHnteaBD4mzTjmrEMw0C/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> This email message may contain legally privileged and/or confidential 
> infor

[Bioc-devel] Packages removing documentation

[Lluís Revilla]

Dear Bioconductor community,

One of the oldest requirements of Bioconductor is a vignette with some
executed code.

Recently I found some packages that do not have examples for some
functions and vignettes with executed code in the current release
while they did some versions ago. The vignette was replaced with a
link to resources outside the Bioconductor repository.
These resources might not be in sync with the released code of the
package or might not work. Users, as I did, might get confused if code
linked from the vignette does not work or is not found in the package.

This is possible because submitted packages need to pass all checks
specified by R CMD check and by BioCheck() in the BiocCheck package.
However, once accepted, checks are no longer done with BiocCheck() and
just with R CMD check.

I think it would be desirable to keep the initial high quality of the
packages after the peer review and with the BiocCheck. If authors need
to move their code to a book they can use the book infrastructure set
up by Bioconductor too.
Perhaps Bioconductor checks on existing packages could use the same
version of BiocCheck that was initially used or some specific tests to
ensure that documentation is not dismissed.

I would appreciate your thoughts on this.

Best,

Lluís

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Re: [Bioc-devel] ERROR: More than one VignetteEngine specified.

[Lluís Revilla]

Hi Witek,

Probably it is a false positive, caused by a commented VignetteEngine on
https://github.com/protViz/prozor/blob/master/vignettes/TargetDecoyFDR_Example.Rmd#L16

If you delete it (and the line below to be sure) I guess it will go away.

Best,

Lluís

On Fri, 19 Nov 2021 at 14:33, Witold Wolski  wrote:

> Hi,
>
> I am getting the following error when running BiocCheck
> "ERROR: More than one VignetteEngine specified."
>
> But all the vignettes have the same
> %\VignetteEngine{knitr::rmarkdown}
>
> specified.
> Where else does BiocCheck look for vignetteEngine specification?
>
>
>
> Regards
> Witek
>
> PS. the code can be found here.
> https://github.com/protViz/prozor
>
> ___
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>

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Re: [R-pkg-devel] Change package maintainer

[Lluís Revilla]

Hi,

I agree that the email handshake is the best approach (and very
reasonable to expect it).
I thought that maybe in cases like this there was a waiting period
and/or multiple attempts to contact the maintainer and someone on the
mailing list might have had some experience with the process.
When I'm ready to take over the package I will ask the CRAN team and
give them more details.

Many thanks to all.

Lluís Revilla

On Fri, 2 Jul 2021 at 08:38, Uwe Ligges  wrote:
>
>
>
> On 01.07.2021 23:52, Duncan Murdoch wrote:
> > On 01/07/2021 3:11 p.m., Dirk Eddelbuettel wrote:
> >>
> >> On 1 July 2021 at 20:00, Lluís Revilla wrote:
> >> | I have a question related to changing maintainers.
> >> | What happens when the old/current maintainer does not respond to
> >> | emails or other methods of contact?
> >> | Would the new maintainer need to wait until the package is removed
> >> | from CRAN to submit it again?
> >>
> >> Not speaking for CRAN here but my understanding always was that a full
> >> and
> >> complete 'email handshake' with both old and new maintainer was strongly
> >> preferred / the default simply to prevent misunderstandings or
> >> shenanigans.
> >
> > I'd agree in the normal case where the package is still active on CRAN.
> >
> > In the case where a package has unaddressed issues with no response to
> > CRAN from the maintainer, they'd probably be quite happy to have someone
> > volunteer to take over.
>
> ... and if in doubt, ask the CRAN team and give them details.
>
> Best,
> Uwe Ligges
>
>
> > Duncan Murdoch
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [R-pkg-devel] Change package maintainer

[Lluís Revilla]

Thanks Uwe for answering,

I have a question related to changing maintainers.
What happens when the old/current maintainer does not respond to
emails or other methods of contact?
Would the new maintainer need to wait until the package is removed
from CRAN to submit it again?

Best,

Lluís

PS: Not sure if my related question should be in another thread or not.


On Thu, 1 Jul 2021 at 18:00, Uwe Ligges  wrote:
>
> Both ways are fine with us, but the auto confirmation request will be
> sent out in any case.
>
> Best,
> Uwe Ligges
>
>
> On 01.07.2021 17:57, rmendelss gmail wrote:
> > Hi Uwe:
> >
> > Is what you described the preferred way to change maintainers  (I have just 
> > taken over another package),  or would you prefer receiving an email from 
> > the old maintainer before the submission?
> >
> > Thanks,
> >
> > -Roy
> >
> >> On Jul 1, 2021, at 8:38 AM, Uwe Ligges  
> >> wrote:
> >>
> >>
> >>
> >> On 01.07.2021 16:10, Javier García Chamorro wrote:
> >>> Hi there, I have recently uploaded the first version of my R package to
> >>> CRAN. As it is part of my final degree project, I need to change the
> >>> maintainer to my supervisor, now that I have finished the project.
> >>> I changed in the DESCRIPTION file the proper data to do so, but when
> >>> receiving back the email from CRAN the only NOTE I have is this one:
> >>> * checking CRAN incoming feasibility ... NOTE
> >>> Maintainer: 'Fernando Carazo Developer '
> >>> New maintainer:
> >>>Fernando Carazo Developer 
> >>> Old maintainer(s):
> >>>Javier Garcia Developer 
> >>
> >> 1. Correct the name of the new maintainer whose family name is probably 
> >> not "Developer". Apparently nobody spotted this in your initial submission.
> >>
> >> 2. After successful submission to CRAN, the old maintainer will receive a 
> >> confirmation request which you have to respond to.
> >>
> >> Best,
> >> Uwe Ligges
> >>
> >>
> >>
> >>> What do I need to do here?
> >>> Thank you
> >>> Javier
> >>> [[alternative HTML version deleted]]
> >>> __
> >>> R-package-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>>
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
> __
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[Rd] New post not readable

[Lluís Revilla]

Hi all,

It has come to my attention that there is a new post on The R blog: "R
Can Use Your Help: Testing R Before Release".
However, the link returns an error "Not found":
https://developer.r-project.org/Blog/public/2021/04/28/r-can-use-your-help-testing-r-before-release/index.html
Hope this mailing list is the right place to make it known to the authors.

Maybe these new content could be announced on the R-announcement
mailing list? For others interested I created a Twitter account that
uses The R blog's RSS feed to announce new entries: R_dev_news.

Looking forward to reading the new post.
Cheers,

Lluís

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[R-pkg-devel] CRAN submissions

[Lluís Revilla]

Hi all,

Some time ago, there was a question[1] about "how long is the average
waiting time when submitting a new package ("newbies") until you get a
manual reply or it's on CRAN, submitting an update with all OK before
it hits CRAN".

I have analyzed the data provided by cransays[2] (Many thanks!). You
can find it on this post https://llrs.dev/2021/01/cran-review/
Some key points:
 - Most submission happens in the first days of the week and towards
the middle of the month
 - Most of the submissions disappear from the CRAN queue in less than a day.
 - There's a new package submission to CRAN every hour.
 - It was impossible to know when there was a reply from CRAN, as no
information is openly available.
 - Not possible to know when a package is all OK before it hits CRAN
as some packages remain in the queue even after acceptance (perhaps
with metacran this could be answered).

Hope it's a useful guide. Thanks to the CRAN reviewers for their task,
Best,

Lluís


[1]: https://stat.ethz.ch/pipermail/r-package-devel/2020q4/006174.html
[2]: https://lockedata.github.io/cransays/articles/dashboard.html

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Re: [Bioc-devel] Fwd: Bioconductor package EnMCB

[Lluís Revilla]

Hi Xin Yu,

You seem to be using the symbol ≤ somewhere on the documentation,
looking at the repository on GitHub I only found that symbol on two
comments:
https://github.com/whirlsyu/EnMCB/blob/6124a5a237a94d42d935720dc1bf8a44b11f6966/R/metricMCB.R#L239
https://github.com/whirlsyu/EnMCB/blob/6124a5a237a94d42d935720dc1bf8a44b11f6966/R/metricMCB_cv.R#L124
Not sure if this is the right repository or if it is up to date. But
there they shouldn't cause this warning, you might have moved those
comments to a help page.
You probably should replace them by the corresponding unicode encoding.
Hope this helps,

Lluís


On Mon, 28 Dec 2020 at 19:56, xin wwa  wrote:
>
> Dear bioconductor team,
> I am working on our package EnMCB, which recently have some problems on
> developing branch,
> I fixed most of the errors but our package still has a warning in check as
> follows:
>
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
>
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> LaTeX errors found:
> ! Package inputenc Error: Unicode character ≤ (U+2264)
> (inputenc)not set up for use with LaTeX.
>
> See the inputenc package documentation for explanation.
> Type  H   for immediate help.
> ! Package inputenc Error: Unicode character ≤ (U+2264)
> (inputenc)not set up for use with LaTeX.
>
> See the inputenc package documentation for explanation.
> Type  H   for immediate help.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> * DONE
>
> I checked our package on the local computer and looks fine. I can not find
> out which character causes this problem.
>
> Could you please help me to fix this issue?
>
> Thanks in advance.
> Merry Christmas!
> Best Regards,
> Xin Yu
> Ph.D. student of Biomedical Informatics
> College of Bioinformatics - Huazhong Agricultural University
> whirl...@gmail.com
> yu...@webmail.hzau.edu.cn
> tel: (+86) 186-5313-5769
>
>
> xin wwa  于2020年12月23日周三 下午8:26写道：
>
> > Dear  Lori,
> >
> > Thank you for your email, we currently are working on upgrading our
> > package.
> > It should be work fine after our update.
> >
> > Best regards,
> > Xin Yu
> > Ph.D. student of Biomedical Informatics
> > College of Bioinformatics - Huazhong Agricultural University
> > whirl...@gmail.com
> > yu...@webmail.hzau.edu.cn
> > tel: (+86) 186-5313-5769
> >
> >
> > Kern, Lori  于2020年12月23日周三 下午8:20写道：
> >
> >> Hello Package Maintainer,
> >>
> >> The Bioconductor Team would like to notify you that your package is
> >> currently
> >> failing on the devel 3.13 version of Bioconductor, and has been for an
> >> extended
> >> period of time.  Please fix your package to R CMD build and R CMD check
> >> cleanly
> >> immediately to avoid deprecation of your package. While devel is a place
> >> to
> >> experiment with new features, we expect packages to build and check
> >> cleanly in a
> >> reasonable time period and not stay broken for any extended period of
> >> time. If
> >> you are having trouble or have any further questions please do not
> >> hesitate to
> >> reach out to the developers mailing list at bioc-devel@r-project.org.
> >> The package has been failing consistently since 12/04/20
> >>
> >> bioconductor.org/checkResults/devel/bioc-LATEST/EnMCB
> >>
> >>
> >> Lori Shepherd
> >>
> >> Bioconductor Core Team
> >>
> >> Roswell Park Comprehensive Cancer Center
> >>
> >> Department of Biostatistics & Bioinformatics
> >>
> >> Elm & Carlton Streets
> >>
> >> Buffalo, New York 14263
> >>
> >> 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

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Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

[Lluís Revilla]

Dear Pablo,

Sometimes when building a vignette the lines reported are a bit off (I
usually check the code above and below those lines).
I could reproduce the error on R 4.0.1, the error is triggered on
lines 515-519 on the following code:

relationship_plot(qtl_file=out.qtls.filtered, x="Abbrev", y="Ref_ID",
cex=1,gap=2.5,degree = 60,
canvas.xlim = c(-5, 5),
canvas.ylim = c(-3, 3),
grid.col = color.grid)

Hope you can solve it.

Cheers,

Lluís


On Thu, 5 Nov 2020 at 22:00, Pablo Fonseca  wrote:
>
> Dear Lluís Revilla,
>
> Thank you very much for the comments and suggestions. I changed the vignette 
> format from the BiocStyle to a regular html. However, I am still getting an 
> error.  Now, the error is "Input vector too short" and it is related with the 
> same code chunk lines 465-506.
>
> I can't figure out a possible reason for this issue. Any comment or 
> suggestion will be very welcome.
>
> Kind regards.
>
>
> Pablo Augusto de Souza Fonseca, Ph.D.
> Postdoctoral Fellow at University of Guelph
> Centre for Genetic Improvement of Livestock
> E pfons...@uoguelph.ca
> W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca
> 
> From: Lluís Revilla 
> Sent: Thursday, November 5, 2020 11:38 AM
> To: Pablo Fonseca 
> Cc: Duncan Murdoch ; r-package-devel@r-project.org 
> 
> Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
> re-building - The magick package is required to crop
>
> CAUTION: This email originated from outside of the University of Guelph. Do 
> not click links or open attachments unless you recognize the sender and know 
> the content is safe. If in doubt, forward suspicious emails to 
> ith...@uoguelph.ca
>
>
> Hi Pablo,
>
> "The magick package is required to crop"  is related to using
> BiocStyle for your vignette. Not sure what causes it, but I reported
> this error some time ago:
> https://github.com/Bioconductor/BiocStyle/issues/77.
> On related issues and on bioc-devel mailing list
> (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html) it
> is mentioned to use knitr::opts_chunk$set(crop = NULL) to solve it.
> If the package is intended for CRAN I would recommend not using
> BiocStyle template, which would also solve this.
>
> Best,
>
> Lluís
>
> On Thu, 5 Nov 2020 at 17:28, Pablo Fonseca  wrote:
> >
> > Dear Duncan Murdoch,
> >
> > Thank you for the quickly reply. Yes, the package is on Github. Any comment 
> > or suggestion will be very welcome.
> >
> > https://github.com/pablobio/GALLO
> >
> > Kind regards.
> >
> > Pablo Augusto de Souza Fonseca, Ph.D.
> > Postdoctoral Fellow at University of Guelph
> > Centre for Genetic Improvement of Livestock
> > E pfons...@uoguelph.ca  <mailto:pfons...@uoguelph.ca>
> > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
> > <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>
> > 
> > From: Duncan Murdoch 
> > Sent: Thursday, November 5, 2020 11:22 AM
> > To: Pablo Fonseca ; r-package-devel@r-project.org 
> > 
> > Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
> > re-building - The magick package is required to crop
> >
> > CAUTION: This email originated from outside of the University of Guelph. Do 
> > not click links or open attachments unless you recognize the sender and 
> > know the content is safe. If in doubt, forward suspicious emails to 
> > ith...@uoguelph.ca
> >
> >
> > On 05/11/2020 10:55 a.m., Pablo Fonseca wrote:
> > > Dear all,
> > >
> > > Currently I am trying to update my package (GALLO) with some small edits 
> > > in the code. However, the package is not passing in the automatic check. 
> > > I am getting only two warnings:
> > >
> > > The first one is a warning related with the maintainer email (my email in 
> > > the case), which is correct. I really think that this is not the cause of 
> > > the package failure during the automatic checking.
> >
> > The first one is actually about your version number:  you called it
> > version 1.0, but CRAN already has 1.0.  You need to increase the number.
> >
> >
> > >
> > > The second warning is a problem during the vignette rebuilding. The 
> > > warning is "The magick package is required to crop". In my first 
> > > submission I didn't experience this error. In the recent submissions for 
> > > updates, I included the magick package as a dependency of the package. 
> > > However, this did

Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

[Lluís Revilla]

Hi Pablo,

"The magick package is required to crop"  is related to using
BiocStyle for your vignette. Not sure what causes it, but I reported
this error some time ago:
https://github.com/Bioconductor/BiocStyle/issues/77.
On related issues and on bioc-devel mailing list
(https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html) it
is mentioned to use knitr::opts_chunk$set(crop = NULL) to solve it.
If the package is intended for CRAN I would recommend not using
BiocStyle template, which would also solve this.

Best,

Lluís

On Thu, 5 Nov 2020 at 17:28, Pablo Fonseca  wrote:
>
> Dear Duncan Murdoch,
>
> Thank you for the quickly reply. Yes, the package is on Github. Any comment 
> or suggestion will be very welcome.
>
> https://github.com/pablobio/GALLO
>
> Kind regards.
>
> Pablo Augusto de Souza Fonseca, Ph.D.
> Postdoctoral Fellow at University of Guelph
> Centre for Genetic Improvement of Livestock
> E pfons...@uoguelph.ca  
> W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
> 
> 
> From: Duncan Murdoch 
> Sent: Thursday, November 5, 2020 11:22 AM
> To: Pablo Fonseca ; r-package-devel@r-project.org 
> 
> Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
> re-building - The magick package is required to crop
>
> CAUTION: This email originated from outside of the University of Guelph. Do 
> not click links or open attachments unless you recognize the sender and know 
> the content is safe. If in doubt, forward suspicious emails to 
> ith...@uoguelph.ca
>
>
> On 05/11/2020 10:55 a.m., Pablo Fonseca wrote:
> > Dear all,
> >
> > Currently I am trying to update my package (GALLO) with some small edits in 
> > the code. However, the package is not passing in the automatic check. I am 
> > getting only two warnings:
> >
> > The first one is a warning related with the maintainer email (my email in 
> > the case), which is correct. I really think that this is not the cause of 
> > the package failure during the automatic checking.
>
> The first one is actually about your version number:  you called it
> version 1.0, but CRAN already has 1.0.  You need to increase the number.
>
>
> >
> > The second warning is a problem during the vignette rebuilding. The warning 
> > is "The magick package is required to crop". In my first submission I 
> > didn't experience this error. In the recent submissions for updates, I 
> > included the magick package as a dependency of the package. However, this 
> > didn't fixed the issue. Additionally, I can't reproduce the errors in my 
> > machines, even when running R CMD check --as-cran. The error seems to be 
> > related with the lines 465-495 from the vignette. I double checked the code 
> > and introduced some small changes (such as reducing the figure dimensions).
>
> I am not sure about this one; I'd need to look at the package to check.
> Is it on Github?
>
> Duncan Murdoch
>
> >
> > Have ever someone faced a similar issue? However, it seems ineffective. Is 
> > there any possibility to be a false negative?
> >
> > I am sending bellow the links for the check logs.
> >
> > package GALLO_1.0.tar.gz does not pass the incoming checks automatically, 
> > please see the following pre-tests:
> > Windows: 
> > 
> > Status: 2 WARNINGs
> > Debian: 
> > 
> > Status: 2 WARNINGs
> >
> > Last released version's CRAN status: ERROR: 1, WARN: 11
> > See: 
> >
> >
> > Kind regards.
> >
> >
> > Pablo Augusto de Souza Fonseca, Ph.D.
> > Postdoctoral Fellow at University of Guelph
> > Centre for Genetic Improvement of Livestock
> > E pfons...@uoguelph.ca  
> > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
> > 
> >
> >[[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

[Lluís Revilla]

Hi Anthony,

I stumbled with the same issue for a package I submitted recently, the
problem seems to be that LaTex doesn't know how to map this unicode
character to a typesetting.

My unicode character was \u2229 and I tried several ways to avoid this warning.
On the vignette built with knitr I declared the unicode character the
following way:
%\DeclareUnicodeCharacter{2229}{$\cap$}
On the man pages I had to use a bit of code to print the right symbol:
\ifelse{latex}{\out{$\cup$}}{\ifelse{html}{\out{}}{}}.}

This way it passes the CRAN checks on all the machines and I didn't
get any comment from the reviewer.
In your case a similar changing the symbol might work, if there isn't
any symbol you'll probably need to map the ligature in latex:
tex.stackexchange.com/a/230140/178206.
Not sure how to include that map with the package tho.

Hope this helps,

Lluís

On Thu, 29 Oct 2020 at 15:35, Anthony Hammond  wrote:
>
> Hello,
> I'm attempting to upload a package to CRAN and although it passes the R CMD
> checks that I run, it doesn't pass the CRAN check and the response I get is
> pasted below. I've looked online and found numerous solutions; some made no
> sense to me & others didn't work.
> I tried downloading and putting upquote.sty and inconsolata.sty files into
> the latex folder. I also tried typing --no-manual in the project options
> under R CMD check options.
> Still the CRAN submission email response provided the below error.
> What can I do to make this go away and have my package accepted?
> It probably doesn't help that I know next to nothing about LaTeX.
> Incidentally I don't mind not having a pdf manual, so if there is a simple
> way to avoid the check by requesting not to have one, that'll do.
> Any assistance would be greatly appreciated.
>
> Kind Regards
> Anthony
>
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> LaTeX errors found:
> ! Package inputenc Error: Unicode char fl (U+FB02)
> (inputenc)not set up for use with LaTeX.
>
> See the inputenc package documentation for explanation.
> Type  H   for immediate help.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> * checking for detritus in the temp directory ... OK
> * DONE
> Status: 1 ERROR, 1 WARNING, 3 NOTEs
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [Bioc-devel] Bioconductor affy author questions

[Lluís Revilla]

Hi Henry,

This information is on the landing page of the package: https:
bioconductor.org/packages/affy.
There are many authors, but the listed maintainer is Rafael A. Irizarry
whose mail is: rafa at jhu.edu.
However, if you have questions about the package, the best route would be
to post them at https://support.bioconductor.org.

Best regards,

Lluís

On Sun, 20 Sep 2020 at 12:57, Henry Luo  wrote:

> Hi, my name is Henry, I am a master student of NCU in Taiwan.
> My project is probe design about environmental bacteria, and I want to use
> affy package on my project. I want to know who is the authors of affy
> package and what are their email addresses. Thank you.
>
> Best regards,
>
> Henry Luo
>
> [[alternative HTML version deleted]]
>
> ___
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>

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Re: [Bioc-devel] New Package Submission Workflow Updates!

[Lluís Revilla]

Hi Lori and Core Team,

Hope this change will make it easier for all to submit packages to
Bioconductor (and review them).

I have a couple of comments on the documentation. I think that the
extensive documentation available can be confusing and a bit circular.
The README of github.com/Bioconductor/Contributions says: "Review the package
submission 
process"
While on that page under Submission it says: "Submit by opening a new issue
in the *Bioconductor* Contributions
 repository,
following the guidelines  of
the README.md file.".
Perhaps a more lineal documentation will be easier to follow and understand
for new and old contributors.

Another thing that caught my attention: on the README under "What to
expect" there is a link to the new package workflow

where it is explained how to set up the local repository to be able to
update the package for the submission. However, it isn't linked from the
package submission website and it only mentions that it is for
modifications **after moderation**. I think this is the ideal situation
(first time submitted packages pass all the check the first time), but
often new submissions must update the package so that the package passes
all the checks in order to be reviewed/moderated. I think this needs to be
mentioned too.

Best,

Lluís

On Wed, 8 Jul 2020 at 17:03, Shepherd, Lori 
wrote:

> Hello Bioconductor Development Community,
>
> The team has made a significant change to the single package builder
> process for submitting new packages to Bioconductor.
>
> Previously, when submitting a new package, the process was to submit on
> github, add a webhook for interactive building on version bump, acceptance,
> addition to the git.bioconductor.org repository system, and addition to
> the daily builder manifest.
>
> Now upon submission of your package to github, the preapproval process
> will involve immediately adding packages to git.bioconductor.org.
> Subsequent builds of the package during the review process will be
> triggered by a version bump and push to the upstream repository at
> g...@git.bioconductor.org:packages/. Upon acceptance your
> package will be added to the daily builder manifest for official inclusion
> in Bioconductor.
>
>
> The webhook will be deactivated and no longer trigger builds during the
> review process.
> Any package that was previously submitted (Before July 7th, 2020) will not
> have to worry about the new workflow. You can continue your new package
> review as you have been and we will deactivate your webhook once you are
> through the submission process.
> This will only affect packages newly submitted.
>
> Please ask any questions or concerns you may have.
>
> Thank you
> Lori Shepherd on behalf of the Core Team
>
>
>
> 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]]
>
> ___
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>

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Re: [Bioc-devel] How I hide non-exported function from the manual

[Lluís Revilla]

Hi Stefano,

About 1) you can document internal functions but remove them from the index
if you use #' @keywords internal tag.
See the vignette of roxygen2
https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under
Other tags.
About 2) perhaps you have too many/long examples?

Hope this helps,

Lluís



On Thu, 4 Jun 2020 at 05:48, stefano  wrote:

> Hello Community,
>
> I am used to document function although hey are not exported
>
> ```
> #' Get differential transcription information to a tibble using edgeR.
> #'
> #' @import dplyr
> #' @import tidyr
> #' @import tibble
> #' @importFrom magrittr set_colnames
> #' @importFrom stats model.matrix
> #' @importFrom utils installed.packages
> #' @importFrom utils install.packages
> #' @importFrom purrr when
> #'
> #'
> #' @param .data A tibble
> #' @param .formula a formula with no response variable, referring only to
> numeric variables
> #' @param .sample The name of the sample column
> #' @param .transcript The name of the transcript/gene column
> #' @param .abundance The name of the transcript/gene abundance column
> #' @param .contrasts A character vector. See edgeR makeContrasts
> specification for the parameter `contrasts`. If contrasts are not present
> the first covariate is the one the model is tested against (e.g., ~
> factor_of_interest)
> #' @param method A string character. Either "edgeR_quasi_likelihood" (i.e.,
> QLF), "edgeR_likelihood_ratio" (i.e., LRT)
> #' @param significance_threshold A real between 0 and 1
> #' @param minimum_counts A positive integer. Minimum counts required for at
> least some samples.
> #' @param minimum_proportion A real positive number between 0 and 1. It is
> the threshold of proportion of samples for each transcripts/genes that have
> to be characterised by a cmp bigger than the threshold to be included for
> scaling procedure.
> #' @param fill_missing_values A boolean. Whether to fill missing
> sample/transcript values with the median of the transcript. This is rarely
> needed.
> #' @param scaling_method A character string. The scaling method passed to
> the backend function (i.e., edgeR::calcNormFactors;
> "TMM","TMMwsp","RLE","upperquartile")
> #' @param omit_contrast_in_colnames If just one contrast is specified you
> can choose to omit the contrast label in the colnames.
> #'
> #' @return A tibble with edgeR results
> #'
> get_differential_transcript_abundance_bulk <- function
> [...]
> ```
>
> However this leads to 2 problems
>
> 1) The PDF manual includes many function that are not accessible to the
> user. How can I hide documented non-exported function from the manual
> 2) I receive the Biocheck note. "You have  initialised objects".
> Again how can I document an object without initialising it?
>
> Thanks a lot.
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
> [[alternative HTML version deleted]]
>
> ___
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>

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Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

[Lluís Revilla]

Hi,

The maintainer is already aware of this error.
I reported it several months ago
https://github.com/colearendt/xlsx/issues/132 and is reported multiple
times (issues 154, 156, 159)
There is a fix on the github version of the package but the maintainter
hasn't updated the CRAN version yet.

Maybe if you present your case xlsx will be finally updated on CRAN.

Cheers,

Lluís

On Tue, 12 May 2020 at 23:44, Hervé Pagès  wrote:

> Hi Arman,
>
> On 5/7/20 08:57, Arman Shahrisa wrote:
> > Hi to all,
> >
> > I�m maintainer of the package  �cbaf�. I have pushed changes to both
> devel and stable branches almost two days ago. The package check has only
> been carried out for the stable release so far. There has been only one
> error on macOS server as a result of the version of Java used on the server.
>
> Not sure what is wrong with the version of Java used on our Mac server
> machv2. cbaf fails to load with the following error message:
>
>Error: .onLoad failed in loadNamespace() for 'xlsx', details:
>  call: fun(libname, pkgname)
>  error: Your java version is 14.  Need 1.5.0 or higher.
>Execution halted
>ERROR: lazy loading failed for package ‘cbaf’
>
> Obviously version 14 is higher than version 1.5.0 so to me it just looks
> like the Java checking code in xlsx is broken. Something you might want
> to report to the xlsx maintainer.
>
> Alternatively you might want to choose the packages you depend on more
> carefully.
>
> Cheers,
> H.
>
>
> > Despite this, the older version is listed on the cbaf web page for BioC
> 3.11.
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_html_cbaf.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=A59d3JuLgSK3niLkKLga7vyA-vcQsy8q7riknf75RJ0=UAhMnh0UmS_h5m4zNRZ_6GE4yemBR0PNGc1WWIARybI=
> >
> > Am I missing something?
> >
> > Best regards,
> > Arman
> >
> >
> >   [[alternative HTML version deleted]]
> >
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=A59d3JuLgSK3niLkKLga7vyA-vcQsy8q7riknf75RJ0=A-xLxbM3GGrLmBYZzTnC17RTyvyKEL4QRFNK8DoDq8A=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
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[Bioc-devel] Package coverage

[Lluís Revilla]

Dear Lori and all,

Some years ago there was a coverage badge, which disappeared when
transitioning to git. Afterwards there were some mails about including the
coverage badge on package's landing page again (
https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012417.html), but
still there isn't one.

As there is some interest from the core, and I don't know how to add it to
the package builder: https://github.com/Bioconductor/packagebuilder. (I
guess somewhere in builder.py?) I would like to contribute some lines to
bring back the coverage badge:

library(covr)p <- package_coverage("yourpackage", "all")
# This will return the % of coverage of the package
percent_coverage(tally_coverage(p))

Adding this will probably slow down the building of the new landing pages,
but it shouldn't take much longer than the time used for the tests and the
vignette.

Hope this helps,

Lluís

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[Bioc-devel] Bioconductor package review

[Lluís Revilla]

Hi,

Recently I was looking how package reviews are done. Specifically those
packages from developers on the Bioconductor team, or listing the
Bioconductor Package Maintainer as the maintainer.

Some of those packages become the backbone of other packages and perhaps
there are some experiences on the reviewing the 50 packages that
Bioconductor is currently maintaining. However, I couldn't find if there
are under the same review process than other packages? Or are there any
other expectations on the review of those packages?

Sorry if this has been described before, I couldn't come up with a good
search term, and didn't find anything on the Package Submission website.
And as a fairly new contributor I don't know how package reviews were done
before github.

Many thanks,

Lluís

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[Bioc-devel] Error building the vignette

[Lluís Revilla]

Dear Bioconductor team and list,

I found that my package on devel (BioCor) fails to build on all the OS. The
error message is  related to creating figures of the vignette (see below).

I haven't touched the vignettes in a while. and building the package on my
machine passes all the checks. In addition, I found the same type of error
happens to other packages (metagene, and yesterday to restfulSE). I don't
know where to look at to solve this problem. Do you have any recommendation?

Many thanks,

Lluís


PS: Errors on the devel branch:

Linux:
* creating vignettes ... ERROR
Quitting from lines 271-282 (BioCor_1_basics.Rmd)
Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors

Windows:
* creating vignettes ... ERROR
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "BioCor_1_basics_files/figure-html/hclust1-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust1-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "BioCor_1_basics_files/figure-html/hclust3-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust3-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "BioCor_1_basics_files/figure-html/hclust3b-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust3b-1.png"' execution failed with
error code 4
Quitting from lines 271-282 (BioCor_1_basics.Rmd)
Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors

MacOS
* creating vignettes ... ERROR
sh: line 1:  8065 Abort trap: 6   'convert'
'BioCor_1_basics_files/figure-html/hclust1-1.png' -trim
'BioCor_1_basics_files/figure-html/hclust1-1.png' > /dev/null
sh: line 1:  8098 Abort trap: 6   'convert'
'BioCor_1_basics_files/figure-html/hclust3-1.png' -trim
'BioCor_1_basics_files/figure-html/hclust3-1.png' > /dev/null
sh: line 1:  8163 Abort trap: 6   'convert'
'BioCor_1_basics_files/figure-html/hclust3b-1.png' -trim
'BioCor_1_basics_files/figure-html/hclust3b-1.png' > /dev/null
Quitting from lines 271-282 (BioCor_1_basics.Rmd)
Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors

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Re: [Bioc-devel] Why bioconductor?

[Lluís Revilla]

Some people is lost even when and how many updates are and differences
between different packages. See this question for instance (
https://www.biostars.org/p/287871/)
Compared to CRAN or PyPi, which don't have release cycles, Bioconductor
workflow is a bit more complicated to learn.

Related to Bioconductor style there is a issue on lintr to build one for
bioconductor: https://github.com/jimhester/lintr/issues/43
I think that with a few more tweaks to this file (
https://github.com/llrs/customizations/blob/master/.lintr) it could be
ready for the community. Pull requests are welcome.

There is also the styler package (https://github.com/r-lib/styler) which
automatically changes of style according to some rules.
I opened an issue about having Bioconductor style:
https://github.com/r-lib/styler/issues/331 but I couldn't manage to build
one style. It could be interesting to have one too.

Hope this helps





On Wed, 10 Oct 2018 at 23:43, Morgan, Martin 
wrote:

> I think pull requests on
>
>
>
> https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md
>
> would be welcome.
>
> Martin
>
> On 10/10/18 11:51 AM, Ludwig Geistlinger wrote:
> > While this might be obvious to most of us, it seems to be less clear to
> others.
> >
> > In particular, those who worked out their first package and wonder
> what's the difference between having a package available on Github, CRAN,
> or Bioconductor.
> >
> >
> > I wonder whether it would be helpful for the Bioc webpage to pick up on
> the benefits of submitting to CRAN by Hadley
> >
> >
> > http://r-pkgs.had.co.nz/release.html
> >
> >
> > and several considerations with respect to Bioconductor
> >
> >
> > https://bioinformatics.stackexchange.com/questions/639/why-bioconductor
> >
> >
> > (Maybe FAQ?)
> >
> >
> >   Just a thought.
> >
> >
> >   [[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] NEWS.md

[Lluís Revilla]

e is formatted incorrectly.  from the
> ?news
> > > >
> > > >
> > > >  The plain text 'NEWS' files in add-on packages use a variety of
> > > >  different formats; the default news reader should be capable to
> > > >  extract individual news entries from a majority of packages from
> > > >  the standard repositories, which use (slight variations of) the
> > > >  following format:
> > > >
> > > > • Entries are grouped according to version, with version
> header
> > > >   "Changes in version" at the beginning of a line, followed
> by
> > > >   a version number, optionally followed by an ISO 8601 format
> > > >   date, possibly parenthesized.
> > > >
> > > > • Entries may be grouped according to category, with a
> category
> > > >   header (different from a version header) starting at the
> > > >   beginning of a line.
> > > >
> > > > • Entries are written as itemize-type lists, using one of
> 'o',
> > > >   '*', '-' or '+' as item tag.  Entries must be indented, and
> > > >   ideally use a common indentation for the item texts.
> > > >
> > > >
> > > >
> > > >
> > > > Please remove the pound sign (# ) from the header entry -  and use
> "Changes in version"  not "BioCor"
> > > >
> > > >
> > > > so for example:
> > > >
> > > >
> > > >
> > > > # BioCor 0.99.25
> > > >
> > > > * Update Vignette to just output html
> > > >
> > > > # BioCor 0.99.24
> > > >
> > > > * Submit the package to the Bioconductor project
> > > >
> > > > # BioCor 0.99.23
> > > >
> > > > * Add the Bioconductor webhook
> > > >
> > > >
> > > > Would become
> > > >
> > > >
> > > > Changes in version 0.99.25
> > > >
> > > > * Update Vignette to just output html
> > > >
> > > > Changes in version 0.99.24
> > > >
> > > > * Submit the package to the Bioconductor project
> > > >
> > > > Changes in version 0.99.23
> > > >
> > > > * Add the Bioconductor webhook
> > > >
> > > >
> > > >
> > > >
> > > > Lori Shepherd
> > > >
> > > > Bioconductor Core Team
> > > >
> > > > Roswell Park Cancer Institute
> > > >
> > > > Department of Biostatistics & Bioinformatics
> > > >
> > > > Elm & Carlton Streets
> > > >
> > > > Buffalo, New York 14263
> > > >
> > > > 
> > > > From: Bioc-devel  on behalf of
> Lluís Revilla 
> > > > Sent: Tuesday, September 25, 2018 3:20:39 AM
> > > > To: bioc-devel
> > > > Subject: [Bioc-devel] NEWS.md
> > > >
> > > > Dear Bioconductor team,
> > > >
> > > > I found that the new R version 3.5.1, to be used with the new
> release of
> > > > Bioconductor, supports the ‘NEWS.md' files.
> > > >
> > > > I updated my package (BioCor) to use `NEWS.md`. However, on the devel
> > > > landing page of the package stills shows the old file NEWS file.
> This is
> > > > consistent with the developer page (
> > > > https://www.bioconductor.org/developers/package-guidelines/#news).
> > > >
> > > > Will this be a requirement or can I keep the NEWS.md file?
> > > >
> > > > Many thanks,
> > > >
> > > > Lluís
> > > >
> > > > [[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
> > >
> > >
> > > --
> > > Laurent Gatto | @lgatt0
> > > http://lgatto.github.io/
> > >
> > > ___
> > > 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
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[Bioc-devel] NEWS.md

[Lluís Revilla]

Dear Bioconductor team,

I found that the new R version 3.5.1, to be used with the new release of
Bioconductor, supports the ‘NEWS.md’ files.

I updated my package (BioCor) to use `NEWS.md`. However, on the devel
landing page of the package stills shows the old file NEWS file. This is
consistent with the developer page (
https://www.bioconductor.org/developers/package-guidelines/#news).

Will this be a requirement or can I keep the NEWS.md file?

Many thanks,

Lluís

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Re: [Bioc-devel] Transition from Google Sheet to Web App

[Lluís Revilla]

Many thanks Valerie for the feedback!

On 7 May 2018 at 15:03, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Lluis,
>
> A little follow up on this. When a new package is submitted, the email in
> DESCRIPTION is checked against the Support Site so those 2 fields are in
> sync for new packages ... at least for awhile. Right now we don't have
> plans to sync the App with DESCRIPTION and the Support Site but it may be
> considered in the future.
>
> Valerie
>
>
>
> On 04/19/2018 07:59 AM, Obenchain, Valerie wrote:
>
> Hi Lluis,
>
> We (or at least I) had not considered linking the profile in the
> credentials app with the profile in the Support Site and currently they are
> not aware of each other. The email in DESCRIPTION was used to get some
> emails for the credentials app but it is not the case that an email change
> in the app will propagate to DESCRIPTION.
>
> We do require package maintainers to be registered on the Support Site in
> order to submit a package but I'm not sure if this email is checked against
> the DESCRIPTION.
>
> I see what you mean by having this information in 3 places, DESCRIPTION
> file, credentials app and Support Site. I think the 'if' and 'how' of
> connecting these pieces needs some thought. I'll discuss with the group at
> our next meeting and will follow up here.
>
> Thanks for bringing this up.
>
> Valerie
>
>
>
>
> On 04/19/2018 06:35 AM, Lluís Revilla wrote:
>
> Hi all,
>
> I have a couple of doubts related to the new app.
>
> I've seen that one can update mail, and github id, and add new keys
> (Nice!). However I couldn't find if this account will be somehow linked to
> the user profile in the support site. Are there any plans in this direction?
> At the moment the email of the maintainer of a package should be
> registered in the support site, which is the same one used for the app.
> When someone updates the email in the app is it updated in other sites of
> Bioconductor? Will the email of the Description files of the packages  and
> the account in the support site be updated?
>
> Many thanks,
>
> Lluís
>
>
> On 18 April 2018 at 17:13, Obenchain, Valerie <Valerie.Obenchain@
> roswellpark.org> wrote:
>
>> The Web App for managing SSH keys is now available at
>>
>>   https://git.bioconductor.org/BiocCredentials/
>>
>> Accounts have been created for all package maintainers. Note the central
>> identifier, i.e., how you login is your email. This email was taken from
>> the DESCRIPTION of your package or the Google Sheet if you registered a key
>> there.
>>
>> When you first visit the App you'll need to activate your account. An
>> activation link will be sent to your email. Once your account is activated
>> you can login. Trying to login without activation will lead to an error.
>>
>> Let us know if you have any questions or problems.
>>
>>
>>
>> On 04/18/2018 05:56 AM, Obenchain, Valerie wrote:
>> This transition will start at 9am EST today. We'll post back when it's
>> done.
>>
>> Valerie
>>
>>
>> On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:
>>
>> Hi developers,
>>
>> Tomorrow we are bringing a web app online to help with the management of
>> SSH keys. The app will replace the Google Sheet currently used to add keys.
>> Through the web interface you'll be able to add keys and change your email
>> or github username. There is also an option to see what packages you have
>> access to.
>>
>> Using the app is not a requirement. It's intended to help package authors
>> get setup with keys and access to their package in the Bioconductor git
>> repository. Those of you already set up with keys and access may never need
>> to use it.
>>
>> Tomorrow, April 18, we'll have downtime from 9-11am EST while we take
>> down the Google Sheet and bring up the app.
>>
>> Thanks.
>>
>> Valerie and Nitesh
>>
>>
>> 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

Re: [Bioc-devel] Transition from Google Sheet to Web App

[Lluís Revilla]

Hi all,

I have a couple of doubts related to the new app.

I've seen that one can update mail, and github id, and add new keys
(Nice!). However I couldn't find if this account will be somehow linked to
the user profile in the support site. Are there any plans in this direction?
At the moment the email of the maintainer of a package should be registered
in the support site, which is the same one used for the app. When someone
updates the email in the app is it updated in other sites of Bioconductor?
Will the email of the Description files of the packages  and the account in
the support site be updated?

Many thanks,

Lluís


On 18 April 2018 at 17:13, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> The Web App for managing SSH keys is now available at
>
>   https://git.bioconductor.org/BiocCredentials/
>
> Accounts have been created for all package maintainers. Note the central
> identifier, i.e., how you login is your email. This email was taken from
> the DESCRIPTION of your package or the Google Sheet if you registered a key
> there.
>
> When you first visit the App you'll need to activate your account. An
> activation link will be sent to your email. Once your account is activated
> you can login. Trying to login without activation will lead to an error.
>
> Let us know if you have any questions or problems.
>
>
>
> On 04/18/2018 05:56 AM, Obenchain, Valerie wrote:
> This transition will start at 9am EST today. We'll post back when it's
> done.
>
> Valerie
>
>
> On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:
>
> Hi developers,
>
> Tomorrow we are bringing a web app online to help with the management of
> SSH keys. The app will replace the Google Sheet currently used to add keys.
> Through the web interface you'll be able to add keys and change your email
> or github username. There is also an option to see what packages you have
> access to.
>
> Using the app is not a requirement. It's intended to help package authors
> get setup with keys and access to their package in the Bioconductor git
> repository. Those of you already set up with keys and access may never need
> to use it.
>
> Tomorrow, April 18, we'll have downtime from 9-11am EST while we take down
> the Google Sheet and bring up the app.
>
> Thanks.
>
> Valerie and Nitesh
>
>
> 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]]
>
> ___
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> 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]]
>
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Re: [Bioc-devel] repository change after package acceptance

[Lluís Revilla]

Dear Xu,

While you, with your ssh key, keep pushing to the git.bioconductor.org it
doesn't matter where else is stored.
To move a repository within github you need to follow this tutorial:
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization

Regards,

Lluís


On 16 April 2018 at 12:05, Xu Qiao  wrote:

> Hi everyone,
>
> I am the developer of package "PowerExplorer",  it has been accepted last
> week, and now it is visible on Bioconductor git server. However, the
> package was developed in my own personal GitHub repository, now I need to
> move it into our lab repository. Does anyone have any idea how to do this
> smoothly? Since the Bioconductor is expecting to be associated with my
> original GitHub-id.
>
> Kind regards,
> Xu
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[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
> >
>
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Re: [Bioc-devel] Warnings in build for BioCor

[Lluís Revilla]

Thanks Martin for looking into it.
I think that is the reason of the problem, the timeline of the errors
building certainly match.
I couldn't find this documented in Writing R Extensions, is this behavior
documented somewhere?

Lluís

On 28 February 2018 at 15:03, Martin Morgan <martin.mor...@roswellpark.org>
wrote:

> Actually, looking at your github repository, I see you have two vignettes,
> you have renamed one from vignette2.Rmd to BioCor_advanced.Rmd, and that
> this vignette now collates before the original one. I believe that
> vignettes are built in the same R process, so the packages loaded in the
> first vignette are available (and conflict with) packages loaded in the
> second.
>
> Martin
>
>
> On 02/28/2018 08:53 AM, Martin Morgan wrote:
>
>>
>>
>> On 02/28/2018 05:31 AM, Lluís Revilla wrote:
>>
>>> Dear bioconductor core,
>>>
>>> The development version of my package hosted in Github cannot be build.
>>> It
>>> seems that another package is loaded when it shouldn't and masks the
>>> functions that are used in the vignette. (In case anyone wants to help
>>> here
>>> is the link to the StackOverflow question:
>>> https://stackoverflow.com/q/49002455/2886003)
>>>
>>
>> This means that 'another package' is on the search() path. It only gets
>> there if your package attaches it, directly or indirectly. Maybe another
>> package that you attach previously import'ed it, but now depends on it? To
>> narrow this down, step through your vignette code until you see the
>> offending package on the search() path.
>>
>> Maybe you can avoid attaching the intermediate package, or put your
>> package in front of the others on the search path by loading your package
>> last in the vignette.
>>
>> If you're running into these problems, and you're intimately familiar
>> with your package, then one can imagine that users will also run into this
>> problem and the suggestion to mangle your package function names starts to
>> sound appealing.
>>
>>
>>> Additionally the current version hosted in Bioconductor has a warning in
>>> the windows build. Which I hoped to correct for these release.
>>>
>>> I don't know if I will find a solution on time for the next release
>>> (which
>>> I expect in three weeks), but I am worried I won't be able to fix it on
>>> time.
>>>
>>
>> The next Bioconductor release has not been announced (we try to tie these
>> to the R release schedule, and the release of R-3.5 has not yet been
>> announced), but will likely be at the end of April.
>>
>> Martin
>>
>>
>>> The End Of Life page of Bioconductor only talks about errors not
>>> warnings,
>>> and I couldn't find if this has been discussed previously in the
>>> archive. I
>>> would like to know if I can leave the development version as is (until I
>>> find a solution) or should I aim to correct the warning for the next
>>> release?
>>>
>>> Many thanks,
>>>
>>> Lluís Revilla
>>>
>>> [[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.
>

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Re: [Bioc-devel] Warnings in build for BioCor

[Lluís Revilla]

Dear Matthias and Robert,

My namespace doesn't import that package. It is mentioned in the
Description file in Suggests, and on the same vignette it is and loaded but
after the line where the error is reported.
The error is reported on lines 143-148 (BioCor.Rmd) and the library is
loaded on line 260.
But I might end up using the double colon to avoid the error.
Cheers,

Lluís

On 28 February 2018 at 14:26, Robert Castelo <robert.cast...@upf.edu> wrote:

> Lluis,
>
> something you can do in you NAMESPACE to follow the advice below from
> Matthias if you are importing the functionality of a whole package is:
>
> import(pkgyouneed, except=functionmethodyoudefine)
>
> in this way, you're importing everything except that particular function
> or method that you are defining in your own package.
>
> cheers,
>
> robert.
>
>
> On 28/02/2018 12:51, Matthias Döring wrote:
>
>> DearLluis,
>> how is your namespace defined? Do you use 'import' or 'importFrom' to
>> load the package in question? If you are currently using 'import' to load
>> all exports from the package, you could switch to 'importFrom' and exclude
>> the function that causes the problems and then use the double-colon
>> operator when referring to the package's function.
>>
>> Kind regards
>>  Matthias
>>
>> On 02/28/2018 11:31 AM, Lluís Revilla wrote:
>>
>>> Dear bioconductor core,
>>>
>>> The development version of my package hosted in Github cannot be build.
>>> It
>>> seems that another package is loaded when it shouldn't and masks the
>>> functions that are used in the vignette. (In case anyone wants to help
>>> here
>>> is the link to the StackOverflow question:
>>> https://stackoverflow.com/q/49002455/2886003)
>>>
>>> Additionally the current version hosted in Bioconductor has a warning in
>>> the windows build. Which I hoped to correct for these release.
>>>
>>> I don't know if I will find a solution on time for the next release
>>> (which
>>> I expect in three weeks), but I am worried I won't be able to fix it on
>>> time.
>>>
>>> The End Of Life page of Bioconductor only talks about errors not
>>> warnings,
>>> and I couldn't find if this has been discussed previously in the
>>> archive. I
>>> would like to know if I can leave the development version as is (until I
>>> find a solution) or should I aim to correct the warning for the next
>>> release?
>>>
>>> Many thanks,
>>>
>>> Lluís Revilla
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>

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[Bioc-devel] Warnings in build for BioCor

[Lluís Revilla]

Dear bioconductor core,

The development version of my package hosted in Github cannot be build. It
seems that another package is loaded when it shouldn't and masks the
functions that are used in the vignette. (In case anyone wants to help here
is the link to the StackOverflow question:
https://stackoverflow.com/q/49002455/2886003)

Additionally the current version hosted in Bioconductor has a warning in
the windows build. Which I hoped to correct for these release.

I don't know if I will find a solution on time for the next release (which
I expect in three weeks), but I am worried I won't be able to fix it on
time.

The End Of Life page of Bioconductor only talks about errors not warnings,
and I couldn't find if this has been discussed previously in the archive. I
would like to know if I can leave the development version as is (until I
find a solution) or should I aim to correct the warning for the next
release?

Many thanks,

Lluís Revilla

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Re: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

[Lluís Revilla]

Great work and happy new year!!

I checked both RSS feeds and the random links I tried all point to the home
page of Bioconductor.
I am unsure if the links in the feed should point to a section on the
gitlog page or to any other page (or is an issue on my end).

Thanks,

Lluís


On 2 January 2018 at 21:38, Turaga, Nitesh 
wrote:

> Hello Maintainers,
>
> Happy new year!
>
> The GIT logs are available as RSS feeds, or as markdown on the website at
>
> http://bioconductor.org/developers/gitlog/
>
> This is across all the packages on the bioconductor git server. It allows
> developers to keep track of their package development, and for the
> community to keep track of their favorite packages. The website shows only
> the most recent 200 commits.
>
> Please note that the website rebuilds every 20 mins, so it will take 20
> mins for your commit to show up on the website.
>
>
> Best,
>
>
> Nitesh Turaga
> Bioconductor Core Team
>
> 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.
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Support site question can't be edited: Language "ca" is not one of the supported languages ['en']!

[Lluís Revilla]

This seems related to this issue:
https://github.com/Bioconductor/support.bioconductor.org/issues/33

On 20 September 2017 at 11:54, Martin Morgan 
wrote:

> On 09/19/2017 10:30 PM, Gordon K Smyth wrote:
>
>> As a Bioc support site moderator, I tried to edit the following post to
>> fix the tags in the original question:
>>
>>https://support.bioconductor.org/p/edit/100572/
>>
>> However any attempt by me to edit the question elicits the error message:
>> "Language "ca" is not one of the supported languages ['en']!"
>>
>> I have checked the message at the source level and there appears to be no
>> language setting. The error persists even if I delete all the text and
>> replace it with new text or if I don't edit the text at all.
>>
>> Any ideas?
>>
>
> I see this too but don't have any solutions. Martin
>
>
>> Gordon
>>
>> --
>> Professor Gordon K Smyth
>> Head, Bioinformatics Division
>> Walter and Eliza Hall Institute of Medical Research
>>
>>
>> ___
>> 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}}
>
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] BioCor devel timeout

[Lluís Revilla]

Dear developers,

The package I maintain (BioCor) builds correctly on malbec1 (Linux) and
veracruz1 (OS X) in the development but not in tokay1 (Windows machine)
server. It timesout.

I am not sure what causes this, I don't fetch anything from the website.
Last Windows downloadable version is 1.1.0 and on later versions of the
package I haven't add anything that could modify the time it takes to build
on Windows.

I can't test the package on a Windows computer. Is there a way to know if
it is due to something on my code? Could somebody advise me how to find
what can I do?

Many thanks,

Lluís Revilla

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Re: [Bioc-devel] Maintainers submit your SSH public keys

[Lluís Revilla]

Hi,

Yes, Jason your Github username is the Github id.

I have a question about one social feature of github: the topics of a
repository. Should we tag the repositories with packages included (or
intended to be included) in Bioconductor with the tag "bioconductor" or
"biocondcutor-package"?
I am asking this because some repositories might be related to bioconductor
but they aren't a package.

Regards,

Lluís

On 13 July 2017 at 11:43, Jason Serviss  wrote:

> Hello,
>
> What exactly is ment with “Github id”? My Github username?
>
> Kind Regards,
> Jason
>
>
> On 12 Jul 2017, at 18:16, Turaga, Nitesh  > wrote:
>
> Hi Samuel,
>
>
> This is a great question.
>
>
> You are not required to create a Github repository for your package. But,
> if you are actively maintaining your package, and would like to take
> advantage of the social coding features and the extended Bioconductor
> community it is a really good idea.
>
>
> If you want to just maintain it on our Git server, once you have SSH
> access, you are welcome to do that as well. This is highlighted in our
> documentation https://github.com/Bioconductor/bioc_git_
> transition/blob/master/doc/scenario-11-maintain-without-github.md.
>
>
> We welcome feedback on the documentation, and FAQ section (
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq.md
> )
>
>
>
> Best Regards,
>
>
> Nitesh
>
>
>
> 
> From: Samuel E Zimmerman >
> Sent: Wednesday, July 12, 2017 11:49 AM
> To: Turaga, Nitesh; Ramon Diaz-Uriarte; bioc-devel@r-project.org bioc-devel@r-project.org>
> Subject: RE: [Bioc-devel] Maintainers submit your SSH public keys
>
> Dear Nitesh,
>
> This may seem like an obvious question, but if we have not created a
> repository for our packages yet, should we create a GitHub repository using
> the directions here:
>
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/
> scenario-1-svn-to-github.md
>
>
> Thank you.
>
> Best,
> Sam
> 
> From: Bioc-devel [bioc-devel-boun...@r-project.org bioc-devel-boun...@r-project.org>] on behalf of Turaga, Nitesh
> [nitesh.tur...@roswellpark.org]
> Sent: Wednesday, July 12, 2017 11:29 AM
> To: Ramon Diaz-Uriarte; bioc-devel@r-project.org bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] Maintainers submit your SSH public keys
>
> Hi Ramon,
>
> This is a good question. Your key will be processed every 24 hours. If you
> have already submitted, then, you should be able to work through the
> documentation provided
> (https://github.com/Bioconductor/bioc_git_transition/tree/master/doc).
> Working through the documentation to check everything is in order helps
> everyone in the Bioconductor community too.
>
> Or a simple way to check is, make a change in your cloned package, ideally
> it is a �version bump� in the DESCRIPTION file. Then, try to git add �>
> commit �> push the change up to the new git server. These steps are given
> in our documentation,
>
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/
> scenari
> o-11-maintain-without-github.md#clone-and-setup-the-
> package-on-your-local-m
> achine
>
>
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/
> scenari
> o-11-maintain-without-github.md#make-and-commit-changes-to-
> your-local-repos
> itory
>
>
> We appreciate feedback on this.
>
> Best,
>
> Nitesh
>
> P.S We have already processed your previous submission. Don�t worry, we
> don�t process duplicate submissions.
>
>
> Dear Nitesh,
>
> I just filled it up again, though I think I did fill up and hit
> send/submit
> a few days ago. Is there a way for me to confirm it has worked?
>
>
> Best,
>
>
> R.
>
>
>
> On Wed, 12-07-2017, at 14:50:14, Turaga, Nitesh
> >
> wrote:
> Hi Maintainers,
>
> Please submit your (SSH public key or GitHub id) and SVN id in this
> google
> form https://goo.gl/forms/eg36vcBkIUjfZfLe2. It will only take a minute
> [https://lh6.googleusercontent.com/aTIh4yWF4TsFYR95qIA_
> lBuCgvLJ88Q4WzDmdBuie6ndQirxWI0jhfRBF7eO-n3W6SE=w1200-h630-p]<
> https://goo.gl/forms/eg36vcBkIUjfZfLe2>
>
> git / svn transition: ssh keys
> goo.gl
> Use this form to link your existing svn credentials with access
> permissions to the new Bioconductor git repository. To do this, we need an
> ssh public key. You might have added these to github, see
> https://github.com/your-github-id.keys. Alternatively, you may provide
> the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To
> generate ssh key pairs, see https://help.github.com/
> articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/
>
>
>
> or
> less.
>
> This is a crucial step to the transition, 

Re: [Bioc-devel] Bioconductor stats

[Lluís Revilla]

Hi Hervé,

I wasn't aware of the discrepancy between the monthly number of IPs and the
yearly number of IPs.
I didn't realize that my own package showed this distinction between
monthly and yearly number of IPs.
Thanks for pointing it.

Yes, usually the effect of a package being in several categories is quite
low.
But in some packages it is more frequent than once a year and in some
others more than just one download each time it happens.

Cheers,

Lluís



On 30 June 2017 at 11:44, Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi LLuis,
>
> As Sean already said mirrors are not included in the stats. The
> monthly nb of distinct IPs are reset every month and the yearly
> nb of distinct IPs are reset every year.
>
> Some packages are indeed in two categories. Category assignment is
> based on the download URL only. For some mysterious reason the Apache
> logs contain some lines that indicate that AnnotationDbi was downloaded
> from an URL that points to a data experiment repository. These lines
> are very rare though (1 or 2 per year) so overall don't have any
> significant impact on the stats. Anyway that's something we'll need
> to dig into at some point.
>
> Cheers,
> H.
>
>
> On 06/27/2017 04:34 AM, Lluís Revilla wrote:
>
>> Hi,
>>
>> I have been looking at the stats of Bioconductor, and I would like to know
>> more about how are they calculated.
>>
>> Do these stats account for the mirror sites? Are there any stats of the
>> usage of mirrors?
>>
>> I found some packages that for the same month they have downloads in two
>> categories. For instance AnnotationDbi has some downloads as experimental
>> data package:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>> ctor.org_packages_stats_data-2Dexperiment_AnnotationDbi_=
>> DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA=psknpX6b5M14sI3qf3U_bWP0s-rn_fEEnRsPoYrD
>> 2bw=Vn8nr1PNCdozt0465LZB9CXnGpPGdoEu_QskcQ6ehZA=  while
>> most of the downloads are in the software category (The right one). It
>> seems that near 500 packages have downloads in two categories.
>>
>> The "Nb of distinct IPs" if I understand correctly is for each package and
>> month. So if the same IP downloads again the package is listed as a new
>> IP,
>> isn't it? I assume that if mirrors are counted either no one downloads the
>> same packages from different mirrors in the same IP or that these
>> information is shared across mirrors for these stats.
>>
>> Regards,
>>
>> Lluís
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ps
>> knpX6b5M14sI3qf3U_bWP0s-rn_fEEnRsPoYrD2bw=fX6Iawm0pI8-QEOm
>> Pe6TjPRFoKmYDYtrW6As8eHJ59o=
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

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[Bioc-devel] Bioconductor stats

[Lluís Revilla]

Hi,

I have been looking at the stats of Bioconductor, and I would like to know
more about how are they calculated.

Do these stats account for the mirror sites? Are there any stats of the
usage of mirrors?

I found some packages that for the same month they have downloads in two
categories. For instance AnnotationDbi has some downloads as experimental
data package:
http://bioconductor.org/packages/stats/data-experiment/AnnotationDbi/ while
most of the downloads are in the software category (The right one). It
seems that near 500 packages have downloads in two categories.

The "Nb of distinct IPs" if I understand correctly is for each package and
month. So if the same IP downloads again the package is listed as a new IP,
isn't it? I assume that if mirrors are counted either no one downloads the
same packages from different mirrors in the same IP or that these
information is shared across mirrors for these stats.

Regards,

Lluís

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Re: [Bioc-devel] Commiting from git to svn

[Lluís Revilla]

Dear Stephanie,

Maybe I didn't pick the right commit but it didn't solve my error, and
the same message appeared.
Thanks for the suggestion.

Lluís

On 6 April 2017 at 18:34, Stephanie M. Gogarten
<sdmor...@u.washington.edu> wrote:
> Try following the steps under "Dealing with prior history / merge conflicts"
> on the git mirror page:
> http://www.bioconductor.org/developers/how-to/git-mirrors/
>
> Using "git cherry-pick" instead of rebase seems to avoid a lot of errors.
>
> Stephanie
>
>
> On 4/5/17 8:18 AM, Lluís Revilla wrote:
>>
>> Dear all,
>>
>> Short problem: I am a trying to sync my new package BioCor git repository
>> with the Bioconductor svn repository. But I am failing when I do git svn
>> dcommit.
>>
>> Long history of the problem
>> I did some changes on my master branch (where I developed until now) then
>> I
>> used the update_remotes.sh which created a new branch.
>> I changed to that branch (git checkout devel), changed its name (git
>> branch
>> -m devel bioc/devel) and used (git svn rebase) following the instructions.
>> I brought the changes by merging the branches (git merge master)and wanted
>> to push it to the svn server with (git svn dcommit --add-author-from) .
>> As expected I had some merge conflicts (apparently originated because the
>> initial commit to that repository wasn't with the code I submitted)
>> I skipped them (git rebase --skip) until it ended the rebase at the moment
>> I am only with the changes I performed after submitting the package, as
>> compared with the Bioconductor-mirror (previously the branch was ahead of
>> 'bioc/master' by 173 commits):
>> git status
>> Your branch is ahead of 'bioc/master' by 11 commits.
>>
>> However when I try to sync and commit with svn I can't (BTW it wasn't
>> clear
>> to me how to add my username for git svn repository otherwise I am
>> prompted
>> with tue username of my machine, so maybe it is still wrong):
>>
>> git svn dcommit --add-author-from --username l.revilla
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
>> Subversion Repository
>> Password for 'l.revilla':
>>
>> ERROR from SVN:
>> URL access forbidden for unknown reason: POST of '/bioconductor/!svn/me':
>> 403 Forbidden (https://hedgehog.fhcrc.org)
>> W: 3d12099bda0c61d0a63a787ebb9cbe3b2e06770d and refs/remotes/svn differ,
>> using rebase:
>> :04 04 985b6b2986a31a3eff4161563a5585ea10467787
>> c8d818d0ed3196d391f914996dd26354004df665 MR
>> :100644 00 8e2bef6bf185b9bbc9da7e500bdb394396ccad99
>>  Dbio_cor.R
>> :04 04 ed161436ea9089f70f74f2e1ea79e53a796eed5b
>> 378a5b97d68ecfa7430bebdaba2c5b6540e6051e Mman
>> :04 04 65b109ed754cd8aa35a2fcaceea8c05fdbe91899
>> 594d15d7838d2096afda7b5697242e48bb7fce42 Mtests
>> :04 04 474a6a48c23f1bce377071b58e0b87f161b2a5cf
>> 6be3cd535391595a962f610dad103e88b2fc32bd Mvignettes
>> Current branch bioc/devel is up to date.
>> ERROR: Not all changes have been committed into SVN, however the committed
>> ones (if any) seem to be successfully integrated into the working tree.
>> Please see the above messages for details.
>>
>>
>> How can I push the new commits to the svn repository?
>>
>> Many thanks!
>>
>> Lluís
>>
>> [[alternative HTML version deleted]]
>>
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>>
>

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[Bioc-devel] Commiting from git to svn

[Lluís Revilla]

Dear all,

Short problem: I am a trying to sync my new package BioCor git repository
with the Bioconductor svn repository. But I am failing when I do git svn
dcommit.

Long history of the problem
I did some changes on my master branch (where I developed until now) then I
used the update_remotes.sh which created a new branch.
I changed to that branch (git checkout devel), changed its name (git branch
-m devel bioc/devel) and used (git svn rebase) following the instructions.
I brought the changes by merging the branches (git merge master)and wanted
to push it to the svn server with (git svn dcommit --add-author-from) .
As expected I had some merge conflicts (apparently originated because the
initial commit to that repository wasn't with the code I submitted)
I skipped them (git rebase --skip) until it ended the rebase at the moment
I am only with the changes I performed after submitting the package, as
compared with the Bioconductor-mirror (previously the branch was ahead of
'bioc/master' by 173 commits):
git status
Your branch is ahead of 'bioc/master' by 11 commits.

However when I try to sync and commit with svn I can't (BTW it wasn't clear
to me how to add my username for git svn repository otherwise I am prompted
with tue username of my machine, so maybe it is still wrong):

git svn dcommit --add-author-from --username l.revilla

Authentication realm:  The bioconductor
Subversion Repository
Password for 'l.revilla':

ERROR from SVN:
URL access forbidden for unknown reason: POST of '/bioconductor/!svn/me':
403 Forbidden (https://hedgehog.fhcrc.org)
W: 3d12099bda0c61d0a63a787ebb9cbe3b2e06770d and refs/remotes/svn differ,
using rebase:
:04 04 985b6b2986a31a3eff4161563a5585ea10467787
c8d818d0ed3196d391f914996dd26354004df665 MR
:100644 00 8e2bef6bf185b9bbc9da7e500bdb394396ccad99
 Dbio_cor.R
:04 04 ed161436ea9089f70f74f2e1ea79e53a796eed5b
378a5b97d68ecfa7430bebdaba2c5b6540e6051e Mman
:04 04 65b109ed754cd8aa35a2fcaceea8c05fdbe91899
594d15d7838d2096afda7b5697242e48bb7fce42 Mtests
:04 04 474a6a48c23f1bce377071b58e0b87f161b2a5cf
6be3cd535391595a962f610dad103e88b2fc32bd Mvignettes
Current branch bioc/devel is up to date.
ERROR: Not all changes have been committed into SVN, however the committed
ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.


How can I push the new commits to the svn repository?

Many thanks!

Lluís

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[Bioc-devel] reusing topGO objects

[Lluís Revilla]

Dear Adrian and all

I am using the package topGO and I would like to know if you could help me
to reuse the same object to perform several test, see the examples below:

library("topGO")
data(GOdata)
geneSelectionFun(GOdata) <- function(x) {x == 1L}
GOdata
resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes1 <- GenTable(GOdata, resultKS.elim)
geneSelectionFun(GOdata) <- function(x) {x > 0.5}
GOdata
resultKS.elim2 <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes2 <- GenTable(GOdata, resultKS.elim2)
ontology(GOdata) <- "CC"
resultKS.elim3 <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes3 <- GenTable(GOdata, resultKS.elim3)
all.equal(score(resultKS.elim), score(resultKS.elim2)) # Shouldn't it be
different?

all(names(score(resultKS.elim3)) == names(score(resultKS.elim2))) # Should
the GO terms be different?
sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=es_ES.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] topGO_2.26.0 SparseM_1.74 GO.db_3.4.0
[4] AnnotationDbi_1.36.2 IRanges_2.8.1S4Vectors_0.12.1
[7] Biobase_2.34.0   graph_1.52.0 BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9matrixStats_0.51.0 lattice_0.20-34
digest_0.6.12
[5] grid_3.3.2 DBI_0.5-1  RSQLite_1.1-2
tools_3.3.2
[9] memoise_1.0.0


The object GOdata have different number of "Significant" genes annotated
when I change the geneSelectionFun, thus I would expect different p-values
but there are the same p-values in allRes2 and allRes1.

Also the test on the cellular component returns the same genes ontologies
as the previous test, which should be different because it is performed in
a different GO subcategory. Maybe that's the reason why the Term column is
NA.

I am doing something wrong? How can I reuse the same object with different
tests?

Thanks your help


Lluís

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Re: [Bioc-devel] Code quality and bug reports

[Lluís Revilla]

Dear Valerie,

When I talked about maintenance status I thought something on the line of
this badges at http://www.repostatus.org/ :
Maybe only the last three status are relevant to Bioconductor :

  - Active: The project has reached a stable, usable state and is being
actively developed.
  - Inactive: The project has reached a stable, usable state but is no
longer being actively developed; support/maintenance will be provided as
time allows.
  - Unsupported: The project has reached a stable, usable state but the
author(s) have ceased all work on it. A new maintainer may be desired.

Tweaking a bit the description it could be used to classify the support
given to a package. Given these categories and the information there is in
the repositories and in support site I suggest the following:

Giving the Active badge when there are commits (not done by the
Bioconductor project) in 6 months. Excluding the Bioconductor team is done
to prevent having packages as Active which are not, because the only change
is the version number or minor changes done by the Bioconductor team (Also,
is not the responsibility of the Bioconductor team to maintain the
packages, is it?). Or when at least once every six months the package
maintainer answers or comments a question (tagged with the package tag) in
the support site if there is any.As an example edgeR would be Active, it
has commits from the maintainers in the last 6 months.

If a question tagged with a package tag is unanswered and the maintainer
hasn't answered/commented in the last 6 months or there isn't any commit in
the last 6 months the package (by the maintainer or other than the
Bioconductor team) could be set to Inactive. CorMut would be Inactive and
close to the Unsupported status.

If there is any unanswered question tagged with a package tag and the
maintainer hasn't answered/commented in the last year and there isn't any
commit from the maintainer in the last 2 years, I would give the
Unsupported tag to that package. topGO would be in that category.

Once Unsupported status is reached the team could try to contact the
maintainer to let him/her know that the maintainer position could be taken
by somebody else willing to. Of course, if he/she makes commits or
answers/comment questions in the support site to make the status of the
package back to Active he/she could keep the maintainer status.

This system could be along with the current End of Life Policy, or not, but
gives an opportunity to the community of users to maintain a package they
deem useful. It is a bit more complex but would guide much better on what
packages are well supported and not only used. and those used but not
supported could be saved from Deprecation.

HTH,

Lluís

On 18 January 2017 at 17:52, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi,
>
> On 01/14/2017 03:01 AM, Lluís Revilla wrote:
> > Dear Valerie and all,
> >
> > If I understood the page you kindly linked correctly, a package is
> deprecated:
> > 1) When it fails to build and check (unless it is fixed).
> > 2) When the maintainer asks for it.
> > 3) If the maintainer is unresponsive (I assume when a mail is not
> > delivered) and(/or?) doesn't answers questions about the package (How
> > is this tracked? Which is the threshold for unanswered questions, 1
> > year? )
> We contact maintainers when a package fails on the build system. There
> isn't a set rule on the number of times contacted with no response
> because there are so many exceptions, e.g., transferred maintainer ship,
> away from email due to travel, etc. I'd say the average number of
> contacts is 3 before getting the final 2 week notice.
>
> >
> > In some packages, it seems the maintainers receive the mails, and the
> > packages build and past the daily checks of Bioconductor, but there
> > are bugs and issues with those packages that are left unanswered and
> > unsolved in support.bioconductor.org. Those packages that are still
> > functional and used but don't receive maintenance are then kept ? How
> > should the community help to solve those issues?
> A primary motivation for implementing badges on the landing pages was to
> provide the "maintenance status" you mention below. The badge stats give
> an idea of how active the maintainer is (posts, commits, coverage) as
> well as the level of use by others (downloads). The 'posts' badge shows
> support site activity over that past 6 months in terms of 4 fields:
> tagged questions / average answers per question / average comments per
> question / accepted answers.
>
> The CorMut package has no tagged questions:
>
>   http://www.bioconductor.org/packages/3.5/bioc/html/CorMut.html
>
> If Guangchuang had asked questions on the support site instead of
> posting comments in a gist there would be a number of ta

Re: [Bioc-devel] Code quality and bug reports

[Lluís Revilla]

Dear Valerie and all,

If I understood the page you kindly linked correctly, a package is deprecated:
1) When it fails to build and check (unless it is fixed).
2) When the maintainer asks for it.
3) If the maintainer is unresponsive (I assume when a mail is not
delivered) and(/or?) doesn't answers questions about the package (How
is this tracked? Which is the threshold for unanswered questions, 1
year? )

In some packages, it seems the maintainers receive the mails, and the
packages build and past the daily checks of Bioconductor, but there
are bugs and issues with those packages that are left unanswered and
unsolved in support.bioconductor.org. Those packages that are still
functional and used but don't receive maintenance are then kept ? How
should the community help to solve those issues?

Thanks,

Lluís

On 6 January 2017 at 18:56, Obenchain, Valerie
<valerie.obench...@roswellpark.org> wrote:
> On 01/04/2017 07:53 AM, Lluís Revilla wrote:
>> Dear Guangchuang and all,
>>
>> Quality of the packages has been a preoccupation of the project from
>> the  beginning  (see
>> https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for
>> more references and other discussions about bug reports.) Despite not
>> being in a goal of the project, it is necessary to do a reproducible
>> research, which it is a goal: "To further scientific understanding by
>> producing high-quality documentation and reproducible research.".
>> Although it seems that this discussion appears periodically
>> Bioconductor I don't know any solution in the project.
>>
>> I have never submitted a package to Bioconductor or CRAN, and I am
>> quite new to R (and is my first mail to the list), but one thing that
>> I keep thinking (before publishing a package) is the maintainability
>> of it. I don't know how much time/desires will I have to dedicate to a
>> package (if it is accepted) in the future, but at the same time I want
>> to make useful code to be used in further research beyond my own
>> project.
>>
>> However the Bioconductor core team may be already too busy to deal
>> with the issues of all packages. Maybe it would be better to bring
>> CRAN's policy to orphan packages (see:
>> https://cran.r-project.org/src/contrib/Orphaned/README):
>
> Bioconductor does have a system for dealing with orphaned packages
> called End of Life:
>
>   http://www.bioconductor.org/developers/package-end-of-life/
>
> Deprecated packages have a strikethrough the name on the build reports,
> e.g., the saps package,
>
>   http://www.bioconductor.org/checkResults/devel/bioc-LATEST/
>
>
> Valerie
>
>>
>> "Possible reasons for orphanizing a package:
>>
>> 1) The current maintainer actively wants to orphanize the package,
>>e.g., due to no longer having time or interest to act as package
>>maintainer.
>>
>> 2) Emails sent to the current maintainer by the CRAN admins bounced, or
>>were not answered for longer periods of time.
>> "
>> Example of an orhpan package is clusterRepro.
>>
>> To orphanize a package the current maintainer could post it here on
>> the devel list and ask for a maintainer on the support site, and it is
>> his/her decision to whom is passed the responsibility.
>> Otherwise, maybe the limit of time without answering mails/posts in
>> support could be 3 months/6 months. (I don't know the CRAN decision
>> when not answering mails)
>>
>> Once the orphaned status is reached maybe however who wants could send
>> patches or take the maintenance of the package for another 3 months or
>> more.
>>
>> This status would not make bugs easier to fix or control, but could
>> mark that a package is not in the best maintenance status.
>>
>> Hope this helps,
>>
>> Lluís
>>
>>
>> 
>> Date: Wed, 4 Jan 2017 15:38:53 +0800
>> From: "Yu, Guangchuang" <g...@connect.hku.hk>
>> To: bioc-devel <bioc-devel@r-project.org>
>> Subject: [Bioc-devel] report package issue to Bioconductor
>> Message-ID:
>> <caef2yodeq9loa3nfblbvnddtltkmz-yivkcf7umjrrpfqp7...@mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Dear all,
>>
>> Some packages never updated after they publish a paper, and they just
>> ignore bug report.
>>
>> I think we need somewhere, maybe on github, to post code review and
>> Bioconductor core team can take action if maintainer fail to fix issue.
>>
>> Here is a quick look of the CorMut package:
>> https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.
&

[Bioc-devel] Code quality and bug reports

[Lluís Revilla]

Dear Guangchuang and all,

Quality of the packages has been a preoccupation of the project from
the  beginning  (see
https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for
more references and other discussions about bug reports.) Despite not
being in a goal of the project, it is necessary to do a reproducible
research, which it is a goal: "To further scientific understanding by
producing high-quality documentation and reproducible research.".
Although it seems that this discussion appears periodically
Bioconductor I don't know any solution in the project.

I have never submitted a package to Bioconductor or CRAN, and I am
quite new to R (and is my first mail to the list), but one thing that
I keep thinking (before publishing a package) is the maintainability
of it. I don't know how much time/desires will I have to dedicate to a
package (if it is accepted) in the future, but at the same time I want
to make useful code to be used in further research beyond my own
project.

However the Bioconductor core team may be already too busy to deal
with the issues of all packages. Maybe it would be better to bring
CRAN's policy to orphan packages (see:
https://cran.r-project.org/src/contrib/Orphaned/README):

"Possible reasons for orphanizing a package:

1) The current maintainer actively wants to orphanize the package,
   e.g., due to no longer having time or interest to act as package
   maintainer.

2) Emails sent to the current maintainer by the CRAN admins bounced, or
   were not answered for longer periods of time.
"
Example of an orhpan package is clusterRepro.

To orphanize a package the current maintainer could post it here on
the devel list and ask for a maintainer on the support site, and it is
his/her decision to whom is passed the responsibility.
Otherwise, maybe the limit of time without answering mails/posts in
support could be 3 months/6 months. (I don't know the CRAN decision
when not answering mails)

Once the orphaned status is reached maybe however who wants could send
patches or take the maintenance of the package for another 3 months or
more.

This status would not make bugs easier to fix or control, but could
mark that a package is not in the best maintenance status.

Hope this helps,

Lluís



Date: Wed, 4 Jan 2017 15:38:53 +0800
From: "Yu, Guangchuang" 
To: bioc-devel 
Subject: [Bioc-devel] report package issue to Bioconductor
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Dear all,

Some packages never updated after they publish a paper, and they just
ignore bug report.

I think we need somewhere, maybe on github, to post code review and
Bioconductor core team can take action if maintainer fail to fix issue.

Here is a quick look of the CorMut package:
https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.

There should be more issues than I can found with quick look of the source
code.

Best wishes,
Guangchuang
?
--
--~--~-~--~~~---~--~~
Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: https://guangchuangyu.github.io
-~--~~~~--~~--~--~---

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