Re: [Bioc-devel] Flexibility for submitting a new ExperimentData-package

[Marcel Ramos]

Hi Teemu Daniel,

Those packages were developed before ExperimentHub.

Please follow the current standard for experiment data packages at

https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html

You may want to take a look at curatedTCGAData as an example 
(disclaimer: I developed the package).
It is advisable to split the resources into more modular components, 
e.g., colData, sampleMap, data assays
rather than distribute serialized MultiAssayExperiment objects.

IMO, there should be no compatibility issues as the changes would only 
affect the underlying code and
not the user interface.

Best regards,

Marcel


On 11/24/22 1:57 AM, Daniel Laajala wrote:
> Dear Bioconductor devs,
>
> thanks for all the hard work. Regarding if there's any leeway in how 
> ExperimentData-packages are structured:
>
> We started working a few years back on a "curatedPCaData" R-package for 
> curating prostate cancer multi-'omics datasets. We followed the structure of 
> a family of similar packages, e.g. readily on bioc:
> https://bioconductor.org/packages/release/data/experiment/html/curatedBreastData.html
> https://bioconductor.org/packages/release/data/experiment/html/curatedOvarianData.html
>
> With the data in a satisfactory form, we were now hoping to submit the 
> package to Bioconductor. However, due to the size of 
> MultiAssayExperiment-objects, the package is auto-rejected:
> https://github.com/Bioconductor/Contributions/issues/2804
>
> The data-raw/-files we can discard, as we provided these just for extra user 
> convenience.
> However, the mae_*.rda files are essential MultiAssayExperiment objects (as a 
> standard format for multi-'omics in Bioc), but these are right now too large 
> for the bot.
>
> Reading the package structure instructions, we were under the impression that 
> this old structure for ExperimentData would still be ok for Bioconductor; the 
> package passed checks (R CMD check and BiocCheck) with minor NOTEs. Our 
> current GitHub is at:
> https://github.com/Syksy/curatedPCaData
>
> Our package already has citations (with code provided there-in for extracting 
> and processing relevant data from the package), has been forked, has 
> collaborators using it as-is, etc, so revamping it to e.g. 
> ExperimentHub-structure would most likely cause quite major compatibility 
> issues.
>
>
> Would there be any chance of approaching Bioconductor with the package 
> roughly in its current format inspired by these older curated-packages, even 
> if it is not in the updated ideal ExperimentData-format?
>
> Kind regards,
> Teemu Daniel Laajala
>
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Flexibility for submitting a new ExperimentData-package

[Marcel Ramos]

Hi Teemu Daniel,

Those packages were developed before ExperimentHub.

Please follow the current standard for experiment data packages at

https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html

You may want to take a look at curatedTCGAData as an example 
(disclaimer: I developed the package).
It is advisable to split the resources into more modular components, 
e.g., colData, sampleMap, data assays
rather than distribute serialized MultiAssayExperiment objects.

IMO, there should be no compatibility issues as the changes would only 
affect the underlying code and
not the user interface.

Best regards,

Marcel


On 11/24/22 1:57 AM, Daniel Laajala wrote:
> Dear Bioconductor devs,
>
> thanks for all the hard work. Regarding if there's any leeway in how 
> ExperimentData-packages are structured:
>
> We started working a few years back on a "curatedPCaData" R-package for 
> curating prostate cancer multi-'omics datasets. We followed the structure of 
> a family of similar packages, e.g. readily on bioc:
> https://bioconductor.org/packages/release/data/experiment/html/curatedBreastData.html
> https://bioconductor.org/packages/release/data/experiment/html/curatedOvarianData.html
>
> With the data in a satisfactory form, we were now hoping to submit the 
> package to Bioconductor. However, due to the size of 
> MultiAssayExperiment-objects, the package is auto-rejected:
> https://github.com/Bioconductor/Contributions/issues/2804
>
> The data-raw/-files we can discard, as we provided these just for extra user 
> convenience.
> However, the mae_*.rda files are essential MultiAssayExperiment objects (as a 
> standard format for multi-'omics in Bioc), but these are right now too large 
> for the bot.
>
> Reading the package structure instructions, we were under the impression that 
> this old structure for ExperimentData would still be ok for Bioconductor; the 
> package passed checks (R CMD check and BiocCheck) with minor NOTEs. Our 
> current GitHub is at:
> https://github.com/Syksy/curatedPCaData
>
> Our package already has citations (with code provided there-in for extracting 
> and processing relevant data from the package), has been forked, has 
> collaborators using it as-is, etc, so revamping it to e.g. 
> ExperimentHub-structure would most likely cause quite major compatibility 
> issues.
>
>
> Would there be any chance of approaching Bioconductor with the package 
> roughly in its current format inspired by these older curated-packages, even 
> if it is not in the updated ideal ExperimentData-format?
>
> Kind regards,
> Teemu Daniel Laajala
>
>
>   [[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] Package dependencies error during BiocCheck

[Marcel Ramos]

Hi Sarvesh,

The error has something to do with an interaction between internal base 
R code
and checking for dependencies in BiocCheck with `loadNamespace`.
Either way, this check in BiocCheck is redundant with R CMD check.
It will soon get removed but for now, you can disable it by running:

BiocCheck("./seqArchRplus", `no-check-dependencies` = TRUE)

Best,

Marcel


On 10/25/22 12:27 PM, Sarvesh Nikumbh wrote:
> Hi all,
>
> I am trying to resolve an issue with dependencies of my package which is
> under review at the moment (Issue 2790
> , latest report
> ).
> I was wondering if somebody else also encountered this issue (see details
> below), and were successful resolving it. Any help in this regard would be
> greatly appreciated.
>
> *The issue:*
> Running BiocCheck throws the following error:
>
> Error in completeSubclasses(classDef2, class1, obj, where) :
>trying to get slot "subclasses" from an object of a basic class
> ("NULL") with no slots
> Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
>call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
>error: error in contained classes ("character") for class ident;
> class definition removed from dbplyr
> Execution halted
>
> which going by info at
> tidyverse/dbplyr#779  is
> caused by Brobdingnag, and
> resolved with version 1.2-9, which is now also available on CRAN (see here
> ).
>
> I saw this error earlier on my debian machine only using bioc-devel. Here,
> I could resolve this by re-installing Matrix, dbplyr and Brobdingnag.
>
> On bioc-side, the error can be seen on Ubuntu (latest report
> ).
> Maybe, it would occur on other OSs as well, but that stage is not reached.
> Thanks to Lori and Jennifer from bioc-team, the same re-installation
> solution was attempted, but this did not resolve it there.
>
> Since I do not have access to a machine running Ubuntu around, I have set
> up GHA. There, interestingly, the same error is encountered on macOS and
> Windows, but not on Ubuntu -- details here
> 
> .
>
>
> Any leads?
>
> Thanks in advance.

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Re: [Bioc-devel] Interpreting BiocCheck output

[Marcel Ramos]

Hi Giulia,

Thanks for sharing.
I took a look at https://github.com/calabrialab/ISAnalytics and I'm glad 
you resolved the issue.

Just a reminder, you can also use `utils::globalVariables('.')` in your 
package for functions
that use `'.'` (and other symbols) as a variable, e.g. in `purrr::pmap`.

Best regards,

Marcel


On 10/6/22 4:34 AM, Giulia Pais wrote:
>
> Hi, thanks for the reply. I managed to fix the first error as it was a 
> minor issue in the code, while for the second one I don’t have a 
> solution since the problem appears only locally and not on Biconductor 
> after the build.
>
> Just for reference the package is ISAnalytics and the BiocCheck 
> version is the latest one.
>
> Thanks again,
>
> Giulia
>
> *From: *Bioc-devel  on behalf of 
> Marcel Ramos 
> *Date: *Wednesday, 2022October5 at 23:48
> *To: *bioc-devel@r-project.org 
> *Subject: *Re: [Bioc-devel] EXTERNAL: Interpreting BiocCheck output
>
> Hi Giulia,
>
> Are you using a recent version of BiocCheck?
>
> If so, check the bottom of the BiocCheck::BiocCheck():
>
> ---
> See the .BiocCheck folder and run
>  browseVignettes(package = 'BiocCheck')
> for details.
> ---
>
> Can you provide more details, e.g., the repository of the package?
>
> Thanks.
>
> Best regards,
>
> Marcel
>
> On 10/4/22 4:44 AM, Giulia Pais wrote:
> > Hello,
> > I�m having some issues in interpreting BiocCheck outputs, maybe 
> someone can tell me how to fix the issues.
> >
> > I�ve got 2 main issues that cause the check to fail after normal 
> CRAN check has passed:
> >
> >    1.  I get this error message
> >
> > * Checking if other packages can import this one...
> >
> >  * ERROR: Packages providing 2 object(s) used in this package 
> should be imported in the NAMESPACE file, otherwise packages importing
> >
> >    this package may fail.
> >
> >
> >
> > However it is nowhere mentioned which packages they are and where 
> those objects are instantiated so I have no clue how to solve this one
> >
> >    1.  Since previous version of the package, which built and passed 
> checks without issues, I�ve been using a custom *.Rmd file placed in 
> inst/rmd in the vignette to recycle the same chunk of code and 
> optimizing time in phase of update (I update info only once instead of 
> 4 times). Even if the package passes CRAN checks, BiocCheck errors 
> telling me it can�t find this Rmd file and therefore can�t evaluate 
> the chunk where it is mentioned. Any suggestion on this?
> >
> > Thanks in advance
> > Giulia
> >
> >    [[alternative HTML version deleted]]
> >
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> <https://secure-web.cisco.com/1BHJN2d_YaqvKQMHULUaRH7QNYQJdOhBmii2EQbiAbqa5Lkeb8i3hiUIfaWofD4P7qtrIBd4DMzICkiL7nxBM9QffrsbPxL3_kbkQFAg-yuAopFfphrSrtxM2B2Z0qp-DcUG2pechJ5QE0wfC6p5VsjrRr4nhPCl3WjsqZcBETYfmUItDeY_Br3CVecmoCk5k1gglA7riYZaVCfjP1NsjpliHO07urMoNlQIYYEyGXtdcZP0VSYaKiMgyYU41JtU_ZqKBSRUTtRknaIU5cZSeS6gHT4j4gobUCm1A0EVQToHkI-c8MgdgesyootE6ZRVht1uNPHivzeujJGoWsZJUQA/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel>
>
>
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>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
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Re: [Bioc-devel] EXTERNAL: Interpreting BiocCheck output

[Marcel Ramos]

Hi Giulia,

Are you using a recent version of BiocCheck?

If so, check the bottom of the BiocCheck::BiocCheck():

---
See the .BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.
---

Can you provide more details, e.g., the repository of the package?

Thanks.

Best regards,

Marcel

On 10/4/22 4:44 AM, Giulia Pais wrote:

Hello,
I�m having some issues in interpreting BiocCheck outputs, maybe someone can 
tell me how to fix the issues.

I�ve got 2 main issues that cause the check to fail after normal CRAN check has 
passed:

   1.  I get this error message

* Checking if other packages can import this one...

 * ERROR: Packages providing 2 object(s) used in this package should be 
imported in the NAMESPACE file, otherwise packages importing

   this package may fail.



However it is nowhere mentioned which packages they are and where those objects 
are instantiated so I have no clue how to solve this one

   1.  Since previous version of the package, which built and passed checks 
without issues, I�ve been using a custom *.Rmd file placed in inst/rmd in the 
vignette to recycle the same chunk of code and optimizing time in phase of 
update (I update info only once instead of 4 times). Even if the package passes 
CRAN checks, BiocCheck errors telling me it can�t find this Rmd file and 
therefore can�t evaluate the chunk where it is mentioned. Any suggestion on 
this?

Thanks in advance
Giulia

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Re: [Bioc-devel] Vignettes with many output graphics - How to fulfill the Bioc build requirements, best practises?

[Marcel Ramos]

Hi Christian,

Thanks for reaching out.

 From what I gather, perhaps a workflow package submission is more 
appropriate for the
details that you would like to submit within the vignette. We recommend 
vignettes that have
small and run-able examples (possibly from simulated data) that 
demonstrate package functionality.

I haven't taken a look at the 'mysterious' package but perhaps consider 
breaking up the functionality
into separate packages, if possible. For example, you could have one 
package for each of the facilities
(e.g., stats, viz, utils, etc).

As for producing PDFs from plotting functions, this is generally 
discouraged.
Plotting functions should work like plot(1:10) and should output a 
single plot (or grouped plots)
to the graphics device. The user should then be free to choose the file 
format for any plot produced.
This approach may in turn resolve the issues you describe with plots in 
the vignette.

It may require some time re-designing the package(s) but I think your 
users would benefit
in the long run.

Best regards,

Marcel

On 3/22/22 4:05 PM, James W. MacDonald wrote:
> If the pages from the PDF are essentially static (for your vignette, that 
> is), why not run it once, get the pngs, save them somewhere, and use eval = 
> FALSE in the knitr headers for the plot* fuctions. Then you will speed things 
> up, there won't be all this extra PDF documentation that's +/- not part of 
> the vignette, and it should run much faster.
>
> -Original Message-
> From: Bioc-devel  On Behalf Of Christian 
> Arnold
> Sent: Tuesday, March 22, 2022 3:33 PM
> To:bioc-devel@r-project.org
> Subject: [Bioc-devel] Vignettes with many output graphics - How to fulfill 
> the Bioc build requirements, best practises?
>
> Hi, I wanted to reach out for some thoughts on the following problem I am 
> facing with a package I recently submitted to Bioc. In essence, I am 
> struggling with the 15 minutes time limit for R CMD check as well as the 
> package size limit of 5 MB. The latter is more important, so let's focus on 
> that:
>
> It is a quite large package with many functions, a full workflow for building 
> gene-regulatory networks, and we want to include a detailed workflow vignette 
> where the most important output plots are shown and explained, to make it 
> user-friendly and easy to apply.
>
> For various plot* functions produce PDFs that have many pages (sometimes 
> dozens or even hundreds), only some of which should be shown in the vignette 
> (say page 2 and 5 from PDF A, and page 1 and 2 from PDF B, etc). Including 
> selected pages from a PDF doesnt seem to be possible with BiocStyle (please 
> correct me if I am wrong), so currently, I am automatically converting each 
> page of each of the various PDFs as a png image, to include selected pages 
> then in the Vignette via knitr::include_graphics. This works well, but leads 
> to the repo being too big (currently 11 MB) when being build - because the 
> original images as well as the resulting htmls in the inst folder contain the 
> images, making it bigger than 5 MB. I could reduce the resolution of the 
> images much further, but this feels wrong also. In total, we talk about 40 or 
> so images that I wanted to share across the different vignettes.
>
> Are there any thoughts on how I can proceed here without spending a lot of 
> time on re-designing the package logic (which I unfortunately dont have at 
> this point) and without sacrificing the usability of the package (I could 
> just remove the Workflow vignette or host it externally I guess)?
>
>
> Thanks, your input is very appreciated.
>
>
> Best
>
> Christian
>
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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Re: [Bioc-devel] EXTERNAL: R: release of new version of package

[Marcel Ramos]

Hi Emanuela,

You should not be pushing new features to the RELEASE_3_14 branch.
This is meant to be stable throughout the course of the release cycle.

Make sure you are pushing your new commits to the devel branch of
Bioconductor with:

  git push upstream master

Based on your git history, it looks like you were able to make changes.

Do not forget to bump the Z version of your package, e.g.,

1.5.1

in devel so that the new version of the package propagates. This can 
take between 24 - 48 hours.

Best regards,

Marcel

On 12/20/21 1:43 PM, Emanuela Iovino wrote:
> Dear Nitesh
> thank you for your answer.
>   I followed Bioconductor instruction but when I pushed on
>
> upstream/RELEASE_3_14 I received always  Everything up-to-date.
>
> Before to follow Bioconductor instruction I already had pushed all my 
> modification on my Github repository and I don't know if it  got me a problem 
> in next steps.
>
> I checked the last commit 
> onhttp://bioconductor.org/checkResults/release/bioc-LATEST/uncoverappLib/  
> and it doesn't match with my last modification.
>
> Have I to repeat all steps?
>
> Thanks
>
> Emanuela
>
>
>
> 
> Da: Nitesh Turaga
> Inviato: luned� 20 dicembre 2021 15:36
> A: Emanuela Iovino
> Cc:bioc-devel@r-project.org  
> Oggetto: Re: [Bioc-devel] release of new version of package
>
> Hi,
>
> You�ll want these two tutorials since I�m guessing you have a Github Repo and 
> along with the git.bioconductor repo.
>
> So you�ll first have to sync (1), then push your updates to both Github and 
> Bioc server(2)
>
> (1)http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
> (2)https://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> Best
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
>> On Dec 20, 2021, at 9:32 AM, Emanuela Iovino  
>> wrote:
>>
>> Hello everyone
>> I'm the developer and the maintainer of Bioconductor package uncoverappLib .
>> I recently added some features to package and I would like to know how 
>> update to Biocondunctor . Do I follow new package workflow ? 
>> (https://bioconductor.org/developers/how-to/git/new-package-workflow/).
>> Many thanks in advance
>>
>> Emanuela Iovino
>> PhD Student in Data Science and Computation
>> Division of Medical Genetics
>> Dept. Medical and Surgical Sciences - DIMEC
>> University of Bologna
>> Pol.S.Orsola-Malpighi, via Massarenti 9,
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
>   [[alternative HTML version deleted]]
>
>
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
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Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

[Marcel Ramos]

Hi Witold,

I am not sure what the use case is for loading data in the yaml header.
If you're swapping out data for your vignettes, perhaps your introduction
chunks could contain the code to load the data.

In any case, I recommend that you use `data("dataset", package = "package")`
to load the data with LazyData turned off.

Best regards,

Marcel

On 11/18/21 9:51 AM, Witold Wolski wrote:
> Hi,
>
> I with BiocCheck I am getting a warning that my packages uses 
> LazyData: true.
>
> So far some of the package vignettes loaded the data in the params 
> section of the Rmd file e.g.,
>
> ---
> title:
> ...
> ...
> params:
>   configuration:  !r data(prolfqua::data_ionstar); 
> quote(prolfqua::data_ionstar$filtered()$config )
>   project_conf: NULL
>   data: !r quote( prolfqua::data_ionstar$filtered()$data )
> ...
> ---
>
>
> However, this will not work with LazyData false. What is the 
> bioconductor way of loading the data in the Rmd file Yaml section?
>
> If anyone wonders, why do I need it. By this I can reuse the vignette 
> with a different dataset.
>
> Best Witold
>
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
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Re: [Bioc-devel] EXTERNAL: Re: Too many dependencies / MultiAssayExperiment + rtracklayer

[Marcel Ramos]

>>>> "combinat" 1 13 7.69 0.01 1
>>>> "MultiAssayExperiment" 4 46 8.7 0.22 1
>>>> "foreach" 2 23 8.7 0.02 0
>>>> "graphics" 8 87 9.2 0.01 0
>>>> "GenomicRanges" 15 106 14.15 0.08 0
>>>> "rappdirs" 1 7 14.29 0.01 0
>>>> "reshape2" 1 6 16.67 0.05 0
>>>> "RColorBrewer" 1 4 25 0.01 0
>>>> "netSmooth" 1 3 33.33 0.82 3
>>>> "Rtsne" 1 3 33.33 0.02 0
>>>> "doParallel" 1 2 50 0.03 0
>>>> "ROCR" 2 3 66.67 0.05 4
>>>> "clusterExperiment" NA 122 NA 0.74 0
>>>> "IRanges" NA 255 NA 0.04 0
>>>>
>>>>
>>>> --
>>>>
>>>> *Shraddha Pai, PhD*
>>>> Principal Investigator, OICR
>>>> Assistant Professor, Department of Molecular Biophysics, University of
>>>> Toronto
>>>> shraddhapai.com; @spaiglass on Twitter
>>>> https://pailab.oicr.on.ca
>>>>
>>>>
>>>> *Ontario Institute for Cancer Research*
>>>> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada
>>> M5G
>>>> 0A3
>>>> *@OICR_news*<https://twitter.com/oicr_news>  | *www.oicr.on.ca*
>>>> <http://www.oicr.on.ca/>
>>>>
>>>>
>>>>
>>>> *Collaborate. Translate. Change lives.*
>>>>
>>>>
>>>>
>>>> This message and any attachments may contain confidential and/or
>>> privileged
>>>> information for the sole use of the intended recipient. Any review or
>>>> distribution by anyone other than the person for whom it was originally
>>>> intended is strictly prohibited. If you have received this message in
>>>> error, please contact the sender and delete all copies. Opinions,
>>>> conclusions or other information contained in this message may not be
>>> that
>>>> of the organization.
>>>> ___
>>>> Bioc-devel@r-project.org  mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>> --
>>> Michael Lawrence
>>> Principal Scientist, Director of Data Science and Statistical Computing
>>> Genentech, A Member of the Roche Group
>>> Office +1 (650) 225-7760
>>> micha...@gene.com
>>>
>>> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>>>
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Re: [Bioc-devel] EXTERNAL: ERROR: Avoid references to external hosting platforms

[Marcel Ramos]

nsider multiples of 4 spaces for line indents, 2531
   lines(34%) are not.
     First 6 lines:
   R/app_config.R:8   system.file(..., package = "InterCellar")
   R/app_config.R:22   value,
   R/app_config.R:23   config = Sys.getenv("R_CONFIG_ACTIVE", 
"default"),
   R/app_config.R:24   use_parent = TRUE
   R/app_config.R:26   config::get(
   R/app_config.R:32   )
     See http://bioconductor.org/developers/how-to/coding-style/
     See styler package: https://cran.r-project.org/package=styler as
   described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
     * NOTE: Cannot determine whether maintainer is subscribed to the
   bioc-devel mailing list (requires admin credentials). Subscribe
   here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
     Maintainer is registered at support site.
     Package name is in support site watched tags.


Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "Packages providing 1 object(s) used in this package should be 
imported in the NAMESPACE file, otherwise packages importing this 
package may fail."

$warning
[1] "The following files are over 5MB in size: 
'.git/objects/pack/pack-a1161a04bfe06bb12a006c137aadfb94cb26e254.pack'"

$note
  [1] "Consider clarifying how 89 object(s) are initialized. Maybe they 
are part of a data set loaded with data(), or perhaps part of an object 
referenced in with() or within()."
  [2] " 'sessionInfo' not found in vignette(s)"
  [3] " Avoid sapply(); use vapply()"
  [4] " Avoid redundant 'stop' and 'warn*' in signal conditions"
  [5] "Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)"
  [6] "Recommended function length <= 50 lines."
  [7] "Consider adding runnable examples to the following man pages 
which document exported objects:"
  [8] "Usage of dontrun{} / donttest{} found in man page examples."
  [9] "Use donttest{} instead of dontrun{}."
[10] "Consider shorter lines; 326 lines (4%) are > 80 characters long."
[11] "Consider multiples of 4 spaces for line indents, 2531 lines(34%) 
are not."
[12] "Cannot determine whether maintainer is subscribed to the 
bioc-devel\nmailing list (requires admin credentials). Subscribe 
here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel;



On 10/16/21 6:20 AM, Marta Interlandi wrote:
> Dear Marcel,
>
> I have updated BiocCheck to version 1.29.16, but the error persists. 
> Here my lines of code that are causing this issue, in red the lines 
> indicated by BiocCheck:
>
> dropdownMenu(type="tasks",
>  icon=icon("info"),
>  badgeStatus=NULL,
>  headerText="Check out",
>  notificationItem(
>  text="InterCellar",
>  icon=icon("github"),
>  status="primary",
> href="https://github.com/martaint/InterCellar 
> <https://secure-web.cisco.com/13EM8WN4sg9TPE_mRHA3XhLcgRiPAZnSaYXuDyd31DF6tVXGznKttF7a_TQ3qkTNDJ1T9BieebuO1PDE5h5-5FbJxFVciVVsQCQ4ZzkB1ID2tRchkUtbT1Eexi3Ymdx_oP7ofK0EgxUjBUtgJo0eVH9WUm9uRkzCKwO00XrlNXUsPvWvD5CB6gX_LJ6-Bp_YXArfptCPQXpazPSCdE6THzFhVDUFbT1eXXIXzxwF5QAUfrVTWhwgLnBAHqZl7J_QP2LTOwRN3dv2d7wJAa1Rn_TThrvGlPh58M3wcildjKgipasszzBq58sDYT-aGkLiP/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar>"
>                                                ),
>  notificationItem(
>  text="InterCellar-reproducibility",
>  icon=icon("github"),
>  status="primary",
>    href="https://github.com/martaint/InterCellar-reproducibility 
> <https://secure-web.cisco.com/1V9uFOQ1rnml0F7UCooserQqX2TGusszy2SHG9RpCd-iWF_S7IdltUepuqw8a8zlnxJZ7d1oQRAdjAzMisLM3y392gW-Fvhmv3_njfTB6cjrfeX38csHrTAKwwurEo15wRDhq_rOrwp33T8CokQiEgjwzIn3UJ9cucpAVJihGYoA421tb1gd0dzqTnh8xDoFEsfdm__83oKghIe5TH3Wb1EqBAzuf3eSdTcBgK6bl0bR9lGQGLfQzzGfxpN8FWGLFcrqhL6VV_fHwQpfRZ267LbpkMTJ0BNTwHkI00LJmMuq-7m2YvCs1NyxzR8ls2M5q/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar-reproducibility>"
>                                                ),
>  notificationItem(
>  text="Bioconductor package",
>  icon=icon("cube"),
>  status="primary",
>                                                 
>  href="https://bioconductor.org/packages/InterCellar/;
>                                                )
> These are part of the app UI.
>
> Thank you very much for taking a look at this!
>
> Best regards,
>
> M

Re: [Bioc-devel] EXTERNAL: ERROR: Avoid references to external hosting platforms

[Marcel Ramos]

Hi Marta,

Thank you for bringing this to our attention.
We've made an update to BiocCheck to minimize these false positives.
Please use BiocCheck version >= 1.29.16 which should propagate in a
day or so.

Best regards,

Marcel

On 10/14/21 10:39 AM, Marta Interlandi wrote:

Hi everybody,

My package *InterCellar *is currently getting the error "Avoid references
to external hosting platforms" when running BiocCheck.
The error is caused by href items pointing towards the github repos of the
package itself, in the form of clickable links (the package is a Shiny app).
These 3 links however are not used to get any data, but are simply nice
features for the shiny app users.

Do you have any suggestions on how I could still include these links
without getting an error?

Thank you so much for your help!!

Best regards,

Marta

[[alternative HTML version deleted]]

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Bioconductor Core Team
Roswell Park Comprehensive Cancer Care
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263



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Re: [Bioc-devel] EXTERNAL: Bioconductor build system using old commit

[Marcel Ramos]

Hi Eric,

This is the devel build report and it includes a commit from Mon Aug 16:
https://bioconductor.org/checkResults/devel/bioc-LATEST/slinky/ 
<https://bioconductor.org/checkResults/devel/bioc-LATEST/slinky/>

If you need to patch the release version as well, follow the guide that 
Jim kindly posted:
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ 
<http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/>

Best regards,

Marcel

On 9/17/21 2:14 PM, Kort, Eric wrote:
> Good day. I have made updates to my package, slinky. I pushed my changes both 
> to my github rep, and the Bioconductor git repository.
>
> My remotes are set up as follows:
>
>> git remote -v
> origin https://github.com/vanandelinstitute/slinky (fetch)
> origin https://github.com/vanandelinstitute/slinky (push)
> upstream g...@git.bioconductor.org:packages/slinky.git (fetch)
> upstream g...@git.bioconductor.org:packages/slinky.git (push)
>
> Following directions here: 
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>
> I then did
>
> git fetch upstream
> git merge upstream/master
> git push origin master
>
> But on the build system 
> (https://bioconductor.org/checkResults/3.13/bioc-LATEST/) where errors are 
> being encountered, the git_last_commit shows an old commit and commit date.
>
> Do I have the wrong remote? Or is there another mistake I am making?
>
> -Eric
>
>
>
>
>   [[alternative HTML version deleted]]
>
> _______
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

---
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



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Re: [Bioc-devel] EXTERNAL: Not possible to create runnable examples for package

[Marcel Ramos]

Hi Kelsey,

One of the main reasons we have that 80% check is to induce modularity 
in a package.
You can chain examples from several R files / functions in sequence 
according to
collation order (collation field in the DESCRIPTION or alphabetical order).

Ideally, you can use a small dataset for the examples and demonstrate 
the use
of the functions in your package. In the end, these examples will be very
useful for your users.

We do make rare exceptions to this rule mainly for non code based packages
e.g., ExperimentHub.

One could argue that if the functions are very complicated or difficult,
it may not be a package that users will find easy to use and that
some redesign would be apt.

Best regards,

Marcel


On 8/10/21 11:48 AM, Kelsey Chetnik via Bioc-devel wrote:
> I am preparing a package for submission to Bioconductor. One of the errors I 
> got from running BioCheck() was "At least 80%of man pages documenting 
> exported objects must have runnable examples". The way our package is 
> constructed makes meeting this requirement practically impossible.
>
> Our package is designed to create pipelines by chaining functions and saving 
> intermediate results in an object. These functions are not meant to be run in 
> small examples - many require a series of other functions to be run before 
> they can be called. It wouldn't be possible to make the examples runnable 
> without either large intermediate objects that would cause our package to 
> exceed the size limit of 5 MB or long examples that could consist of 20+ 
> lines of code. It would also be very complicated and difficult to maintain 
> these examples.
>
> Is it possible for our package to be accepted without resolving this issue if 
> we provide justification for it?
>
> Thank you,
> Kelsey
>
>   [[alternative HTML version deleted]]
>
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---
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
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Re: [Bioc-devel] EXTERNAL: Build errors when running examples that call circlize

[Marcel Ramos]

Hi Giulia,

It seems that the issue is further down the callstack, likely in circlize.
To reproduce, you can enable _R_CHECK_LENGTH_1_* from 
https://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc

You might have to open an issue at https://github.com/jokergoo/circlize


Note. FWIW write temporary files using tempfile() rather than getwd().

Best regards,

Marcel

On 8/3/21 4:10 AM, Giulia Pais wrote:
> Hope somebody can help with this.
> I�ve implemented a function in the package I�m developing that uses circlize. 
> The function simply draws a basic circos plot with genomic densities, nothing 
> fancy. Even if in my local dev environment I have no build issues, the build 
> fails on all platforms when running the example in the documentation of such 
> function, here are the details of the error 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/merida1-checksrc.html
>
> I have no clue how to fix this issue other than declare the example not 
> runnable, does anybody have suggestions on this?
>
> Also, I noticed that sometimes Windows builds fail due to some tests that 
> need to write temporary files on disk, should I skip such tests on Windows?
> Thank you
> Giulia Pais
>
>   [[alternative HTML version deleted]]
>
>
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Elm St. & Carlton St.
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Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

[Marcel Ramos]

t;>>> consider it a bug,  I encourage you to reach out to their maintainer 
>>>> directly as well.
>>>>
>>>> Please ask further git access issues on bioc-devel@r-project.org mailing 
>>>> list as there are dedicated members of the team to assist with access. To 
>>>> start,  make sure you have a valid ssh key on the computer you are using, 
>>>> and that the key is uploaded to the git credentials app.  If you have not 
>>>> activated the git credentials app, be sure to activate your account first. 
>>>>  Links to the app and other useful git workflow can be found here:
>>>> http://bioconductor.org/developers/how-to/git/new-package-workflow/
>>>>
>>>> Cheers,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Lori Shepherd
>>>>
>>>> Bioconductor Core Team
>>>>
>>>> Roswell Park Comprehensive Cancer Center
>>>>
>>>> Department of Biostatistics & Bioinformatics
>>>>
>>>> Elm & Carlton Streets
>>>>
>>>> Buffalo, New York 14263
>>>>
>>>> 
>>>> From: Mattia Chiesa 
>>>> Sent: Tuesday, July 27, 2021 5:06 AM
>>>> To: Kern, Lori 
>>>> Subject: R: Bioconductor package DaMiRseq
>>>>
>>>> Dear Lori,
>>>> Since I haven't modified DaMiRseq for several months, I think the the 
>>>> problem could be related to some Damirseq dependencies.
>>>> Anyway, I tried to go deep into the problem, but when I type:
>>>> git pull upstream master
>>>> a connection error occurs:
>>>> ssh_exchange_identification: read: Connection reset by peer
>>>> fatal: Could not read from remote repository.
>>>> Please make sure you have the correct access rights
>>>> and the repository exists.
>>>>
>>>> It's the first time I have experinced this problem. What should I do?
>>>> Thanks In advance.
>>>> Mattia
>>>>
>>>>
>>>> 
>>>> Da: Kern, Lori 
>>>> Inviato: luned� 26 luglio 2021 16:55
>>>> A: mattia.chi...@hotmail.it 
>>>> Oggetto: Bioconductor package DaMiRseq
>>>>
>>>> We would like to bring to your attention that your package is failing to 
>>>> build
>>>> or check on our release and devel build machines:
>>>>
>>>> Devel:
>>>> http://bioconductor.org/checkResults/3.14/bioc-LATEST/<http://secure-web.cisco.com/1UyHFFpElhlwoJASYNWNnZo294YfOAS2eA-p2cjmz_DSDOF7yfSSvnTsaWfgpR1F03jqoFKgAspBBEeYNfj1PZhObI9jNDtfIEciWCb5icLfNgkIPsjNScxTtUrhAiUJfpwX1edKaYyjjfRmcH0tpo8_bG7MbqZWqkyL1PcWBQwLbjU_fO4UKLxjBmK_VXNwz6SsMCrYCO27DgHBRWvvQi5im5uzCiGg1HlXwSSVi_1Y5fDp8kh52CbA_eo7SuaKaCcjsfEn5qVvTrl6YIlBCANzv2HubDATSyRHIu9nGNZG7mF3Ky8x4fk2dXP45/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
>>>>
>>>> Release:
>>>> http://bioconductor.org/checkResults/3.13/bioc-LATEST/<http://secure-web.cisco.com/1h7aSKHWtsfb4cOI13Zh8EU4a5W856Zce40L3uyRNdZTtbeGJQMra08tCbRLlaKugtrt2IECy6CVe6neRyat4TcRkKG4IEZyrSEipziS7yH_RNNvEAkRC8zauoM6Ai7f_9UZojDR7tXXczshLqKDLZteLqLDX9baox4e-VZG8wMfuKwpTvE6cNGtDHFMEZ3rzhOR1IT3M_3xSYbknmx0Q71qZxihn2YtiYhjU4Up9pe4bXUjhWRxl6LOhqp9PgND-GKfgV5YeyM3XFZKfynGIEcs8lF-8eZl1GbgEzIcKHUJ1FupgfLANKtUF7v_ibzB6/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
>>>>
>>>> Would you mind taking a look at this? Don't hesitate to ask on the 
>>>> bioc-devel mailing list if you have any question or need help.
>>>>
>>>> This is very problematic.   If no action is taken over the next few weeks 
>>>> we will begin the deprecation process for your package. We appreciate your 
>>>> assistance on pushing changes to remedy these errors.
>>>>
>>>>
>>>>
>>>>
>>>> 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.
>>>>
>>>> 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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>
>   [[alternative HTML version deleted]]
>
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Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
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Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio

[Marcel Ramos]

le_1.8-4
>>>>   [63] progress_1.2.2rsvd_1.0.5
>>>>   [65] bit_4.0.4 glmnet_4.1-1
>>>>   [67] netSmooth_1.10.0  httr_1.4.2
>>>>   [69] RColorBrewer_1.1-2ellipsis_0.3.2
>>>>   [71] scuttle_1.0.4 pkgconfig_2.0.3
>>>>   [73] XML_3.99-0.6  R.methodsS3_1.8.1
>>>>   [75] dbplyr_2.1.1  locfit_1.5-9.4
>>>>   [77] utf8_1.2.1RJSONIO_1.3-1.4
>>>>   [79] howmany_0.3-1 tidyselect_1.1.1
>>>>   [81] rlang_0.4.11          softImpute_1.4-1
>>>>   [83] reshape2_1.4.4later_1.2.0
>>>>   [85] AnnotationDbi_1.52.0  munsell_0.5.0
>>>>   [87] BiocVersion_3.12.0tools_4.0.5
>>>>   [89] cachem_1.0.5  generics_0.1.0
>>>>   [91] RSQLite_2.2.7 ExperimentHub_1.16.1
>>>>   [93] ade4_1.7-16   evaluate_0.14
>>>>   [95] stringr_1.4.0 fastmap_1.1.0
>>>>   [97] yaml_2.2.1knitr_1.33
>>>>   [99] bit64_4.0.5   purrr_0.3.4
>>>> [101] sparseMatrixStats_1.2.1   nlme_3.1-152
>>>> [103] mime_0.10 R.oo_1.24.0
>>>> [105] pracma_2.3.3  xml2_1.3.2
>>>> [107] compiler_4.0.5beeswarm_0.3.1
>>>> [109] curl_4.3.1interactiveDisplayBase_1.28.0
>>>> [111] tibble_3.1.2  RNeXML_2.4.5
>>>> [113] stringi_1.6.2 RSpectra_0.16-0
>>>> [115] lattice_0.20-41   Matrix_1.3-2
>>>> [117] vctrs_0.3.8   pillar_1.6.1
>>>> [119] lifecycle_1.0.0   rhdf5filters_1.2.1
>>>> [121] BiocManager_1.30.15   combinat_0.0-8
>>>> [123] BiocNeighbors_1.8.2   zinbwave_1.12.0
>>>> [125] data.table_1.14.0 irlba_2.3.3
>>>> [127] bitops_1.0-7  httpuv_1.6.1
>>>> [129] R6_2.5.0  promises_1.2.0.1
>>>> [131] gridExtra_2.3 vipor_0.4.5
>>>> [133] codetools_0.2-18  MASS_7.3-53.1
>>>> [135] assertthat_0.2.1  pkgmaker_0.32.2
>>>> [137] withr_2.4.2   GenomeInfoDbData_1.2.4
>>>> [139] locfdr_1.1-8  hms_1.1.0
>>>> [141] beachmat_2.6.4grid_4.0.5
>>>> [143] tidyr_1.1.3   DelayedMatrixStats_1.12.3
>>>> [145] rmarkdown_2.8 Rtsne_0.15
>>>> [147] clusterExperiment_2.10.1  shiny_1.6.0
>>>> [149] ggbeeswarm_0.6.0  tinytex_0.31
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *Shraddha Pai, PhD*
>>>> Principal Investigator
>>>> shraddhapai.com; @spaiglass on Twitter
>>>>
>>>>
>>>> *Ontario Institute for Cancer Research*
>>>> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada
>>>> M5G
>>>> 0A3
>>>> *@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
>>>> <http://www.oicr.on.ca/>
>>>>
>>>>
>>>>
>>>> *Collaborate. Translate. Change lives.*
>>>>
>>>>
>>>>
>>>> This message and any attachments may contain confidentia...{{dropped:11}}
>>>>
>>>> ___
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
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>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine
>>> at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
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---
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Bioconductor Core Team
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Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



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Re: [Bioc-devel] EXTERNAL: [BULK] genefu Warning

[Marcel Ramos]

Hi Christopher,

It would be a good idea to remove the `LazyData: yes` from the DESCRIPTION.

https://bioconductor.org/developers/package-guidelines/#description 
<https://bioconductor.org/developers/package-guidelines/#description>

One that is set make sure there is no pollution in function environments 
e.g., `sbt.model=scmod1.robust`
in `R/genius.R`. Create an empty data environment where you can load 
package data for the
function to use with `new.env(parent = emptyenv())`.


Best,

Marcel

On 5/18/21 6:21 PM, Eeles, Christopher wrote:
> Hello Bioc Core Team,
>
> I just noticed that one of our lab package, genefu, has a WARNING on devel 
> for all build machines.
>
> The warning is:
>
> LazyData DB of 5.0 MB without LazyDataCompression set
>See �1.1.6 of 'Writing R Extensions'
>
> I wanted to make sure that this will not affect the inclusion of genefu in 
> the 3.13 release.
>
> I have already started researching the issue and will push a fix as soon as 
> the release is complete on Thursday.
>
> ---
> Christopher Eeles
> Software Developer
> BHK 
> Laboratory<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=nGXPfLnlbcaLQdDOHFDmp4lZ7lD9H29uFeVCAqjT9Ds%3D=0>
> Princess Margaret Cancer 
> Centre<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=b2ZjA%2FPDKjTZmAWGbnQAY1SjVtCDQGQmXu2Thz%2FXQkI%3D=0>
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>
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Re: [Bioc-devel] EXTERNAL: Re: Best practice use pkgdown, docker with Bioconductor

[Marcel Ramos]

Thank you Jianhong for the clean solution.

I would encourage Alan to check out the biocthis::use_bioc_github_action
to set up the Docker build and pkgdown.

Best,

Marcel

On 4/6/21 12:48 PM, Jianhong Ou, Ph.D. wrote:
> Hi Alan,
>
> Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. 
> Hope this help.
>
> You may want to add one more step after check and before pkgdown to push to 
> your dockerhub by:
>
> - name: push to docker
> - uses: docker/build-push-action@v1
>  with:
>username: ${{ secrets.DOCKER_USERNAME }}
>password: ${{ secrets.DOCKER_TOKEN }}
>repository: your/docker/path
>tag_with_ref: true
>tag_with_sha: true
>tags: latest
> [https://avatars.githubusercontent.com/u/5640707?s=400=4]<https://github.com/jianhong/HMMtBroadPeak/tree/staging>
> jianhong/HMMtBroadPeak<https://github.com/jianhong/HMMtBroadPeak/tree/staging>
> call broad peak by a modified Baum_Welch algorithm that supports 
> multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
> github.com
> 
>
> 
> From: Bioc-devel  on behalf of Murphy, Alan 
> E 
> Sent: Tuesday, April 6, 2021 10:24 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
>
> Hi all,
>
> I'm working on the development of 
> (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$
>  ] and have a question regarding a reviewer note. My package currently uses 
> pkgdown to create a website through the master branch. I also create and push 
> a new docker image from the main branch when the package successfully builds 
> on travis.
>
> My reviewer has asked to remove the related files 
> _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any 
> issues with these external configurations and Bioconductor. My reviewer has 
> suggested to put these in another branch. It's not clear to me how best to do 
> this? Ideally, if they are in a separate branch, is there a way to run them 
> once there is an update and successful build on the master branch? If this 
> isn't possible, is there a way to avoid manually duplicating new changes in 
> the master branch in this separate branch and instead, just push the changes 
> from master to this separate branch and trigger pkgdown and docker build that 
> way? Sorry, I realise this last part more so relates to github commands but I 
> was thinking someone else has probably already foudn a way around this issue.
>
> Kind regards,
> Alan.
>
> Alan Murphy
> Bioinformatician
> Neurogenomics lab
> UK Dementia Research Institute
> Imperial College London
>
>  [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] EXTERNAL: Resolve mismatch between master and release branches

[Marcel Ramos]

Hi Sarah,

The release branch is meant for bug fixes that ensure the stability of 
the code.
It does not usually include 'updates' from the devel.

The way to cleanly do this is to hard reset to a previous commit. The 
commit
where your packages version was bumped for the 3.12 release. You
can then force push the release branch to your GitHub repository
RELEASE_3_12 branch.
https://bioconductor.org/developers/how-to/git/abandon-changes/ 
<https://bioconductor.org/developers/how-to/git/abandon-changes/>

After emailing Nitesh and he would apply a force push to the Bioc git
repo.

You will then be able to apply your changes from the devel branch by
cherry-picking those changes** onto the release branch.

** your changes in the devel branch should be atomic, meaning they do not
include version bumps, so that cherry-picking is easier, if that is not 
the case
you may have to apply a diff or manually update the version.

https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ 
<https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/>

Hope that helps.

Best,

Marcel



On 3/22/21 4:43 PM, Sarah Voisin wrote:
> Hi,
>
> I have updated the master branch of my MEAT package yesterday (
> https://github.com/sarah-voisin/MEAT), and I tried updating the release
> branch as well (RELEASE_3_12), but I must have messed up since the release
> branch is now 7 commits behind master and 3 commits ahead, and I am stuck.
> How do I do this again cleanly so I can push all changes from the master
> branch to the release branch without messing up further?
>
> Thank you for your help.
>
> Kind regards,
>
> *Sarah Voisin*
> *Senior Lecturer*
> Institute for Health and Sport (IHES)
> Victoria University, Footscray Park Campus, VIC 3011 Australia
> *Email*: sarah.voisin.ae...@gmail.com
> *Office phone*: +61 3 9919 5744
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] EXTERNAL: %>%.html': Invalid argument Multiple platform

[Marcel Ramos]

Hi Stefano,

It seems like you are re-exporting the pipe operator.
You should try using usethis::use_pipe instead. There, they change the 
name of the documentation to "pipe" to
avoid this issue. If you're documenting manually, you could use @name 
%>% and @rdname pipe as
shown with usethis::use_pipe.

https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html 
<https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html>

Best,

Marcel

On 3/11/21 2:10 PM, stefano wrote:
> Hello,
>
> I get this warning for tidySummarized Experiment:
>
> Rd warning: cannot open file
> 'D:/biocbuild/bbs-3.13-bioc/meat/tidySummarizedExperiment.buildbin-libdir/00LOCK-tidySummarizedExperiment/00new/tidySummarizedExperiment/help/%>%.html':
> Invalid argument
>
> Multiple platform build/check report for BioC 3.13 - CHECK report for
> tidySummarizedExperiment on riesling1 (bioconductor.org)
> <http://bioconductor.org/checkResults/devel/bioc-LATEST/tidySummarizedExperiment/riesling1-checksrc.html>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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Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

[Marcel Ramos]

2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3Dreserved=0
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>
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Re: [Bioc-devel] EXTERNAL: Re: Encountering Issues with Github sync

[Marcel Ramos]

Hi Krithika,

Regarding Step #10:

It is a good idea to have a release branch checkout in your GitHub 
(origin) repository
in case you need to commit bug fixes to that branch:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ 
<http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/>

Best,

Marcel

On 2/25/21 3:02 PM, Krithika Bhuvaneshwar wrote:
> Thank you for catching that !  That was very helpful
>
> I have now completed Steps# 1 - 7 and Step # 9 from here:
> *http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> <http://bioconductor.org/developers/how-to/git/sync-existing-repositories/>
> *(I think Step # 8 does not apply to me)
>
> I don't exactly understand what Step # 10 is. Is this what I should do , or
> can I skip this ? Please advise.
>
>
> *10. Repeat for the release branch, replacing master with the name of the
> release branch, e.g., RELEASE_3_6. It may be necessary to create the
> release branch in the local repository.*
>
> git checkout RELEASE_13_3
>   git merge upstream/RELEASE_13_3
>   git merge origin/RELEASE_13_3
>   git push upstream RELEASE_13_3
>   git push origin RELEASE_13_3
>
>
> Thanks,
> Krithika
>
>
>
> On Thu, Feb 25, 2021 at 12:33 PM Martin Morgan 
> wrote:
>
>> The Bioconductor remote should not include 'ICBI,
>>
>>  git remote remove upstream
>>  git remote add upstream g...@git.bioconductor.org:packages/CINdex.git
>>
>> On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" <
>> bioc-devel-boun...@r-project.org on behalf of kb...@georgetown.edu> wrote:
>>
>>  Hello,
>>
>>  We are the package maintaines for the CINdex package.  We have made
>> changes
>>  in our package to address the build errors for the upcoming release.
>> The
>>  latest code is here in our Gtithub account *
>> https://github.com/ICBI/CINdex
>>  <https://github.com/ICBI/CINdex>  . *I'm trying to sync it with the
>> BioC
>>  Github repo, but encountering errors. Would appreciate some help
>>
>>  These are the steps I did:
>>
>>  1) Updated code so that there are no build errors. Updated version
>>  information in DESCRIPTION File (changed from 1.19.0 to 1.19.1). The
>> latest
>>  code is here in our Gtithub account *https://github.com/ICBI/CINdex
>>  <https://github.com/ICBI/CINdex> *
>>
>>  2)  I generated new ssh keys , and then added the ssh information from
>> my
>>  *id_rsa.pub* file in this link.
>>  https://git.bioconductor.org/BiocCredentials/account_activation/
>>
>>  3) I'm currently following the steps mentioned here:
>>  bioconductor.org/developers/how-to/git/sync-existing-repositories/.
>> *I have
>>  an error when I try git fetch*
>>
>>  #Configure the “remotes” of the GitHub clone. --- completed step
>>  git remote add upstream g...@git.bioconductor.org:
>> packages/ICBI/CINdex.git
>>
>>  $ git remote -v
>>  origin https://github.com/ICBI/CINdex (fetch)
>>  origin https://github.com/ICBI/CINdex (push)
>>  upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (fetch)
>>  upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (push)
>>
>>  $ git fetch --all
>>  Fetching origin
>>  Fetching upstream
>>  FATAL: R any packages/ICBI/CINdex k.bhuvaneshwar DENIED by fallthru
>>  (or you mis-spelled the reponame)
>>  fatal: Could not read from remote repository.
>>
>>  Please make sure you have the correct access rights
>>  and the repository exists.
>>  error: Could not fetch upstream
>>
>>  Thanks,
>>  Krithika
>>  kb...@georgetown.edu
>>
>>  [[alternative HTML version deleted]]
>>
>>  ___
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Re: [Bioc-devel] Recent change in MultiAssayExperiment for inferred MAE-level colData

[Marcel Ramos]

Hi all,

Apologies for the delay. I hope you had a nice break.

This should be fixed in 1.17.4.

Bonne année!

Best,

Marcel

On 1/2/21 1:18 PM, Levi Waldron wrote:

Hi Dario and Andrea, I don't think you'll have to do anything - it was
meant to be a feature that shouldn't have affected your use cases
of not specifying the sampleMap.  I've opened an issue at
https://github.com/waldronlab/MultiAssayExperiment/issues/291.


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Re: [Bioc-devel] Unsure about why package is not updating

[Marcel Ramos]

Hi Krutik,

Version numbers are not considered a decimal values. Therefore 5 < 4158. 
See here for further details:


https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file

Bump the version to 0.99.4159 and try again.

Best,

Marcel

On 10/8/20 4:09 PM, Krutik Patel (PGR) wrote:

Dear Bioconductor,

Thank you for all the help so far. Unfortunately, I have a few more issues. I 
updated the version of my package to 0.99.5, found here 
http://www.bioconductor.org/checkResults/3.12/bioc-LATEST/TimiRGeN/, but the 
new version is not being built, regardless of check successes or errors.

When I did git clone g...@git.bioconductor.org:packages/TimiRGeN, version 
0.99.5 was downloaded so I think the update was successful.

However, I am getting a message "NO, built version is lower than internal 
version". The previous version was 0.99.4158, so I think the version bump should 
have worked. What is the issue here, and how can the version update be completed properly?

Best,

Krutik

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Re: [Bioc-devel] EXTERNAL: Author name displayed incorrectly in package landing page

[Marcel Ramos]

Hi Lara,

I often recommend the use of the `Authors@R` field in the DESCRIPTION file
which will give you more control:

```
Authors@R: c(
    person(given = "Lara", family = "Selles Vidal", ...),
    ...
    )
```

Best,

Marcel


On 4/22/20 4:00 PM, Selles Vidal, Lara wrote:
> Dear Bioconductor team,
>
> I have recently realized the first author name in my rfaRm package is not 
> displayed as intended in its landing page 
> (https://bioconductor.org/packages/rfaRm).
>
> In short, I put my name as “Lara Selles Vidal” in the Author: field of the 
> DESCRIPTION file. My first name is just “Lara”, and “Selles Vidal” are my 
> surnames. However, it has been interpreted as Vidal, LS. The intended 
> behaviour would have been Selles Vidal, L
>
> Is there any workaround for this?
>
> Thanks a lot in advance!
>
> Best wishes,
>
> Lara
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] rankprod package update

[Marcel Ramos]

Hi Francesco,

Please wait at least 24 hours before seeing an effect on the build report.
We should have a build report with your changes later today.
Check around 2 PM EST or https://everytimezone.com/s/3eab3407

Best regards,

Marcel

On 2/14/20 11:32 AM, Francesco Del Carratore wrote:
> Dear support team,
> I am the maintainer of the RankProd package and yesterday I submitted a bug
> fix on the development branch.
> How long will it take for the fix to appear on the development page of the
> package?
> (https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html)
> Many thanks,
> Francesco Del Carratore
>


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Re: [Bioc-devel] EXTERNAL: Re: warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic

[Marcel Ramos]

Hi Stefano,

I'm no roxygen expert either but you could try using the
`usethis::use_pipe(export = TRUE)`
functionality developed by actual roxygen experts ;)

Best,
Marcel

On 2/13/20 2:28 AM, Felix Ernst wrote:
> Hi,
>
> I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to 
> implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also 
> work in this case. 
>
> The case above is used for a package external link. For an internal explicit 
> link use \code{\link[=something]{or other}}.
>
> Felix
>
> -Ursprüngliche Nachricht-
> Von: Bioc-devel  Im Auftrag von Martin 
> Morgan
> Gesendet: Donnerstag, 13. Februar 2020 04:46
> An: stefano ; bioc-devel@r-project.org
> Betreff: Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr' does 
> not exist and so has been treated as a topic
>
> This warning
>
> * checking whether package 'ttBulk' can be installed ... WARNING Found the 
> following significant warnings:
>   Rd warning: 
> C:/Users/pkgbuild/AppData/Local/Temp/Rtmp6Js8e8/R.INSTALL1ddcdee5581/ttBulk/man/reexports.Rd:19:
>  file link '%>%' in package 'magrittr' does not exist and so has been treated 
> as a topic See 
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1330/8048f88/ttBulk.Rcheck/00install.out'
>  for details.
>
> is actually about the documentation for '%>%'. In your previous 'man' page 
> you had
>
>   \code{\link[magrittr]{\%>\%}}
>
> which from reading 'Writing R Extensions' RShowDoc("R-exts") section 2.5 
> 'Cross-references' indicates that you're trying to link to an html page named 
> '%>%.html' in the magrittr package, but actually the man page is 'pipe.html' 
> (e.g., by using help.start() and browsing manually to the help page). While 
> it's possible to link to that help page, you should instead just 
> \code{\link{\%>\%}} and R (possibly with the user choosing the package) will 
> generate the correct link.
>
> Your package is too deep into the roxygen foo for me to know what you need to 
> do to generate the appropriate link (or even where the link is generated...); 
> maybe there's a roxygen expert on the mailing list who can help (or you can 
> perhaps post here where you generate the reexports.Rd page from).
>
> Also, your github repository seems VERY LARGE (I lost patience trying to 
> clone it, although my current link is quite slow); this 
> http://bioconductor.org/developers/how-to/git/remove-large-data/ might 
> provide some hints for removing large commits.
>
> Hope that helps,
>
> Martin
>
>
> On 2/12/20, 9:51 PM, "Bioc-devel on behalf of stefano" 
>  
> wrote:
>
> Hello Community,
> 
> The CHECK Windows server gives me a warning when I try to reexport an
> existing operator magrittr::`%>%`
> 
> ```
> #' @importFrom magrittr %>%
> 
> #' @export
> 
> magrittr::`%>%`
> ```
> 
> okay2 Windows Server 2012 R2 Standard/x64
>   OK
>   WARNINGS
>   OK
>   OK
> 
> malbec2 Linux (Ubuntu 18.04.3 LTS)/x86_64
>   OK
>   OK
>   skipped
>   OK
> 
> 
> Here is the log
> 
> http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
> 
> I looked online but I could not find a definitive answer. An advice will 
> be
> highly appreciated.
> 
> Thanks!
> 
> 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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Re: [Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

[Marcel Ramos]

Hi Charles,

Thank you for your post and for providing a reproducible example.

I was able to reduce the example to behavior from the coerce method on
`list`/`ANY` objects to `SimpleList`.

Here is the reduced example:

``` r
suppressPackageStartupMessages({
    library(SummarizedExperiment)
})
example(SummarizedExperiment, echo = FALSE)
mylist <- list(exo1 = rse, exo2 = se0)

simple <- as(mylist, "SimpleList")

simple[[1]]
#> class: SummarizedExperiment
#> dim: 200 6
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(1): feature_id
#> colnames(6): A B ... E F
#> colData names(1): Treatment

vapply(simple, class, character(1L))
#>   exo1   exo2
#> "SummarizedExperiment" "SummarizedExperiment"
```

Created on 2019-09-03 by the [reprex
package](https://reprex.tidyverse.org) (v0.3.0)

It appears that `S4Vectors:::coerceToSimpleList` looks for the
`S4Vectors:::lowestListElementClass` and coerces all classes in the list
to be the base `SummarizedExperiment` class. I'm not sure what the
reasoning is behind the behavior.

Can you chime in Hervé? Thanks.

- Marcel



On 8/28/19 1:28 AM, Charles Plessy wrote:
> Hello,
>
> I am using MultiAssayExperiment as a base class in the CAGEr package.
>
> In Bioconductor 3.10, CAGEr is broken because updates of
> RangeSummarizedExperiment experiments trigger their silent conversion
> to SummarizedExperiment objects (basically discarding the ranges).  This 
> only happens when there is another experiment slot that contains a plain 
> SummarizedExperiment.
>
> Here is a toy example to reproduce the issue:
>
> ```{r}
> library("MultiAssayExperiment")
> (DF   <- DataFrame(sample1=c(1,2), sample2=c(1,3)))
> (rRanges  <- GPos("chr1", 1:2, "+"))
> (cData<- DataFrame(type=c("control", "treatment"), row.names = 
> c("sample1", "sample2")))
> (rSE  <- SummarizedExperiment(SimpleList(DF), rowRanges = rRanges, 
> colData = cData))
> (SE   <- SummarizedExperiment(SimpleList(DF), colData = cData))
> (m<- MultiAssayExperiment(ExperimentList(exp1=rSE)))
> (m[[1]]   <- m[[1]])
> m # No change
> (m<- c(m, exp2=SE))
> (m[[1]]   <- m[[1]])
> m # RangedSummarizedExperiment replaced with SummarizedExperiment
> sessionInfo()
> ```
>
> Am I misusing the MultiAssayExperiment objects, or is this a bug ?
>
> Have a nice day,
>
> Charles
>


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Re: [Rd] GitHub passwords in .git/config?

[Marcel Ramos]

Hi Spencer,

The first line in the `[remote "origin"]` section should read:

```

url = 
g...@github.com:sbgraves237/Ecdat.git

```

Generally, I add these configs by doing a clone on the command line such as:

> git clone 
> g...@github.com:sbgraves237/Ecdat.git

so that I don't have to mess with the config file.


Best,

Marcel

On 7/15/19 1:48 PM, Spencer Graves wrote:
I'm diverging:  Now I get:


>>> git pull
ssh: Could not resolve hostname github.com:sbgraves237: nodename nor servname 
provided, or not known
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


  ** With .git/config as follows:


[core]
repositoryformatversion = 0
filemode = true
bare = false
logallrefupdates = true
ignorecase = true
precomposeunicode = true
[remote "origin"]
url = 
ssh://g...@github.com:sbgraves237/Ecdat.git
fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
remote = origin
merge = refs/heads/master


  I have an SSH key on my GitHub account, which says it was "Added on Jul 
3, 2019 Last used within the last 2 weeks — Read/write".


  Should I delete my current local copies and clone them fresh from GitHub?
  Spencer


On 2019-07-15 12:01, Brian G. Peterson wrote:
it would be:

ssh://g...@github.com:sbgraves237/Ecdat.git


On Mon, 2019-07-15 at 11:41 -0500, Spencer Graves wrote:
On 2019-07-15 10:56, Dirk Eddelbuettel wrote:



Don't write passwords down like this. Your error is likely in
expecting _ssh_
authentication over _https_ -- when it works only over ssh. Use the
alternate
form for a remote e.g. one that looks like 
g...@github.com:emacs-
ess/ESS.git
I'm confused.  I changed that line to:


  url =
https://g...@github.com:sbgraves237/sbgraves237/Ecdat


Then when I did "git pull" I got:


fatal: unable to access
'https://g...@github.com:sbgraves237/sbgraves237/Ecdat/':
 Port number
ended with 's'


???
Thanks,
Spencer

Hth, Dirk

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Re: [Rd] Suggested Patch: Library returns matching installed packages when typo present

[Marcel Ramos]

Hi Luke,

Thank you for your response.

On 6/21/19 10:56 AM, Tierney, Luke wrote:

Thanks for the suggestion. However I don't think it is the right way
to go. I also don't care for what install.packages() does. Signaling a
warning and then an error means someone has to catch both the error
and the warning, or suppress the warning, in order to handle the error
programmatically.

I do care for what install.packages() does because it's preferable
to have consistency in the user interface.

I see that the proposed patch does return both an error and a warning
but as far as I understand it, library()'s main/intended use is interactive and
there are other functions available for programmatic use cases.



Now that library() signals a structured error there are other options.
One possibility, at least as an interim, is to define a
conditionMessage method, e.g. as

conditionMessage.packageNotFoundError <- function(c) {
 lib.loc <- c$lib.loc
 msg <- c$message
 package <- c$package
 if(length(lib.loc)) {
 allpkgs <- .packages(TRUE, lib.loc)
 if (!is.na(w <- match(tolower(package), tolower(allpkgs {
 msg2 <- sprintf("Perhaps you meant %s ?", sQuote(allpkgs[w]))
 return(paste(msg, msg2, sep = "\n"))
 }
 }
 msg
}

This is something you can do yourself, though it is generally not a
good idea to define a method when you don't own either the generic or
the class.

Something that would be useful and is being considered is having a
mechanism for registering default condition handlers. This would allow
the condition to be re-signaled with a custom class and then having
a custom conditionMessage method is less likely to cause conflicts.

I'd argue that this is quite useful especially for new users and that creating
condition handlers may involve more than what is needed for interactive use.


Best,

Marcel



Also worth looking into is establishing a restart around the error
signal.  This would allow an IDE, for example, to provide a dialog for
choosing the alternate package and retrying without the need to call
library() again. This is currently done in loadNamespace() but not yet
in library(). Can have downsides as well -- if the library() call is
in a notebook, for example, then you do want to fix the call ...  It
is arguably more useful in loadNamespace since that can get called
implicitly inside a longer computation that you don't necessarily want
to start over.

Best,

luke

On Fri, 21 Jun 2019, Marcel Ramos wrote:



Dear R-core devs,

I hope this email finds you well.

Please see the proposed patch to R-devel below:

Scenario:

When loading a package using `library`, a package may not be found if the cases 
are not matching:

```


library(ORG.Hs.eg.db)


Error in library(ORG.Hs.eg.db) :
 there is no package called 'ORG.Hs.eg.db'
```


Suggested Patch:

Returns a message matching what `install.packages` returns in such situations:

```


library("ORG.Hs.eg.db")


Error in library("ORG.Hs.eg.db") :
  there is no package called 'ORG.Hs.eg.db'
In addition: Warning message:
Perhaps you meant 'org.Hs.eg.db' ?
```

This patch will be helpful with 'fat-finger' typos. It will match a package
called with `library` against installed packages.


svn diff:

Index: src/library/base/R/library.R
===
--- src/library/base/R/library.R(revision 76727)
+++ src/library/base/R/library.R(working copy)
@@ -300,8 +300,13 @@
pkgpath <- find.package(package, lib.loc, quiet = TRUE,
verbose = verbose)
if(length(pkgpath) == 0L) {
-if(length(lib.loc) && !logical.return)
+if(length(lib.loc) && !logical.return) {
+allpkgs <- .packages(TRUE, lib.loc)
+if (!is.na(w <- match(tolower(package), tolower(allpkgs
+warning(sprintf("Perhaps you meant %s ?",
+sQuote(allpkgs[w])), call. = FALSE, domain = NA)
stop(packageNotFoundError(package, lib.loc, sys.call()))
+}
txt <- if(length(lib.loc))
gettextf("there is no package called %s", sQuote(package))
else


Thank you!

Best regards,

Marcel



--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


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this message 

[Rd] Suggested Patch: Library returns matching installed packages when typo present

[Marcel Ramos]

Dear R-core devs,

I hope this email finds you well.

Please see the proposed patch to R-devel below:

Scenario:

When loading a package using `library`, a package may not be found if the cases 
are not matching:

```
> library(ORG.Hs.eg.db)
 Error in library(ORG.Hs.eg.db) :
  there is no package called 'ORG.Hs.eg.db'
```


Suggested Patch:

Returns a message matching what `install.packages` returns in such situations:

```
> library("ORG.Hs.eg.db")
 Error in library("ORG.Hs.eg.db") :
   there is no package called 'ORG.Hs.eg.db'
 In addition: Warning message:
 Perhaps you meant 'org.Hs.eg.db' ?
```

This patch will be helpful with 'fat-finger' typos. It will match a package
called with `library` against installed packages.


svn diff:

Index: src/library/base/R/library.R
===
--- src/library/base/R/library.R(revision 76727)
+++ src/library/base/R/library.R(working copy)
@@ -300,8 +300,13 @@
 pkgpath <- find.package(package, lib.loc, quiet = TRUE,
 verbose = verbose)
 if(length(pkgpath) == 0L) {
-if(length(lib.loc) && !logical.return)
+if(length(lib.loc) && !logical.return) {
+allpkgs <- .packages(TRUE, lib.loc)
+if (!is.na(w <- match(tolower(package), tolower(allpkgs
+warning(sprintf("Perhaps you meant %s ?",
+sQuote(allpkgs[w])), call. = FALSE, domain = NA)
 stop(packageNotFoundError(package, lib.loc, sys.call()))
+}
 txt <- if(length(lib.loc))
 gettextf("there is no package called %s", sQuote(package))
     else


Thank you!

Best regards,

Marcel



--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


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Re: [Bioc-devel] Dashes in GFF attributes

[Marcel Ramos]

Hi Valentino,

You will have to provide more details concerning the issue.
It may be as simple as removing the dashes with `gsub` before using 
`featureCount`.

Please review the posting guidelines for a better idea on how to get help:

https://bioconductor.org/help/support/posting-guide/

And consider using `support.bioconductor.org` to post.

Best regards,

Marcel


On 4/17/19 10:51 AM, Valentino Giudice wrote:

Hi, I hope this is the right place to write.

The featureCount function of Rsubread doesn't work if the GFF file contains
dashes in the 9th column.
https://github.com/Bioconductor/BiocManager/issues/45

I was told to write in bioc-devel.

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[Rd] Suggested Patch: Adding commas to list of packages after R CMD check

[Marcel Ramos]

Dear R-devs,


Scenario:

When checking a package via `R CMD check package_tar.ball`, required / 
suggested packages may be missing. R subsequently returns a list of packages 
that are missing (delimited by spaces).

Example:

```
R CMD check glmSparseNet_0.99.13.tar.gz
* using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck'
* using R Under development (unstable) (2018-06-06 r74855)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file 'glmSparseNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmSparseNet' version '0.99.13'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Packages required but not available:
  'MultiAssayExperiment' 'glmnet' 'SummarizedExperiment' 'STRINGdb'
  'biomaRt' 'futile.logger' 'sparsebn' 'sparsebnUtils' 'forcats'
  'dplyr' 'readr' 'ggplot2' 'ggfortify' 'reshape2' 'rlang' 'loose.rock'

Packages suggested but not available:
  'testthat' 'knitr' 'rmarkdown' 'survcomp' 'pROC' 'devtools'
  'VennDiagram' 'BiocStyle' 'curatedTCGAData'

VignetteBuilder package required for checking but not installed: 'knitr'

The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE

Status: 1 ERROR
See
  '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck/00check.log'
for details.
```


Suggested Patch:

To return a list of missing dependencies delimited by a comma and a space (", 
") so to make it easier for the user to copy and paste this list.
This would be especially helpful when the list of missing dependencies is 
extensive.


Example output:

```
R CMD check glmSparseNet_0.99.13.tar.gz
* using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck'
* using R Under development (unstable) (2018-09-18 r75322)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file 'glmSparseNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmSparseNet' version '0.99.13'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Packages required but not available:
  'MultiAssayExperiment', 'glmnet', 'SummarizedExperiment', 'STRINGdb',
  'biomaRt', 'futile.logger', 'sparsebn', 'sparsebnUtils', 'forcats',
  'dplyr', 'readr', 'ggplot2', 'ggfortify', 'reshape2', 'stringr',
  'rlang', 'loose.rock'

Packages suggested but not available:
  'testthat', 'knitr', 'rmarkdown', 'survcomp', 'pROC', 'devtools',
  'roxygen2', 'VennDiagram', 'BiocStyle', 'curatedTCGAData'

VignetteBuilder package required for checking but not installed: 'knitr'

The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE

Status: 1 ERROR
See
  '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck/00check.log'
for details.
```


svn diff:


Index: src/library/tools/R/QC.R
===
--- src/library/tools/R/QC.R(revision 75322)
+++ src/library/tools/R/QC.R(working copy)
@@ -8536,13 +8536,13 @@
 .pretty_format <-
 function(x)
 {
-strwrap(paste(sQuote(x), collapse = " "),
+strwrap(paste(sQuote(x), collapse = ", "),
 indent = 2L, exdent = 2L)
 }
 .pretty_format2 <-
 function(msg, x)
 {
-xx <- strwrap(paste(sQuote(x), collapse = " "), exdent = 2L)
+xx <- strwrap(paste(sQuote(x), collapse = ", "), exdent = 2L)
 if (length(xx) > 1L || nchar(msg) + nchar(xx) + 1L > 75L)
 c(msg, .pretty_format(x))
 else paste(msg, xx)



PS. I would also advocate for setting `useFancyQuotes` to `FALSE` by default 
but it would be better to get more
input from the community.

Thanks!


Best regards,

Marcel

--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


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Re: [Bioc-devel] BiocManager updates / changes

[Marcel Ramos]

Dear Bioc-devs,

We have successfully completed the migration from BiocInstaller to
BiocManager.
Together, we modified about 570 packages that were using old
BiocInstaller code.

Please ensure that your package(s) install / build / check without
errors and that all
dependencies are properly documented in the DESCRIPTION file.

If you have any issues with your package related to our BiocManager
commits. Feel
free to reach out to me.


Thank you all for your continued cooperation.


Best regards,

Marcel


--
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

On 08/31/2018 01:28 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> Thank you to all maintainers who have made appropriate changes to their
> packages *in devel*.
>
> This is an ongoing effort to replace any outdated BiocInstaller,
> biocLite, etc.
> code from packages as we transition to `BiocManager` before the next
> release.
>
> You may have noticed a recent commit to your package. These commits are
> the result
> of a script to automatically replace a set number of lines of code with
> BiocManager code.
>
> These lines include `library(BiocInstaller)`,
> `source("https://bioconductor.org/biocLite.R;)`, and
> `biocLite("pkgname")`.
>
> All in all, we have changed about 314 packages from about 578 packages.
> There are still
> about 264 packages left with `BiocInstaller` and `biocLite` calls.
>
> Please DO ensure that:
>
>     * The language around these new changes is in concordance with the
> actual code
>
>     * You update your package to use BiocManager, if you haven't already
>
>     * Your package is building and dependencies are accounted for
>
>
> For a list of outstanding packages please see:
> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>
> For example code see devel landing pages such as:
> http://bioconductor.org/packages/devel/bioc/html/RaggedExperiment.html
>
>
> Best regards,
> Marcel
>
> --
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
> On 07/13/2018 05:11 PM, Marcel Ramos wrote:
>> Dear bioc-devs,
>>
>> About 4 weeks ago, I notified maintainers to make changes to their
>> bioc-devel vignettes and package code to support the use of
>> `BiocManager`.
>>
>> There are a number of packages that haven't made the transition in
>> Bioc-devel.
>>
>> Please see this GitHub gist for a list of outstanding packages:
>>
>> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>>
>> Best regards,
>>
>> Marcel
>>
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Dept. of Biostatistics & Bioinformatics
>> Elm St. & Carlton St.
>> Buffalo, New York 14263
>>
>>
>> On 06/20/2018 12:23 PM, Marcel Ramos wrote:
>>> Dear bioc-devs,
>>>
>>>
>>> A month ago we notified you about our "next generation" changes to
>>> BiocInstaller.
>>>
>>> Thanks to all beta testers and those who provided feedback and
>>> suggestions for a new package name.
>>>
>>>
>>> I am pleased to inform you that BiocManager is now on CRAN:
>>> https://cran.r-project.org/web/packages/BiocManager/index.html
>>>
>>>
>>> As mentioned in our last email, you can now install BiocManager using:
>>>
>>> ```
>>> install.packages("BiocManager")
>>> BiocManager::install("YourPackageNameHere")
>>> ```
>>>
>>> Action Item:
>>>
>>>     -   Please modify the vignettes in your bioc-devel packages to
>>> reflect the use of BiocManager
>>>
>>>
>>> After the next couple of weeks or so, we will be identifying packages in
>>> bioc-devel (3.8) that still
>>> mention BiocInstaller / biocLite.
>>>
>>>
>>> Best regards,
>>> Marcel
>>>
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Dept. of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>>
>>>
>>> On 05/09/2018 06:11 PM, Martin Morgan wrote:
>>>> Developers --
>>>>
>>>> A preliminary heads-up and request for comments.
>>>>
>>>> Almost since project inception, we've used the commands
>>>>
>>>>    source("htt

[Bioc-devel] BiocManager updates / changes

[Marcel Ramos]

Dear bioc-devs,

Thank you to all maintainers who have made appropriate changes to their
packages *in devel*.

This is an ongoing effort to replace any outdated BiocInstaller,
biocLite, etc.
code from packages as we transition to `BiocManager` before the next
release.

You may have noticed a recent commit to your package. These commits are
the result
of a script to automatically replace a set number of lines of code with
BiocManager code.

These lines include `library(BiocInstaller)`,
`source("https://bioconductor.org/biocLite.R;)`, and
`biocLite("pkgname")`.

All in all, we have changed about 314 packages from about 578 packages.
There are still
about 264 packages left with `BiocInstaller` and `biocLite` calls.

Please DO ensure that:

    * The language around these new changes is in concordance with the
actual code

    * You update your package to use BiocManager, if you haven't already

    * Your package is building and dependencies are accounted for


For a list of outstanding packages please see:
https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653

For example code see devel landing pages such as:
http://bioconductor.org/packages/devel/bioc/html/RaggedExperiment.html


Best regards,
Marcel

--
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

On 07/13/2018 05:11 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> About 4 weeks ago, I notified maintainers to make changes to their
> bioc-devel vignettes and package code to support the use of
> `BiocManager`.
>
> There are a number of packages that haven't made the transition in
> Bioc-devel.
>
> Please see this GitHub gist for a list of outstanding packages:
>
> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>
> Best regards,
>
> Marcel
>
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
>
> On 06/20/2018 12:23 PM, Marcel Ramos wrote:
>> Dear bioc-devs,
>>
>>
>> A month ago we notified you about our "next generation" changes to
>> BiocInstaller.
>>
>> Thanks to all beta testers and those who provided feedback and
>> suggestions for a new package name.
>>
>>
>> I am pleased to inform you that BiocManager is now on CRAN:
>> https://cran.r-project.org/web/packages/BiocManager/index.html
>>
>>
>> As mentioned in our last email, you can now install BiocManager using:
>>
>> ```
>> install.packages("BiocManager")
>> BiocManager::install("YourPackageNameHere")
>> ```
>>
>> Action Item:
>>
>>     -   Please modify the vignettes in your bioc-devel packages to
>> reflect the use of BiocManager
>>
>>
>> After the next couple of weeks or so, we will be identifying packages in
>> bioc-devel (3.8) that still
>> mention BiocInstaller / biocLite.
>>
>>
>> Best regards,
>> Marcel
>>
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Dept. of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>>
>>
>> On 05/09/2018 06:11 PM, Martin Morgan wrote:
>>> Developers --
>>>
>>> A preliminary heads-up and request for comments.
>>>
>>> Almost since project inception, we've used the commands
>>>
>>>    source("https://bioconductor.org/biocLite.R;)
>>>    biocLite(pkgs)
>>>
>>> to install packages. This poses security risks (e.g., typos in the
>>> url) and deviates from standard R package installation procedures.
>>>
>>>
>>> We'd like to move to a different system where a base package, call it
>>> 'BiocManager', is installed from CRAN and used to install Bioconductor
>>> packages
>>>
>>>    if (!"BiocManager" %in% rownames(installed.packages()))
>>>    install.packages("BiocManager")
>>>    BiocManager::install(pkgs)
>>>
>>> This establishes a secure chain from user R session to Bioconductor
>>> package installation. It is also more consistent with base R package
>>> installation procedures.
>>>
>>> BiocManager exposes four functions
>>>
>>>    - install() or update packages
>>>
>>>    - version() version of Bioconductor in use
>>>
>>>    - valid() are all Bioconductor packages from the same Bioconductor
>>> version?
>>>
>>>    - repositories() url location for Bioconducto

Re: [Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Hi Leo,

Thanks for bringing that up and making those changes.
We wanted to emphasize software packages first and then address experiment
data and workflow packages since they are fewer anyhow.

I will be adding those as additional files in the gist.

To update experiment data packages, the commands are the same as if
you were updating a software package.

I will check with the rest of the team about modifying workflow packages
so watch this space.

Regards,

Marcel

PS. See short reponse below.


On 07/24/2018 03:15 PM, Leonardo Collado Torres wrote:

Hi Marcel,

I noticed that https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
doesn't include the experiment data and workflow packages. I updated
mine preemptively (derfinderData and recountWorkflow).

By the way, how do I sync experiment data package updates? I forgot
how to do so. Maybe it's only via svn. I checked
http://bioconductor.org/developers/how-to/git/ and the commit in
question is 
https://github.com/leekgroup/derfinderData/commit/cc0a295a730f8f19a429f28c7b327ee15ccd1e81.
Last time I did it was in 2015.

Also, I suggest changing your grep command to:

grep -rnE "biocLite|biocValid" *

that way you can include biocValid() calls which now should be
BiocManager::valid(). I had included several of them in my package
vignettes.

I've checked on this and the packages that use `biocValid` intersect with
those that use `BiocInstaller|biocLite`. Thanks.

Best,
Leo

On Mon, Jul 16, 2018 at 1:06 PM Gabe Becker  wrote:


Ah, of course. I should have realized that. Makes sense. I'll get that
fixed in devel soon.

Thanks and sorry for the noise.
~G

On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos 
wrote:


Hi Gabe,

Please note that we are only making changes to packages in *bioc-devel*.

BiocManager wouldn't fail for users with earlier versions of R because
it doesn't apply to them. These users
should be using the respective bioc-release versions and consequently
`BiocInstaller`.

BiocManger is currently supported only for `devel` and all /bioc-devel/
users have R 3.5.0 or greater going forward.


Regards,
Marcel


On 07/16/2018 11:51 AM, Gabe Becker wrote:

Marcel et al,

My genbankr package is one of the ones that mentions biocLite (in
README.md, actually, not the vignette proper, but still...).
Historically this was just because I had missed your email and hadn't
updated it, but when I sat down to do it I ran into an issue:

BiocManager, while a huge step forward, requires R >3.5.0. That is
still relatively new, and my package (along with all Bioc packages
from the corresponding release) works fine under 3.4.x (and previous).
I'm somewhat loath to completely remove the biocLite based
instructions because install.packages("BiocManager") will fail (well,
not with an error, but it doesn't install anything...) for users with
earlier versions of R, wherease
source("http://bioconductor.org/biocLite.R;) works and gets the
correct version for them IIRC.

The `biocLite` instructions only apply the current and previous release
versions of Bioconductor.

Is there guidance on how to handle this issue?

Thanks,
~G

On Sun, Jul 15, 2018 at 10:53 AM, Marcel Ramos
mailto:marcel.ramospe...@roswellpark.org>> wrote:

 Hi Jason,

 Please check all of your package files and not just the vignette.

 The criteria involve a simple `grep` search of all package files for
 the words `biocLite` and `BiocInstaller`.

 ~/Bioconductor/ClusterSignificance (master) $ grep -rn "biocLite" *
 README.md:52:source("https://bioconductor.org/biocLite.R
 <https://bioconductor.org/biocLite.R>")
 README.md:53:biocLite("ClusterSignificance")
 README.Rmd:45:source("https://bioconductor.org/biocLite.R
 <https://bioconductor.org/biocLite.R>")
 README.Rmd:46:biocLite("ClusterSignificance")

 As I've mentioned in the previous emails, you can use:

 install.packages("BiocManager")
 BiocManager::install("YourPackageNameHere")

 to replace the source function call.

 You may also refer to the "Installation" section of the devel
 landing pages
 for an additional example:

 http://bioconductor.org/packages/devel/bioc/html/

ClusterSignificance.html

 <http://bioconductor.org/packages/devel/bioc/html/

ClusterSignificance.html>

 Best regards,
 Marcel


 On 07/14/2018 03:31 AM, Jason Serviss wrote:
 > Hello Marcel,
 >
 > I notice that the package I maintain, ClusterSignificance, is
 included
 > in this list although I am unsure why. In your previous mail you
 say:
 >
 >> After the next couple of weeks or so, we will be identifying
 packages in
 >> bioc-devel (3.8) that still
 >> mention BiocInstaller / biocLite.
 >
 > I don’t find any mention of BiocInstaller or biocLit

[Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Dear bioc-devs,

About 4 weeks ago, I notified maintainers to make changes to their
bioc-devel vignettes and package code to support the use of `BiocManager`.

There are a number of packages that haven't made the transition in
Bioc-devel.

Please see this GitHub gist for a list of outstanding packages:

https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653

Best regards,

Marcel

Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


On 06/20/2018 12:23 PM, Marcel Ramos wrote:

Dear bioc-devs,


A month ago we notified you about our "next generation" changes to
BiocInstaller.

Thanks to all beta testers and those who provided feedback and
suggestions for a new package name.


I am pleased to inform you that BiocManager is now on CRAN:
https://cran.r-project.org/web/packages/BiocManager/index.html


As mentioned in our last email, you can now install BiocManager using:

```
install.packages("BiocManager")
BiocManager::install("YourPackageNameHere")
```

Action Item:

    -   Please modify the vignettes in your bioc-devel packages to
reflect the use of BiocManager


After the next couple of weeks or so, we will be identifying packages in
bioc-devel (3.8) that still
mention BiocInstaller / biocLite.


Best regards,
Marcel

Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


On 05/09/2018 06:11 PM, Martin Morgan wrote:

Developers --

A preliminary heads-up and request for comments.

Almost since project inception, we've used the commands

   source("https://bioconductor.org/biocLite.R;)
   biocLite(pkgs)

to install packages. This poses security risks (e.g., typos in the
url) and deviates from standard R package installation procedures.


We'd like to move to a different system where a base package, call it
'BiocManager', is installed from CRAN and used to install Bioconductor
packages

   if (!"BiocManager" %in% rownames(installed.packages()))
   install.packages("BiocManager")
   BiocManager::install(pkgs)

This establishes a secure chain from user R session to Bioconductor
package installation. It is also more consistent with base R package
installation procedures.

BiocManager exposes four functions

   - install() or update packages

   - version() version of Bioconductor in use

   - valid() are all Bioconductor packages from the same Bioconductor
version?

   - repositories() url location for Bioconductor version-specific
repositories

install() behaves like biocLite(), using the most current version of
Bioconductor for the version of R in use. It stores this state using a
Bioconductor package 'BiocVersion', which is nothing more than a
sentinel for the version in use. One can also 'use devel' or a
particular version of Bioconductor (consistent with the version of R)
with

   BiocManager::install(version = "3.8")   # or the synonym "devel"


We intend to phase this in over several release cycles, and to
continue to support the traditional biocLite() route for versions
before BiocManager becomes available.

We also intend to change the overall versioning of 'Bioconductor'
itself, where releases are always even (3.8, 3.10, 3.12, ...) and
'devel' always odd.

Obviously this is a large change, eventually requiring updates to many
locations on our web site and individual vignettes.


Of course the key question is the name of the 'BiocManager' package.
It cannot easily be 'BiocInstaller', because of the differences in way
CRAN and Bioconductor version packages. Some possible names are
'
BiocInstall::install()
BiocPackages::install()
BiocManager
BiocMaestro


Your comments are welcome...

Martin


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

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[Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Dear bioc-devs,


A month ago we notified you about our "next generation" changes to
BiocInstaller.

Thanks to all beta testers and those who provided feedback and
suggestions for a new package name.


I am pleased to inform you that BiocManager is now on CRAN:
https://cran.r-project.org/web/packages/BiocManager/index.html


As mentioned in our last email, you can now install BiocManager using:

```
install.packages("BiocManager")
BiocManager::install("YourPackageNameHere")
```

Action Item:

   -   Please modify the vignettes in your bioc-devel packages to
reflect the use of BiocManager


After the next couple of weeks or so, we will be identifying packages in
bioc-devel (3.8) that still
mention BiocInstaller / biocLite.


Best regards,
Marcel

Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


On 05/09/2018 06:11 PM, Martin Morgan wrote:
> Developers --
>
> A preliminary heads-up and request for comments.
>
> Almost since project inception, we've used the commands
>
>   source("https://bioconductor.org/biocLite.R;)
>   biocLite(pkgs)
>
> to install packages. This poses security risks (e.g., typos in the
> url) and deviates from standard R package installation procedures.
>
>
> We'd like to move to a different system where a base package, call it
> 'BiocManager', is installed from CRAN and used to install Bioconductor
> packages
>
>   if (!"BiocManager" %in% rownames(installed.packages()))
>   install.packages("BiocManager")
>   BiocManager::install(pkgs)
>
> This establishes a secure chain from user R session to Bioconductor
> package installation. It is also more consistent with base R package
> installation procedures.
>
> BiocManager exposes four functions
>
>   - install() or update packages
>
>   - version() version of Bioconductor in use
>
>   - valid() are all Bioconductor packages from the same Bioconductor
> version?
>
>   - repositories() url location for Bioconductor version-specific
> repositories
>
> install() behaves like biocLite(), using the most current version of
> Bioconductor for the version of R in use. It stores this state using a
> Bioconductor package 'BiocVersion', which is nothing more than a
> sentinel for the version in use. One can also 'use devel' or a
> particular version of Bioconductor (consistent with the version of R)
> with
>
>   BiocManager::install(version = "3.8")   # or the synonym "devel"
>
>
> We intend to phase this in over several release cycles, and to
> continue to support the traditional biocLite() route for versions
> before BiocManager becomes available.
>
> We also intend to change the overall versioning of 'Bioconductor'
> itself, where releases are always even (3.8, 3.10, 3.12, ...) and
> 'devel' always odd.
>
> Obviously this is a large change, eventually requiring updates to many
> locations on our web site and individual vignettes.
>
>
> Of course the key question is the name of the 'BiocManager' package.
> It cannot easily be 'BiocInstaller', because of the differences in way
> CRAN and Bioconductor version packages. Some possible names are
> '
> BiocInstall::install()
> BiocPackages::install()
> BiocManager
> BiocMaestro
>
>
> Your comments are welcome...
>
> Martin
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

[Marcel Ramos]

Hi Christian,

It looks like you have to do

*git pull upstream master *

according to your `git remote -v`.

Regards,

Marcel


On 05/14/2018 04:21 PM, cstrato wrote:
> Dear Nitesh,
>
> Thank you for your fast reply. Here is  what I tried now,
> including using 'git pull':
>
> $ cd /Volumes/T3Data/CRAN/GIT/xps
>
> $ git checkout master
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
>
> $ git pull
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Already up-to-date.
>
> $ git commit DESCRIPTION
> On branch master
> Your branch is up-to-date with 'origin/master'.
> Untracked files:
>     .DS_Store
>     xps/
>
> nothing added to commit but untracked files present
>
> $ git push
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Everything up-to-date
>
> $ git push origin master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Everything up-to-date
>
> $ git push upstream master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> To git.bioconductor.org:packages/xps
>  ! [rejected]    master -> master (fetch first)
> error: failed to push some refs to
> 'g...@git.bioconductor.org:packages/xps'
> hint: Updates were rejected because the remote contains work that you do
> hint: not have locally. This is usually caused by another repository
> pushing
> hint: to the same ref. You may want to first integrate the remote changes
> hint: (e.g., 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for
> details.
>
>
> Since I still get the same error I tried the following:
>
> $ git merge upstream/master
> merge: upstream/master - not something we can merge
>
> $ git remote -v
> origin  g...@github.com:cstrato/xps.git (fetch)
> origin  g...@github.com:cstrato/xps.git (push)
> upstream    g...@git.bioconductor.org:packages/xps (fetch)
> upstream    g...@git.bioconductor.org:packages/xps (push)
>
> $ git push -u origin master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Branch master set up to track remote branch master from origin.
> Everything up-to-date
>
> $ git push upstream master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> To git.bioconductor.org:packages/xps
>  ! [rejected]    master -> master (fetch first)
> error: failed to push some refs to
> 'g...@git.bioconductor.org:packages/xps'
> hint: Updates were rejected because the remote contains work that you do
> hint: not have locally. This is usually caused by another repository
> pushing
> hint: to the same ref. You may want to first integrate the remote changes
> hint: (e.g., 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for
> details.
>
>
> Once again I get the same error.
>
> - Do you know what might be the reason?
>
> - Furthermore, why is it not possible to follow exactly the guidelines
> in:
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> Best regards,
> Christian
>
>
> On 05/14/18 20:50, Turaga, Nitesh wrote:
>> Did you try to ‘git pull’ as mentioned in the error message?
>>
>> Best,
>>
>> Nitesh
>>
>>> On May 14, 2018, at 2:48 PM, cstrato  wrote:
>>>
>>> Dear GIT experts,
>>>
>>> On Saturday I wanted to update my development package to xps_1.41.1,
>>> however until now it was not updated in the 'Multiple platform
>>> build/check report' although I could confirm the changes with
>>> Firefox: https://github.com/cstrato/xps
>>>
>>>
>>> For this reason I tried today to update my development package to
>>> xps_1.41.2.
>>>
>>> I did follow exactly the guidelines of:
>>> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>>>
>>>
>>> Here are the results:
>>>
>>> $ cd /Volumes/T3Data/CRAN/GIT/xps
>>>
>>> $ git remote -v
>>> origin  g...@github.com:cstrato/xps.git (fetch)
>>> origin  g...@github.com:cstrato/xps.git (push)
>>> upstream    g...@git.bioconductor.org:packages/xps (fetch)
>>> upstream    g...@git.bioconductor.org:packages/xps (push)
>>>
>>> $ git checkout master
>>> Already on 'master'
>>> Your branch is up-to-date with 'origin/master'.
>>>
>>> $ git add -v DESCRIPTION
>>> add 'DESCRIPTION'
>>>
>>> $ git add -v NEWS
>>> add 'NEWS'
>>>
>>> $ git commit -m "update for NEWS"
>>> [master cf326be] update for NEWS
>>> 2 files changed, 6 insertions(+), 1 deletion(-)
>>>
>>> $ git push origin master
>>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>>> Counting objects: 4, done.
>>> Delta compression using up to 8 threads.
>>> Compressing objects: 100% (4/4), done.
>>> Writing objects: 100% (4/4), 375 bytes | 0 bytes/s, done.
>>> Total 4 (delta 3), reused 0 (delta 0)
>>> remote: Resolving deltas: 100% (3/3), completed with 3 local objects.
>>> To github.com:cstrato/xps.git
>>>    7616d60..cf326be  master -> master
>>>
>>> $ git push upstream master
>>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>>> To git.bioconductor.org:packages/xps
>>> ! [rejected]    

Re: [Bioc-devel] EXTERNAL: Fwd: [Bioconductor/Contributions] GIGSEA (#720)

[Marcel Ramos]

Hi Shijia,

I am assigned to the submission and will be reviewing your package soon.

Please send further correspondence as comments to the issue on GitHub.

Best regards,

Marcel


On 04/18/2018 08:31 PM, Shijia Zhu wrote:
> Hi Everyone,
>
>   My package just passed the check, without errors or warnings.
>
> I am pretty new to Bioconductor. May I ask whether this is done? or
> anything else I need to do for releasing my package?
>
> Any help would be much appreciated.
>
> Best
> Shijia
>
>
>
> -- Forwarded message --
> From: bioc-issue-bot 
> Date: Tue, Apr 17, 2018 at 5:16 AM
> Subject: Re: [Bioconductor/Contributions] GIGSEA (#720)
> To: Bioconductor/Contributions 
> Cc: Shijia Zhu , Mention <
> ment...@noreply.github.com>
>
>
> Dear Package contributor,
>
> This is the automated single package builder at bioconductor.org.
>
> Your package has been built on Linux, Mac, and Windows.
>
> Congratulations! The package built without errors or warnings
> on all platforms.
>
> Please see the build report
> 
> for more details.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> ,
> or mute the thread
> 
> .
>
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>
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[Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

[Marcel Ramos]

Hi Ryan,

Thanks for pointing this out.

I'm not sure what you mean by "structured" or "format". We do have
public facing citations
which can be found at:
http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html

(Thanks Lori for locating these pages!)


And even with a web-browsable git repository (as you mentioned), one
would still only be able
to get the "unprocessed" CITATION file. The best way to programmatically
get these at the moment
is through the git repository via:

git archive
--remote=g...@git.bioconductor.org:packages/MultiAssayExperiment.git \
   HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt

although, we would have to provide the CiteAs service with a key for
read-only access.

Best regards,

Marcel


On 04/17/2018 12:44 PM, Ryan Thompson wrote:
> There's a nice online tool called CiteAs which tries to figure out the
> proper citation for a given URL. I've recently helped the author to add
> support for extracting the DOI from Bioconductor package information pages:
> https://github.com/Impactstory/citeas-api/issues/12
>
> This is a good start, but is suboptimal, since some many packages have
> actual published articles which should be used as the canonical citation
> instead of the package's URL. However, I'm not sure how to get this
> citation information in a structured format short of running R and
> installing the package, which isn't really an option for a web service like
> this, which wants to return a result quickly. Does anyone know a good way
> to access this info?
>
> Thanks,
>
> Ryan Thompson
>
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>
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Re: [Bioc-devel] appveyor CI failing with biocparam

[Marcel Ramos]

Hi Vivek,

Make sure you are using the appropriate version of R.

Your appveyor code says you're using 3.4.4.

https://ci.appveyor.com/project/vivekbhr/icetea#L22

Add a chunk like:

```
environment:
  global: ...
  matrix:
    - R_VERSION: devel

```

after your "global:" tag under the "environment:" field.

Regards,

Marcel



On 03/29/2018 02:39 PM, Vivek Bhardwaj wrote:
> Hi Martin
>
> Thanks for the quick reply. I think that would have been the real issue 
> most probably. I fixed it, though the build still failed, but this time 
> it might be due to build cache or other issues with appveyor? A unit 
> test that was fixed earlier also keeps failing on appveyor.
>
> My travis build .
> My appveyor build .
>
> I am developing on R-3.5 and Bioc3.7 on my local linux system (travis is 
> also using that for linux/mac), but our sysadmin didn't install the 
> devel version on the windows therefore I have to use the older one there 
> for testing.
>
> Thanks for the comment on biocparallel. I would try this.
>
> Best,
> Vivek
>
>
>
>
> On 03/29/2018 03:23 PM, Martin Morgan wrote:
>> Hi Vivek...
>>
>> On 03/29/2018 08:39 AM, Vivek Bhardwaj wrote:
>>> Dear All
>>>
>>> I have travis and appveyor CI running for my upcoming package in
>>> development. I find that the appveyor CI fails for the function
>>> `GenomicAlignments::summarizeOverlaps`, which is called by one of the
>>> functions in my package. It doesn't recognize the BPPARAM argument
>>> (appveyor build is here
>>> ). The same function
>>> passes on my local windows system.
>>>
>> I would guess that the underlying reason is a difference in package 
>> versions.
>>
>> I'd also guess that the problem is at 
>> https://github.com/vivekbhr/icetea/blob/master/R/detect_diffTSS.R#L125 
>> , where summarizeOverlaps hands off the BPPARAM to ResizeReads via 
>> ..., which is then passed to GenomicRanges::resize where the function 
>> is not expecting an argument named BPPARAM. Probably simply replace l 
>> 131 with
>>
>>   GenomicRanges::resize(reads, width = width, fix=fix)
>>
>> Remember that your new package will be added to the 'devel' version of 
>> Bioconductor, so you should be building and testing on R-3.5 /  Bioc 3.7.
>>
>> There seem to be several calls to bplapply in your code; it might pay 
>> to start the parallel back-end at the top of your function, as 
>> mentioned in https://support.bioconductor.org/p/107303/#107322
>>
>> Martin
>>
>>> *appveyor windows build : *
>>>
>>> R version 3.4.4 Patched (2018-03-19 r74453)
>>> Platform: i386-w64-mingw32/i386 (32-bit)
>>> Running under: Windows Server 2012 R2 x64 (build 9600)
>>>
>>> *my local windows info : *
>>>
>>> R version 3.4.3 (2017-11-30)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>
>>> Has anyone encountered this issue? The call to bplapply works in other
>>> functions of the package so I am not sure if this is coming directly
>>> from biocparallel.
>>>
>>>
>>> Best Wishes
>>> Vivek
>>>
>>> 
>>>
>>> *Vivek Bhardwaj*
>>> PhD Candidate | International Max Planck Research School
>>> Max Planck Institute of Immunobiology and Epigenetics
>>> Stübeweg 51, Freiburg
>>> E-mail: bhard...@ie-freiburg.mpg.de
>>>
>>> [[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 
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>



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Re: [Bioc-devel] EXTERNAL: Re: [R-pkg-devel] DESCRIPTION file building problem

[Marcel Ramos]

Hi Dario,

Gabe is right, you shouldn't be building within the package directory.
Although AFAIK, you should be able to do so. Perhaps if you point us
to your package, we might be able to see the issue...

Regards,

Marcel


On 03/21/2018 06:15 PM, Gabe Becker wrote:

Dario,

Does this ever happen if you build in the parent directory? I don't think
building within the package directory is best practice and I'm not sure
it's (officially) supported at all. The error message seems to support that.

~G

On Wed, Mar 21, 2018 at 9:40 AM, Dario Righelli 
wrote:


Hi,

I've a package with a DESCRIPTION file inside of it, as usual.

It's a couple of times that, when I try to build the package on my local
machine or on travis-ci, I get this error:

Building package
Building with: R CMD build
0.74s$ R CMD build .
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘mypackage’:
* checking DESCRIPTION meta-information ...OK
* cleaning src
Error in .read_description(ldpath) :
file 'mypackage/DESCRIPTION' does not exist
Execution halted

Someone knows what does it depends on?

Thanks,
dario


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Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

[Marcel Ramos]

Hi Kevin,

My hunch is that the image that you're working with is old. If you're
working with an
older image, you could run into that problem with different R versions
used to install 'backports'.

I would first ensure that I'm working with a clean image by stopping any
active containers, removing them, and then doing `docker rmi` to remove
the `bioconductor/devel_core2` image.

Pull a clean image from docker hub and run `wercker build` with your
`wercker.yml` file.

Any new changes made by your `yml` file can be saved to a different
image by doing
`docker commit`.
See:
https://stackoverflow.com/questions/26322247/docker-revert-changes-to-container

This allows you to preserve the `devel_core2` image as it was downloaded
and try again with
an updated 'wercker.yml' file.

PS. A correction to the `wecker.yml` file:

```
build:
  steps:
    - script:
    name: Install devtools
    code: R -e "install.packages(c('devtools', 'backports'))"
    - jimhester/r-dependencies
    - jimhester/r-check
    - jimhester/r-coverage
```

Also, the EXTERNAL tag is generated by the Roswell Park email system.


Best regards,

Marcel




On 03/20/2018 05:14 PM, Kevin RUE wrote:
> Hi Marcel,
>
> Thanks for the reply. I tried your `wercker.yml` file (exactly as is),
> and still got the same issue:
>
> * creating vignettes ... ERROR
> Error: processing vignette 'MyPackage-vignette.Rmd' failed with
> diagnostics:
> package ‘backports’ was installed by an R version with different
> internals; it needs to be reinstalled for use with this R version
> Execution halted
> Error: Command failed (1)
> In addition: Warning message:
> `cleanup` is deprecated
> Execution halted
> Check Failed, dumping logs
> find: ‘./*.Rcheck’: No such file or directory
> failed: Check Failed
>
> I'll leave it be for now, and see if I can get it to work with the new
> release in April.
>
> Also, did my email really arrive as  "EXTERNAL" to the bioc-devel
> mailing list? That would be odd, I sent it from my bioc-devel
> registered email address :/
>
> Kind regards,
> Kevin
>
> On Tue, Mar 20, 2018 at 5:03 PM, Marcel Ramos
> <marcel.ra...@roswellpark.org <mailto:marcel.ra...@roswellpark.org>>
> wrote:
>
> Hi Kevin,
>
> Being that I am unable to fully reproduce the issue, I can only
> say that
> I have been successful in running the steps in the Wercker build for a
> different package.
>
> Please do a *clean* pull of the Bioconductor image from docker hub by
> removing any stale images
> first.
>
> Here is the wercker.yml that I used:
>
> >> wercker build --docker-local
>
> box: bioconductor/devel_core2
>
> build:
>   steps:
>     - script:
>     name: Install devtools
>     code: R -e "install.packages('devtools')"
>     - jimhester/r-dependencies:
>     cran_dependencies: backports
>     - jimhester/r-check
>     - jimhester/r-coverage
>
>
> *Note:*I removed the r-lint step because it was having some issues
> with
> xml.
>
>
> Regards,
>
> Marcel
>
>
> On 03/16/2018 07:53 AM, Kevin RUE wrote:
> > Dear all,
> >
> > I'm usually a big Travis CI fan, but I'm having a go at Wercker,
> using the
> > bioconductor/devel_core2 docker (I have also tried the rocker
> 'parent' ones
> > without further success).
> > I am running into the following issue:
> >
> > [...]
> > * creating vignettes ... ERROR
> > Error: processing vignette 'NewPackage-vignette.Rmd' failed with
> > diagnostics:
> > package ‘backports’ was installed by an R version with different
> internals;
> > it needs to be reinstalled for use with this R version
> > Execution halted
> > Error: Command failed (1)
> > In addition: Warning message:
> > `cleanup` is deprecated
> > Execution halted
> > Check Failed, dumping logs
> > find: ‘./*.Rcheck’: No such file or directory
> > failed: Check Failed
> >
> > I've tried adding a task that re-installs the `backports`
> package from
> > source (CRAN), but I still get the same error.
> >
> > My wercker.yml looks like:
> > box: bioconductor/devel_core2
> > build:
> >     steps:
> >         - script:
> >             name: Install devtools
> >             code: R -e "install.packages('devtools')"
> >         - script:
> >             name: Install backports
> >             code: R -e "install.pa

Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

[Marcel Ramos]

Hi Kevin,

Being that I am unable to fully reproduce the issue, I can only say that
I have been successful in running the steps in the Wercker build for a
different package.

Please do a *clean* pull of the Bioconductor image from docker hub by
removing any stale images
first.

Here is the wercker.yml that I used:

>> wercker build --docker-local

box: bioconductor/devel_core2

build:
  steps:
    - script:
    name: Install devtools
    code: R -e "install.packages('devtools')"
    - jimhester/r-dependencies:
    cran_dependencies: backports
    - jimhester/r-check
    - jimhester/r-coverage


*Note:*I removed the r-lint step because it was having some issues with
xml.


Regards,

Marcel


On 03/16/2018 07:53 AM, Kevin RUE wrote:
> Dear all,
>
> I'm usually a big Travis CI fan, but I'm having a go at Wercker, using the
> bioconductor/devel_core2 docker (I have also tried the rocker 'parent' ones
> without further success).
> I am running into the following issue:
>
> [...]
> * creating vignettes ... ERROR
> Error: processing vignette 'NewPackage-vignette.Rmd' failed with
> diagnostics:
> package ‘backports’ was installed by an R version with different internals;
> it needs to be reinstalled for use with this R version
> Execution halted
> Error: Command failed (1)
> In addition: Warning message:
> `cleanup` is deprecated
> Execution halted
> Check Failed, dumping logs
> find: ‘./*.Rcheck’: No such file or directory
> failed: Check Failed
>
> I've tried adding a task that re-installs the `backports` package from
> source (CRAN), but I still get the same error.
>
> My wercker.yml looks like:
> box: bioconductor/devel_core2
> build:
> steps:
> - script:
> name: Install devtools
> code: R -e "install.packages('devtools')"
> - script:
> name: Install backports
> code: R -e "install.packages('backports')"
> - jimhester/r-dependencies
> - jimhester/r-check
> - jimhester/r-lint
> - jimhester/r-coverage
>
>
>
> Any help/advice/experience with Wercker would be greatly appreciated!
>
> Best wishes,
> Kevin
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] EXTERNAL: amplican tokay2 i386 error

[Marcel Ramos]

Hi Kornel,

I downloaded your package from our git repo and ran check locally on
Windows 7.
It seems like there are some issues with the `data.table` (version
1.10.4-3) package.
Here is my result for the `i386` architecture:

>>> R CMD check --force-multiarch --no-vignettes amplican_1.1.6.tar.gz
[truncated]...
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'amplican-Ex.R' failed
The error most likely occurred in:

> ### Name: amplicanPipeline
> ### Title: Wraps main package functionality into one function.
> ### Aliases: amplicanPipeline
>
> ### ** Examples
>
> # path to example config file
> config <- system.file("extdata", "config.csv", package = "amplican")
> # path to example fastq files
> fastq_folder <- system.file("extdata", package = "amplican")
> # output folder
> results_folder <- tempdir()
>
> #full analysis, not knitting files automatically
> amplicanPipeline(config, fastq_folder, results_folder, knit_reports =
FALSE)
Checking write access...
Checking configuration file...
Making alignments...
Aligning reads for barcode_1
Aligning reads for barcode_2
Saving alignments...
Saving parameters...
Saving unassigned sequences...
Saving barcode statistics...
Translating alignments into events...
Saving complete events - unfiltered...
*Error in data.table::foverlaps(aln_fwd, aln_rve, type = "any", which =
TRUE,  :**
**  negative length vectors are not allowed*
Calls: amplicanPipeline -> amplicanConsensus -> 
Execution halted
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 *ERROR*
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:

  Loading required package: data.table

  Attaching package: 'data.table'

  The following object is masked from 'package:IRanges':

  shift

  The following objects are masked from 'package:S4Vectors':

  first, second

  >
  > test_check("amplican")
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
[truncated] ...

## R.version
R.version
   _
platform   x86_64-w64-mingw32
arch   x86_64
os mingw32
system x86_64, mingw32
status Under development (unstable)
major  3
minor  5.0
year   2018
month  03
day    18
svn rev    74422
language   R
version.string R Under development (unstable) (2018-03-18 r74422)
nickname   Unsuffered Consequences

## sessionInfo() header
R Under development (unstable) (2018-03-18 r74422)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1


Regards,

Marcel


On 03/16/2018 05:55 AM, Kornel Labun wrote:
> Hi,
>
> Could you help me diagnose what is wrong with my package, amplican, that
> fails to pass check on tokay2 i386?
>
> I fail to understand what might be wrong from the report
> http://bioconductor.org/checkResults/devel/bioc-LATEST/amplican/tokay2-checksrc.html
> .
> It is long standing problem, since the first moment we moved into devel
> 3.7. I think it might be related to my data.table package which I import as
> I have tried to comment out some tests and examples, but it seems I am
> running in circle.
>
> Best,
> Kornel Labun
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] EXTERNAL: Re: unknown build error novel bioc. package

[Marcel Ramos]

Hi Maarten,

Sorry about the confusion. The link you provided pointed to errors in
*omicRexposome*.

It appears that the errors you're getting for *omicsPrint* have to do
with the `getGEO` call on

line #261 in the vignette.

It can be fixed if you introduce a `fileext` argument to `tempfile()`.

Please see pull request # 3.

Regards,

Marcel



On 12/13/2017 03:25 PM, Maarten van Iterson wrote:
> Hi Marcel,
>
> Thanks for your help, do you mean I should add "bgredata" to our DESCR
> file? omicsPrint should not depend on it?
>
> This sessionInfo when omicsPrint is loaded:
>
> > library(omicsPrint)
> Loading required package: MASS
> in method for ‘coerce’ with signature
> ‘"RangedRaggedAssay","RaggedExperiment"’: no definition for class
> “RaggedExperiment”
> > sessionInfo()
> R Under development (unstable) (2017-09-30 r73418)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.3 LTS
>
> Matrix products: default
> BLAS: /usr/local/lib64/R/lib/libRblas.so
> LAPACK: /usr/local/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C 
>  [3] LC_TIME=nl_NL.UTF-8    LC_COLLATE=en_US.UTF-8   
>  [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8  
>  [7] LC_PAPER=nl_NL.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C   
> [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C  
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] omicsPrint_0.99.30 MASS_7.3-47  
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.14   compiler_3.5.0   
>  [3] GenomeInfoDb_1.12.3    plyr_1.8.4   
>  [5] XVector_0.16.0 bitops_1.0-6 
>  [7] tools_3.5.0    zlibbioc_1.22.0  
>  [9] digest_0.6.12  tibble_1.3.4 
> [11] gtable_0.2.0   lattice_0.20-35  
> [13] rlang_0.1.4    Matrix_1.2-12
> [15] DelayedArray_0.2.7 shiny_1.0.5  
> [17] parallel_3.5.0 gridExtra_2.3
> [19] GenomeInfoDbData_0.99.0    stringr_1.2.0
> [21] UpSetR_1.3.3   S4Vectors_0.14.7 
> [23] IRanges_2.10.5 stats4_3.5.0 
> [25] MultiAssayExperiment_1.2.1 grid_3.5.0   
> [27] shinydashboard_0.6.1   glue_1.2.0   
> [29] Biobase_2.36.2 R6_2.2.2 
> [31] purrr_0.2.4    tidyr_0.7.2  
> [33] magrittr_1.5   reshape2_1.4.2   
> [35] ggplot2_2.2.1  scales_0.5.0 
> [37] matrixStats_0.52.2 htmltools_0.3.6  
> [39] BiocGenerics_0.22.1    GenomicRanges_1.28.6 
> [41] RaggedExperiment_1.0.0 SummarizedExperiment_1.6.5
> [43] mime_0.5   xtable_1.8-2 
> [45] colorspace_1.3-2   httpuv_1.3.5 
> [47] stringi_1.1.6  RCurl_1.95-4.8   
> [49] lazyeval_0.2.1 munsell_0.4.3
>
>
>
>
> On Wed, Dec 13, 2017 at 8:52 PM, Marcel Ramos
> <marcel.ra...@roswellpark.org <mailto:marcel.ra...@roswellpark.org>>
> wrote:
>
> Hi Maarten,
>
> It appears that your vignette is pointing to a package that
> doesn't exist in the build system.
>
> Please reference `package = "brgedata"` instead.
>
> Regards,
>
> Marcel
>
>
> *Note. Apologies if you've received this email twice.
>
> On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
>> Dear all, Our new package, omicsPrint, has been accepted and
>> added to the bioconductor build system but is not passing through
>> on any system. Locally we are able to build install and execute
>> the vignette. We have tried several things without success. The
>> current error we got for version 0.99.29 on malbec2 is: Error:
>> processing vignette 'omicsPrint.Rmd' failed with diagnostics:
>> parsing failed--expected only one '!series_data_table_begin' (
>> 
>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
>> 
>> <https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html>
>>
>> )
>>
>> Anyone idea's or suggestions for debugging?
>>
>> Regards,
>> Maarten and Davy
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-p

[Bioc-devel] unknown build error novel bioc. package

[Marcel Ramos]

Hi Maarten,

It appears that your vignette is pointing to a package that doesn't
exist in the build system.

Please reference `package = "brgedata"` instead.

Regards,

Marcel


*Note. Apologies if you've received this email twice.

On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
> Dear all,
>
> Our new package, omicsPrint, has been accepted and added to the
> bioconductor build system but is not passing through on any system. Locally
> we are able to build install and execute the vignette. We have tried
> several things without success.
>
> The current error we got for version 0.99.29 on malbec2 is:
>
> Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
> parsing failed--expected only one '!series_data_table_begin'
>
> (
> https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
> )
>
> Anyone idea's or suggestions for debugging?
>
> Regards,
> Maarten and Davy
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: unknown build error novel bioc. package

[Marcel Ramos]

Hi Maarten,

It appears that your vignette is pointing to a package that doesn't
exist in the build system.

Please reference `package = "brgedata"` instead.

Regards,

Marcel


On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
> Dear all,
>
> Our new package, omicsPrint, has been accepted and added to the
> bioconductor build system but is not passing through on any system. Locally
> we are able to build install and execute the vignette. We have tried
> several things without success.
>
> The current error we got for version 0.99.29 on malbec2 is:
>
> Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
> parsing failed--expected only one '!series_data_table_begin'
>
> (
> https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
> )
>
> Anyone idea's or suggestions for debugging?
>
> Regards,
> Maarten and Davy
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] MultiAssayExperiment Subsetting Fails if Column Data Has One Column

[Marcel Ramos]

Dear Dario,

Thank you for your report, this is resolved in MultiAssayExperiment 1.3.35.


Sorry for the noise everyone.


Regards,

Marcel


On 09/12/2017 11:00 PM, Dario Strbenac wrote:
> Good day,
>
> Subsetting a MultiAssayExperiment object fails if the column data has one 
> column but not 2 or more columns. Perhaps drop = FALSE is missing for the 
> DataFrame subsetting. A minimal example is:
>
> rowColNames <- list(paste0("Gene", 1:10), paste0("Person", 1:10))
> aTable <- matrix(rnorm(100), ncol = 10, dimnames = rowColNames)
> classes <- data.frame(row.names = paste0("Person", 1:10),
>class = rep(c("Non-Responder", "Recovery"), each = 5))
> measurementsSet <- MultiAssayExperiment(list(RNA = aTable), classes)
> measurementsSet[1, 1, ]
>
> other attached packages:
> [1] S4Vectors_0.15.7BiocGenerics_0.23.1 
> MultiAssayExperiment_1.3.34
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marcel Ramos
Bioconductor Core Team Member
Roswell Park Cancer Institute


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Re: [Bioc-devel] ExperimentList Contructor Failing

[Marcel Ramos]

Hi Dario,

You're using a different version of MultiAssayExperiment which might make
the original problem less reproducible.

I was not able to reproduce the error on the release version of
MultiAssayExperiment. If you do find the issue again. Please let me know.

As a side note, we are using the release version of R for Bioconductor 
development

until the next release (coming up soon).


PS. Package related questions should really go to the support site 
and/or GitHub.


https://support.bioconductor.org/

https://github.com/waldronlab/MultiAssayExperiment


Best regards,

Marcel


On 09/12/2017 10:00 PM, Dario Strbenac wrote:

Good day,

Whatever the problem is, it's gone with R Under Development and all packages 
installed from the development branch of Bioconductor.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] ExperimentList Contructor Failing

[Marcel Ramos]

Hi Dario,

I wasn't able to reproduce this error on my version of Ubuntu. (see below)

Please kindly post any future package inquiries at
support.bioconductor.org.


Best,

Marcel

---


> ExperimentList()
ExperimentList class object of length 0: 

> BiocInstaller::biocValid()

* sessionInfo()

R version 3.4.1 Patched (2017-07-19 r72930)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/libf77blas.so.3.0
LAPACK: /usr/lib/openblas-base/liblapack.so.3

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

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

other attached packages:
[1] MultiAssayExperiment_1.2.1


On 09/12/2017 02:00 AM, Dario Strbenac wrote:
> Good day,
>
> Although the package seems to build without errors, I can't run the basic 
> examples of MultiAssayExperiment successfully.
>
> library(MultiAssayExperiment)
>> example("ExperimentList")
> ExprmL> ## Create an empty ExperimentList instance
> ExprmL> ExperimentList()
> Error in checkSlotAssignment(object, name, value) : 
>   assignment of an object of class �NULL� is not valid for slot 
> �elementMetadata� in an object of class �ExperimentList�; is(value, 
> "DataTableORNULL") is not TRUE
>
> Everything seems fine with the package check:
>
>> BiocInstaller::biocValid()
> * sessionInfo()
>
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.3 LTS
>
> Matrix products: default
> BLAS: /usr/lib/libblas/libblas.so.3.6.0
> LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C   
> LC_TIME=en_AU.UTF-8   
>  [4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8
> LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C  LC_ADDRESS=C   
>
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 
> LC_IDENTIFICATION=C   
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
>
> other attached packages:
> [1] MultiAssayExperiment_1.2.1
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.12   BiocInstaller_1.26.1   compiler_3.4.1 
>
>  [4] GenomeInfoDb_1.12.2plyr_1.8.4 XVector_0.16.0 
>
>  [7] bitops_1.0-6   tools_3.4.1zlibbioc_1.22.0
>
> [10] digest_0.6.12  tibble_1.3.4   gtable_0.2.0   
>
> [13] lattice_0.20-35rlang_0.1.2Matrix_1.2-11  
>
> [16] DelayedArray_0.2.7 shiny_1.0.5parallel_3.4.1 
>
> [19] GenomeInfoDbData_0.99.0gridExtra_2.3  stringr_1.2.0  
>
> [22] UpSetR_1.3.3   S4Vectors_0.14.4   IRanges_2.10.3 
>
> [25] stats4_3.4.1   grid_3.4.1 
> shinydashboard_0.6.1  
> [28] glue_1.1.1 Biobase_2.36.2 R6_2.2.2   
>
> [31] purrr_0.2.3tidyr_0.7.1magrittr_1.5   
>
> [34] reshape2_1.4.2 ggplot2_2.2.1  scales_0.5.0   
>
> [37] matrixStats_0.52.2 htmltools_0.3.6
> BiocGenerics_0.22.0   
> [40] GenomicRanges_1.28.5   SummarizedExperiment_1.6.3 mime_0.5   
>
> [43] xtable_1.8-2   colorspace_1.3-2   httpuv_1.3.5   
>
> [46] stringi_1.1.5  RCurl_1.95-4.8 lazyeval_0.2.0 
>
> [49] munsell_0.4.3 
>
> * Out-of-date packages
>   Package LibPath Installed Built   ReposVer
> rJava "rJava" "/usr/local/lib/R/site-library" "0.9-8"   "3.2.3" "0.9-8" 
>   Repository
> rJava "https://cran.rstudio.com/src/contrib;
>
> update with biocLite()
>
> Error: 1 package(s) out of date
>
> The same example works on another computer using Windows operating system. 
> What's the issue with this Linux environment?
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___

Re: [Bioc-devel] test coverage of a shiny app

[Marcel Ramos]

Hi Sam,
This is a pertinent issue to shiny app development and there are continuing
efforts to create unit tests for shiny applications.

At the moment, there is a package dedicated to providing tests for shiny
applications but it has not been published.
See: https://github.com/rstudio/shinytest

This link may also provide some testing examples:
https://cran.r-project.org/web/packages/RSelenium/vignettes/shinytesting.html

In the meantime, I would advise to simply test the functions and
manipulations that generate the data for your shiny application.
I'm eager to hear other developer's inputs on this subject.

Best regards,
Marcel

On Tue, Apr 11, 2017 at 2:46 AM Samuel Wieczorek 
wrote:

> Hi
>
> I am the developer of the packages Prostar ad DAPAR and I would like to
> write some unit test for Prostar which contains a Shiny application. I
> wrote a test script in the 'test' directory where I am using functions
> from the shiytest package but I don't know how to really test my app
> (Prostar()). And then, the result of packages_coverage is still equal to
> 0%.
>
> Is there anyone who has already developed a Shiny app with unit tests ?
> I would appreciate some examples.
>
>
> Thanks in advance
>
>
> Sam
>
>
> --
> *Samuel Wieczorek
>
> Etude de la Dynamique des Protéomes (EDyP)*
> *Laboratoire Biologie à Grande Echelle (BGE)*
> *U1038 INSERM / CEA / UGA*
> *Biosciences and Biotechnology Institute of Grenoble (BIG)*
> *CEA / Grenoble*
> *17 avenue des Martyrs*
> *F-38054 Grenoble Cedex 9*
> */Tél. : 04.38.78.44.14/*
> */Fax : 04.38.78.50.51/*
>
> http://www.edyp.fr/
>
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>
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Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Marcel Ramos]

Hi Sokratis,

You can resolve this issue by moving `SummarizedExperiment` to the 
Suggests field and

including a `library(SummarizedExperiment)` call in your vignette.

Best regards,

Marcel


On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis 
<s.kario...@sheffield.ac.uk <mailto:s.kario...@sheffield.ac.uk>> wrote:

Hey,

I have submitted the package pathprintGEOData, which got accepted,
but the
build/check report is now producing the following error:



*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics:  chunk 1 Error in assays(result) : could not find function
"assays"*

*assays *is a function from the SummarizedExperiment package which I
have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?

Thank you for any help on the matter!

-Sokratis

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-- 
Marcel Ramos
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Re: [Bioc-devel] SVN repo and git mirror for accepted package

[Marcel Ramos]

Hi Lukas,

You will be receiving SVN credentials soon for upload.
Please expect a message from Martin Morgan.

Regards,
Marcel

On Sat, Oct 15, 2016 at 10:02 AM Lukas Weber  wrote:

> Hi,
>
> Is there anything we need to do to set up the svn repository and git mirror
> for new packages accepted last week? The issue in the GitHub contributions
> repo for our package is closed/accepted (
> https://github.com/Bioconductor/Contributions/issues/128), but the git
> mirror repo isn't there yet (nothing at
> https://github.com/bioconductor-mirror/regsplice or in the build results
> list at https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/). Just
> checking in case I missed something.
>
> Best regards,
> Lukas
>
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>
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Re: [Bioc-devel] "Feature-freeze" deadline for new packages

[Marcel Ramos]

Hi Lukas,
We've been backlogged with package reviews. Your package has been assigned
to me and I will get to your package as soon as possible.

Yes, you will have time to address recommendations/requirements that may
arise during the package review process.

The deadline for package approval is October 12. I will get to it much
sooner.

Regards,
Marcel Ramos
Bioconductor Core Team

On Fri, Sep 30, 2016 at 9:50 AM Lukas Weber <lukmwe...@gmail.com> wrote:

Hi,

I submitted a new package last week, which passed all the checks, but I
haven't heard anything else back since then.

I wanted to confirm how the feature-freeze deadline next week (Friday Oct
7) will work for new packages. If we receive review comments next week,
will there still be some time to address these, either before or after the
feature-freeze deadline? Or will this be too late for the current release?

I would also be grateful for any advice if there is anything further we can
do to assist with the review process. A link to the package/issue is here
(package name "regsplice"):
https://github.com/Bioconductor/Contributions/issues/128

Thanks also for providing all the detailed submission guidelines on the
Bioconductor website -- this was very helpful for preparing our package.

Best regards,
Lukas

Lukas Weber
PhD student
University of Zurich, Switzerland

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