Re: [Bioc-devel] ERROR in the building report of APAlyzer Dev (1.7.3)
Thanks so much for your explanation!
I will probably wait for the newer version of Rsubreads to fix it.
On Mon, Aug 16, 2021 at 9:16 PM Hervé Pagès
wrote:
> Hi Ruijia,
>
> I think this is due to recent changes to Rsubread. You can actually see
> the same error here for Rsubread:
>
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rsubread/nebbiolo2-buildsrc.html
>
> These recent changes to Rsubread did not propagate yet which makes
> things a little hard to reproduce i.e. you can't just use
> BiocManager::install() to get the latest Rsubread. Instead you need to
> install it directly from git.bioconductor.org
> (https://git.bioconductor.org/packages/Rsubread). This is what the build
> system does.
>
> FWIW the reasons the latest changes to Rsubread didn't propagate yet is
> because the package fails to pass 'R CMD build' and also because the
> changes have not been followed by a version bump. Last version bump was
> on July 6 from 2.7.2 to 2.7.3.
>
> Cheers,
> H.
>
>
> On 15/08/2021 17:24, Ruijia Wang wrote:
> > Hi BioC-devel,
> >
> > I am the author of the Bioconductor package APAlyzer (
> > https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). I
> > current noticed there is an ERROR in the building report of our latest
> dev
> > version (1.7.3) on the page of Bioconductor (
> >
> http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html
> > ).
> >
> >>
> >> * Error: object 'fout_annot' not found** Backtrace:*
> >>
> >> * 1. └─APAlyzer::PASEXP_IPA(...) test_IPA_analysis.R:10:8*
> >> * 2. └─Rsubread::featureCounts(...)** 3.
> └─base::file.remove(fout_annot)*
> >
> >
> > However, I can not repeat this error using R 4.1 and Bioconductor 3.14 on
> > my end with either *R CMD check* or
> *BiocCheck("APAlyzer_1.7.3.tar.gz").* And
> > I don't recall any of the code updating would trigger the error of
> > *base::file.remove()*. Could you help me to figure out how to fix/bypass
> > this issue in the building report of Bioconductor? Thanks in advance!
> >
> > Best,
> > Ruijia
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
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Re: [Bioc-devel] ERROR in the building report of APAlyzer Dev (1.7.3)
Hi,
Just trying to give a following up on this issue, any comments/suggestions
on it? Thanks.
On Sun, Aug 15, 2021 at 8:24 PM Ruijia Wang
wrote:
> Hi BioC-devel,
>
> I am the author of the Bioconductor package APAlyzer (
> https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). I
> current noticed there is an ERROR in the building report of our latest dev
> version (1.7.3) on the page of Bioconductor (
> http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html
> ).
>
>>
>> * Error: object 'fout_annot' not found** Backtrace:*
>>
>> * 1. └─APAlyzer::PASEXP_IPA(...) test_IPA_analysis.R:10:8*
>> * 2. └─Rsubread::featureCounts(...)** 3. └─base::file.remove(fout_annot)*
>
>
> However, I can not repeat this error using R 4.1 and Bioconductor 3.14 on
> my end with either *R CMD check* or *BiocCheck("APAlyzer_1.7.3.tar.gz").* And
> I don't recall any of the code updating would trigger the error of
> *base::file.remove()*. Could you help me to figure out how to fix/bypass
> this issue in the building report of Bioconductor? Thanks in advance!
>
> Best,
> Ruijia
>
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Re: [Bioc-devel] Changing package names
Please reconsider. The names of your packages enter components of a
metadata collection
that must be manually altered by our core development staff to accommodate
package name changes.
While it is easy to change names of entities in programs and local file
systems, our package
ingestion, review, compilation, verification, and distribution system is
delivering resources to
thousands of users around the world every day. We do not have the capacity
to make changes
of this kind for any but the most severe errors of name selection, for
example, employing a name
that is legally forbidden. If this is in fact the case, you will have to
withdraw the package, have
it deprecated, and resubmit under another name. We cannot promise rapid
turnaround for this
process.
Thank you
On Tue, Aug 17, 2021 at 10:40 AM Kramer, Nicole Emma
wrote:
> Hello all,
>
> My submitted package BentoBox and its associated data package BentoBoxData
> have been accepted and were just added to Bioconductor's git repository.
> Unfortunately, my group and I would like to change the names of these
> packages/repositories. What would be the appropriate process to change the
> names of these packages if they are already in Bioconductor's git
> repository?
>
> Thank you,
> Nicole Kramer
>
>
>
> Nicole Kramer
>
> Ph.D. Student in Bioinformatics and Computational Biology
>
> University of North Carolina at Chapel Hill
>
> nekra...@live.unc.edu
>
> [[alternative HTML version deleted]]
>
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>
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Re: [Bioc-devel] CITATION error
Hi Hervé,
Thank you for catching the discrepancy between release and dev builds!
How strange - I usually change dev and release build in sync, so wonder how
that happened.
I updated the file and committed -hopefully it fixes the issue.
Best,Shraddha
On Mon, Aug 16, 2021 at 10:27 PM Hervé Pagès
wrote:
> Hi Shraddha,
>
> Note that we only see this error for the release version of netDx:
>
>https://bioconductor.org/packages/3.13/netDx
>
> The devel version does not have it:
>
>https://bioconductor.org/packages/3.14/netDx
>
> With the release version, I get:
>
>> library(netDx)
>
>
>
>Attaching package: ‘netDx’
>
>
>
>The following object is masked from ‘package:stats’:
>
>
>
> predict
>
>
>> packageVersion("netDx")
>
>[1] ‘1.4.2’
>
>
>
>> citation("netDx")
>
>Error in parse(con) : 18:60: unexpected ','
>
>17:pubmed = "30872331",
>
>18:header = "The netDx algorithm is described in:"),
>
> ^
>
> This confirms that the CITATION file is broken in netDx 1.4.2.
>
> FWIW the diff between the release CITATION and the devel CITATION is:
>
>hpages@spectre:~/$ diff CITATION-release CITATION-devel
>
>1c1
>
>< bibentry(bibtype = "Article",
>
>---
>
>> c(bibentry(bibtype = "Article",
>
>43c43
>
>< )
>
>---
>
>> )
>
>\ No newline at end of file
>
>
> So it looks like you've managed to get the file right in devel (netDx
> 1.5.2) but not in release (netDx 1.4.2).
>
> Cheers,
> H.
>
>
> On 16/08/2021 15:48, Shraddha Pai wrote:
> > Hello BioC community,
> >
> > I've recently added a CITATION file for our package "netDx".
> > The package description page on bioconductor.org shows an error
> > message: Important
> > note to the maintainer of the netDx package: An error occured while
> trying
> > to generate the citation from the CITATION file. This typically occurs
> when
> > the file contains R code that relies on the package to be installed e.g.
> it
> > contains calls to things like packageVersion() or packageDate() instead
> of
> > using meta$Version or meta$Date. See R documentation
> > <
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files
> >
> > for
> > more information.
> >
> > However, when I install the package locally and run citation("netDx"), I
> > get the expected output (see below e-mail).
> >
> > The CITATION file does not make function calls. Here are the contents:
> > c(bibentry(bibtype = "Article",
> > key = "netDx-methods",
> > title = "{netDx: interpretable patient classification using
> > integrated patient similarity networks}",
> > author = c(
> > person("Shraddha", "Pai"),
> > person("Shirley", "Hui"),
> > person("Ruth", "Isserlin"),
> > person(c("Muhammad","A"), "Shah"),
> > person("Hussam","Kaka"),
> > person(c("Gary", "D."), "Bader")
> > ),
> > year = 2019,
> > journal = "Molecular Systems Biology",
> > volume = "15",
> > pages = "e8497",
> > doi = "10.15252/msb.20188497",
> > pubmed = "30872331",
> > header = "The netDx algorithm is described in:"),
> > bibentry(bibtype = "Article",
> > key = "netDx-software",
> > title = "{netDx: Software for building interpretable patient
> > classifiers by multi-'omic data integration using patient similarity
> > networks}",
> > author = c(
> > person("Shraddha", "Pai"),
> > person("Philipp", "Weber"),
> > person("Ruth", "Isserlin"),
> > person("Hussam","Kaka"),
> > person("Shirley", "Hui"),
> > person(c("Muhammad","A"), "Shah"),
> > person("Luca", "Giudice"),
> > person("Rosalba", "Giugno"),
> > person(c("Anne","Krogh"), "Nøhr"),"
> > person("Jan", "Baumbach"),
> > person(c("Gary", "D."), "Bader")
> > ),
> > year = 2021,
> > journal = "F1000Research",
> > volume = "9",
> > pages = "1239",
> > doi = "10.12688/f1000research.26429.2",
> > pubmed = "33628435",
> > header = "The netDx package is described in:")
> >
> > )
> >
> > What can I change to fix the error on the bioconductor page?
> >
> > Thank you,
> > Shraddha
> >
> > Output from running citation("netDx") on a local installation:
> >> citation("netDx")
> >
> > The netDx algorithm is described in:
> >
> > Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD (2019). “netDx:
> > interpretable patient classification using integrated patient
> > similarity networks.” _Molecular Systems Biology_, *15*, e8497. doi:
> > 10.15252/msb.20188497 (URL: https://doi.org/10.15252/msb.20188497).
>
[Bioc-devel] Changing package names
Hello all, My submitted package BentoBox and its associated data package BentoBoxData have been accepted and were just added to Bioconductor's git repository. Unfortunately, my group and I would like to change the names of these packages/repositories. What would be the appropriate process to change the names of these packages if they are already in Bioconductor's git repository? Thank you, Nicole Kramer Nicole Kramer Ph.D. Student in Bioinformatics and Computational Biology University of North Carolina at Chapel Hill nekra...@live.unc.edu [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
