Re: [Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

[James Perkins]

Thanks I didn't know about the mouseover hint! It appears that this 
package (miRBaseConverter) is failing the check on linux:


https://bioconductor.org/checkResults/3.18/bioc-LATEST/miRBaseConverter/

Leading to the red light ExpHunterSuite on the linux build only:

https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/

However, what I'm not sure about - is this unavailable dependency the 
reason why the landing page for ExpHunterSuite does not show the 
vignette or source code?


https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html

Or could it be another factor?

Jim

On 2023-11-13 12:08, Martin Grigorov wrote:

Hi,

If you hover over the red LED you will see the following hint: NO,
package depends on 'miRBaseConverter' which is not available"

Regards,
Martin

On Mon, Nov 13, 2023 at 11:31 AM James Perkins 
wrote:


Hi,

I am the maintainer of the Workflow package ExpHunterSuite.

In the build report for the release branch, 3.18, my build and
install
status are green-OK.

However, I have a red LED for Package Propagation. How can I tell
what's
gone wrong, and how could I fix it?



https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/


I've had a look through the documentation and the nearest I've found

was: "propagation is still determined by the results of the nightly
builds." - but I cannot find/workout the relevant section in the
output
of the nightly build report that is related to propagation status.

The landing page of the package is not showing the documentation
(vignette etc.), or letting me download the package source.



https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html


I suspect this is related, because the devel version of the package
IS
showing blue propagation status, and IS showing the
documentation/package source etc.



https://bioconductor.org/packages/3.19/workflows/html/ExpHunterSuite.html


Cheers!

Jim

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[Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

[James Perkins]

Hi,

I am the maintainer of the Workflow package ExpHunterSuite.

In the build report for the release branch, 3.18, my build and install 
status are green-OK.


However, I have a red LED for Package Propagation. How can I tell what's 
gone wrong, and how could I fix it?


https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/

I've had a look through the documentation and the nearest I've found 
was: "propagation is still determined by the results of the nightly 
builds." - but I cannot find/workout the relevant section in the output 
of the nightly build report that is related to propagation status.


The landing page of the package is not showing the documentation 
(vignette etc.), or letting me download the package source.


https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html

I suspect this is related, because the devel version of the package IS 
showing blue propagation status, and IS showing the 
documentation/package source etc.


https://bioconductor.org/packages/3.19/workflows/html/ExpHunterSuite.html

Cheers!

Jim

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Re: [Bioc-devel] devel builds are down

[James Perkins]

Great, thanks for letting me know

Cheers

Jim

On Fri, 26 Mar 2021, 17:56 Hervé Pagès,  wrote:

> Hi Jim,
>
> Workflow builds are back (Linux only for now):
>
>https://bioconductor.org/checkResults/3.13/workflows-LATEST/
>
> Cheers,
> H.
>
>
> On 3/24/21 12:31 PM, James Perkins wrote:
> > Thanks for the info Hervé,
> >
> > Has the workflow build been affected? There appears to have been no
> > build since last Tuesday, I understand there *should* have been one last
> > night:
> >
> > https://bioconductor.org/checkResults/3.13/workflows-LATEST/
> > <https://bioconductor.org/checkResults/3.13/workflows-LATEST/>
> >
> > Cheers,
> >
> > Jim
> >
> >
> >
> > On Wed, 24 Mar 2021 at 19:25, Hervé Pagès  > <mailto:hpages.on.git...@gmail.com>> wrote:
> >
> > The devel builds are up and running again, with nebbiolo1 instead of
> > rex3:
> >
> > https://bioconductor.org/checkResults/3.13/bioc-LATEST/
> > <https://bioconductor.org/checkResults/3.13/bioc-LATEST/>
> >
> > The fate of rex3 is still unclear.
> >
> > Cheers,
> > H.
> >
> >
> > On 3/19/21 1:56 PM, Hervé Pagès wrote:
> >  > Hi maintainers,
> >  >
> >  > If you've not noticed already, the build report for the BioC 3.13
> > builds
> >  > (devel builds) didn't get updated for the last 3 days:
> >  >
> >  > https://bioconductor.org/checkResults/3.13/bioc-LATEST/
> > <https://bioconductor.org/checkResults/3.13/bioc-LATEST/>
> >  >
> >  > This is unusual. The reason is that our build machine rex3 has
> been
> >  > experiencing connectivity issues that have prevented the daily
> > builds
> >  > from running normally. The problem is being investigated and we'll
> >  > provide updates here as the situation evolves.
> >  >
> >  > Thanks for your patience and sorry for the inconvenience.
> >  >
> >  > H.
> >  >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
> >
> > ___
> > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing
> list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >
> >
> >
> > --
> > James R Perkins PhD
> > Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
> > Department of Molecular Biology and Biochemistry
> > <https://goo.gl/maps/UCLQXZLR2W12>
> > Science Faculty, University of Malaga
> > 29071 Malaga, Spain
> >
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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Re: [Bioc-devel] devel builds are down

[James Perkins]

Thanks for the info Hervé,

Has the workflow build been affected? There appears to have been no build
since last Tuesday, I understand there *should* have been one last night:

https://bioconductor.org/checkResults/3.13/workflows-LATEST/

Cheers,

Jim



On Wed, 24 Mar 2021 at 19:25, Hervé Pagès 
wrote:

> The devel builds are up and running again, with nebbiolo1 instead of rex3:
>
>https://bioconductor.org/checkResults/3.13/bioc-LATEST/
>
> The fate of rex3 is still unclear.
>
> Cheers,
> H.
>
>
> On 3/19/21 1:56 PM, Hervé Pagès wrote:
> > Hi maintainers,
> >
> > If you've not noticed already, the build report for the BioC 3.13 builds
> > (devel builds) didn't get updated for the last 3 days:
> >
> >https://bioconductor.org/checkResults/3.13/bioc-LATEST/
> >
> > This is unusual. The reason is that our build machine rex3 has been
> > experiencing connectivity issues that have prevented the daily builds
> > from running normally. The problem is being investigated and we'll
> > provide updates here as the situation evolves.
> >
> > Thanks for your patience and sorry for the inconvenience.
> >
> > H.
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
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>


-- 
James R Perkins PhD
Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
Department of Molecular Biology and Biochemistry

Science Faculty, University of Malaga
29071 Malaga, Spain

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Re: [Bioc-devel] Recently accepted package not appearing in nightly builds

[James Perkins]

OK that makes sense - apologies, it stated in the issue that "Your package
will be included in the next nigthly 'devel' build" and I misinterpreted.

Thanks for clarifying!

Cheers

On Tue, 23 Mar 2021 at 11:40, Kern, Lori 
wrote:

> Your package was identified as a workflow package based you the biocViews
> you selected.  The workflow packages did not build last Friday and next run
> is today.  You should check the following page for your workflow package
> build results:
>
> http://bioconductor.org/checkResults/3.13/workflows-LATEST/
>
> Cheers,
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of James
> Perkins 
> *Sent:* Tuesday, March 23, 2021 4:56 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Recently accepted package not appearing in
> nightly builds
>
> Dear all,
>
> I am the maintainer of the package ExpHunterSuite. This was accepted
> thursday, and on Friday (19/03) the issue raised on the
> Bioconductor/contributions github page was closed (ExpHunterSuite #1835,
>
> https://secure-web.cisco.com/1a7OEZThEU5CLG0ISAyz_rsGl1YpZjHKnXob4DK82SC1JJXcRPx9JMXNkXz1BoRbKGnTU16yAlQ5pxjB_ANH8w_aa7enwKmKs4CrPWV2DIRnf64J8C_Lhv0ugJynT40zYGYvnMURwRkKdVkl6VQUN2TV6FOEZMltNMg5KNAYlJYA-Qo5V1d8V364L_NtC7Hs3h53CQMaahEFYbnPZih0SCXCwr7dpQ1B5RgYukVSwcBhhVqp7co3pHFwSf6V0eSwpKYom_kndyBFBm0cyHnhj8_EWY2fkeezxmDUDkxKui2AspIQiJD_QH9Cmzdt23zLx7kPS8OV2mQJmaLyhQWO1rA/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1835
> ).
>
> The last message on the issue thread told me that the package will be
> included in the next nightly build, to keep an eye on the results and that,
> assuming it builds OK, a landing page will be produced. There was also
> information in the message related to git ssh credentials, but I believe
> that is already solved (I have submitted public key and can clone/push/pull
> the git.bioconductor.org repo without problems).
>
> I've checked the nightly build since then, and it would appear that the
> package has not been included. The latest one uses a git snapshot from
> 21/03 so I assume it should be included?
>
> I know that there have been problems with the devel build as per Hervé
> Pagès's email, I don't know if this is affecting things, or if there is
> something else I have to do, like a bump in version number to trigger
> inclusion or something like that?
>
> Thanks in advance for any help.
>
> Jim
> --
> James R Perkins PhD
> Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
> Department of Molecular Biology and Biochemistry
> <
> https://secure-web.cisco.com/1qJv3gjRb73fkHwItMi7qDYMMMWR_A-afmoGmIQqs68gSEM2Yj_7v-FmFl47C8LVnUGRZQk53-KIAamfJbg2MscBbFYmpJLobhN6mPNbBcaCWqvjFnObTga8eBYSGP45GeL1q0GTGkwf2BFbrDJh3w5IoFOS8dtH8icBLzc-u5pMiDV24xOmw3F0vzDpiJwE_3kQ9PeEkxfaCPqcaNR83tVHYdzT90Fi3gczR4cvs-TMLujB-g8QecNVAm2AM0EAT8wd0_Q3uRX3Ts-8YMjjOiLMnbQn9OdpTFKY_8vmJsRg3kOYpbYtQz6DYW0wco7uhuFVqjuZBxzyCggvaCoLEfA/https%3A%2F%2Fgoo.gl%2Fmaps%2FUCLQXZLR2W12
> >
> Science Faculty, University of Malaga
> 29071 Malaga, Spain
>
> [[alternative HTML version deleted]]
>
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-- 
James R Perkins PhD
Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
Department of Molecular Biology and Biochemistry
<https://goo.gl/maps/UCLQXZLR2W12>
Science Faculty, University of Malaga
29071 Malaga, Spain

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[Bioc-devel] Recently accepted package not appearing in nightly builds

[James Perkins]

Dear all,

I am the maintainer of the package ExpHunterSuite. This was accepted
thursday, and on Friday (19/03) the issue raised on the
Bioconductor/contributions github page was closed (ExpHunterSuite #1835,
https://github.com/Bioconductor/Contributions/issues/1835 ).

The last message on the issue thread told me that the package will be
included in the next nightly build, to keep an eye on the results and that,
assuming it builds OK, a landing page will be produced. There was also
information in the message related to git ssh credentials, but I believe
that is already solved (I have submitted public key and can clone/push/pull
the git.bioconductor.org repo without problems).

I've checked the nightly build since then, and it would appear that the
package has not been included. The latest one uses a git snapshot from
21/03 so I assume it should be included?

I know that there have been problems with the devel build as per Hervé
Pagès's email, I don't know if this is affecting things, or if there is
something else I have to do, like a bump in version number to trigger
inclusion or something like that?

Thanks in advance for any help.

Jim
-- 
James R Perkins PhD
Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
Department of Molecular Biology and Biochemistry

Science Faculty, University of Malaga
29071 Malaga, Spain

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Re: [Bioc-devel] Submitted package under review: linux/Mac builds fine, warning generated in windows

[James Perkins]

I managed to fix the warning in Windows by renaming the function, please
disregard my previous email.

Jim

On Mon, 1 Feb 2021 at 15:57, James Perkins  wrote:

> Hi all,
>
> I have a package under review, ExpHunterSuite. I understand that I must
> get the package running with no warnings or errors during the bioconductor
> builds before I can go to the next stage of the submission process.
>
> I have achieved this for the linux and Mac builds -
> http://bioconductor.org/spb_reports/ExpHunterSuite_buildreport_20210201084100.html
>
> However I have the following warning with the Windows check:
>
> * checking whether package 'ExpHunterSuite' can be installed ... WARNING
> Found the following significant warnings:
>   Rd warning: cannot open file
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1835/ExpHunterSuite_20210201081747/ExpHunterSuite.buildbin-libdir/00LOCK-ExpHunterSuite/00new/ExpHunterSuite/help/%:::%.html':
> Invalid argument
> See
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1835/ExpHunterSuite_20210201081747/ExpHunterSuite.Rcheck/00install.out'
> for details.
>
> Doing a bit of digging, it appears this may be related to a known issue
> with the windows server, as described on the bioc-devel mailing list:
> https://marc.info/?l=bioc-devel=160975009013765=4
>
> Which basically states there isn't much that can be done for now and not
> to worry...
>
> I am therefore not sure how to proceed - the warning appears to be due to
> problems outside of my control and does not indicate a major issue with the
> package, however if I don't solve it, the package will not go to the next
> step.
>
> Does anyone have any suggestions?
>
> Kindest regards,
>
> JIm
> --
> James R Perkins PhD
> Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
> Department of Molecular Biology and Biochemistry
> <https://goo.gl/maps/UCLQXZLR2W12>
> Science Faculty, University of Malaga
> 29071 Malaga, Spain
>
>
>

-- 
James R Perkins PhD
Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
Department of Molecular Biology and Biochemistry
<https://goo.gl/maps/UCLQXZLR2W12>
Science Faculty, University of Malaga
29071 Malaga, Spain

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[Bioc-devel] Submitted package under review: linux/Mac builds fine, warning generated in windows

[James Perkins]

Hi all,

I have a package under review, ExpHunterSuite. I understand that I must get
the package running with no warnings or errors during the bioconductor
builds before I can go to the next stage of the submission process.

I have achieved this for the linux and Mac builds -
http://bioconductor.org/spb_reports/ExpHunterSuite_buildreport_20210201084100.html

However I have the following warning with the Windows check:

* checking whether package 'ExpHunterSuite' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file
'C:/Users/pkgbuild/packagebuilder/workers/jobs/1835/ExpHunterSuite_20210201081747/ExpHunterSuite.buildbin-libdir/00LOCK-ExpHunterSuite/00new/ExpHunterSuite/help/%:::%.html':
Invalid argument
See
'C:/Users/pkgbuild/packagebuilder/workers/jobs/1835/ExpHunterSuite_20210201081747/ExpHunterSuite.Rcheck/00install.out'
for details.

Doing a bit of digging, it appears this may be related to a known issue
with the windows server, as described on the bioc-devel mailing list:
https://marc.info/?l=bioc-devel=160975009013765=4

Which basically states there isn't much that can be done for now and not to
worry...

I am therefore not sure how to proceed - the warning appears to be due to
problems outside of my control and does not indicate a major issue with the
package, however if I don't solve it, the package will not go to the next
step.

Does anyone have any suggestions?

Kindest regards,

JIm
-- 
James R Perkins PhD
Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER)
Department of Molecular Biology and Biochemistry

Science Faculty, University of Malaga
29071 Malaga, Spain

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[Rd] S4 plus tab

[James Perkins]

Dear all,

I set a generic s4 funciton, then add a method.

When I do this, I notice that when pressing tab, the arguments to this
method do not appear like they do for generic functions, instead I get an
elipsis.

i.e.

 setClass(batchFile)
[1] batchFile

 setGeneric(Gen1, function(batchFile, ...) standardGeneric(Gen1))
[1] Gen1

 setMethod(Gen1, signature = batchFile, definition =
+ function(batchFile, xxx, yyy, zzz) { return(batchFile) }
+ )
[1] Gen1
 Gen1(
...=batchFile=


Note that xx, yy and zzz are not displayed when pressing tab after Gen1(

contrast that to

 Gen1 - function(batchFile, xxx, yyy, zzz) { return(batchFile) }
 Gen1(
batchFile=  xxx=yyy=zzz=


Is there a way to allow tab to show the extra options? Or has this been
deliberately disabled in order to allow someone to set a number of different
methods with method specific arguments with a single generic?

Many thanks,

Jim
-- 
James Perkins, PhD student
Institute of Structural and Molecular Biology
Division of Biosciences
University College London
Gower Steet
London, WC1E 6BT
UK

email: jperk...@biochem.ucl.ac.uk
phone: 0207 679 2198

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