Re: [Bioc-devel] compilation of a package

2023-05-22 Thread Kern, Lori 
This has been answered on slack.  
https://community-bioc.slack.com/archives/C35G93GJH/p1684487953056909
Please try not to post the same question in multiple locations so answers can 
be consolodated.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Franck RICHARD 

Sent: Friday, May 19, 2023 7:14 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] compilation of a package

Hello,


I have just finished writing a new package for bioconductor that should
work with Cuda and c++ code. The problem is that the package requires
the installation of many development suites (cuda devtools, Rtools, MSVC
compilations tools) under Windows and the compilation time under Windows
is important (15 minutes or more). I am afraid that this discourages
many people. Also, I would like to provide the Windows executables
directly in the package...

Under linux, the compilation seems to me unavoidable because of the risk
of incompatibility with the libc library...

Is it possible to indicate a compilation under linux and no compilation
under windows in the DESCRIPTION file or should I make two different
packages?

Thanks for your help!

Franck

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Re: [Bioc-devel] No vignette

2023-05-22 Thread Kern, Lori 
The new version doesn't propagate because a dependent package is unavailable.  
If you look on
http://bioconductor.org/checkResults/devel/bioc-LATEST/IsoformSwitchAnalyzeR/
There is a red radio button that if you hoover over, can see more details.  If 
a version cannot be installed by the general community it will not propagate. 
This can happen if a dependency can be installed but is failing in build/check.




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Kristoffer 
Vitting-Seerup 
Sent: Monday, May 22, 2023 5:47 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] No vignette

Hi

I finally have the devel version of my R package IsoformSwitchAnalyzeR
working (sorry I did not make it before the 1.17 release, but a new
dependency was only approved last second).

But now the devel version

does not seem to have a vignette. Does anybody have an idea why that is?
The vignette seems to be build and work during the automated checks.


Once that is fixed I'll push the devel changes into the main branch to have
IsoformSwitchAnalyzeR working again.

--
Cheers
Kristoffer

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Re: [Bioc-devel] rifiComparative

2023-05-22 Thread Vincent Carey 
In RELEASE_3_17 branch your vignette has

devtools::load_all(".")

I don't know why that would be necessary.   1.0.0 in the RELEASE_3_17
branch does not have devtools in Suggests.

On Sun, May 21, 2023 at 3:53 PM Loubna Youssar  wrote:

> Hello,
>
> I am the developer and maintainer of rifiComparative package. I was
> notified by an error and I fixed it then pushed three weeks ago.
> To my surprise I did get the same error with the last package version some
> days ago. This would mean the push did not work even I do remember no error
> was displayed. How can I be sure that my updated package with no error was
> successfully pushed? am I supposed to receive a confirmatory email?
>
> Here is the new version:
>
> Package: rifiComparative
> Title: 'rifiComparative' compares the output of rifi from two different
> conditions.
> Version: 1.1.1
>
> The error sent:
>
> Package: rifiComparative
> Version: 1.0.0
> Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check
> --install=check:rifiComparative.install-out.txt
> --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings
> rifiComparative_1.0.0.tar.gz
> StartedAt: 2023-05-20 00:15:11 -0400 (Sat, 20 May 2023)
> EndedAt: 2023-05-20 00:26:00 -0400 (Sat, 20 May 2023)
> EllapsedTime: 649.2 seconds
> RetCode: 1
> Status:   ERROR
> CheckDir: rifiComparative.Rcheck
> Warnings: NA
>
> Thanks in advance for your assistance
>
> Loubna
>
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>
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Re: [Bioc-devel] rifiComparative

2023-05-22 Thread Sarvesh Nikumbh 
Hi Loubna,

Was the error in release or the devel version?

Devel version report:
http://bioconductor.org/checkResults/3.18/bioc-LATEST/rifiComparative/
Release version report:
http://bioconductor.org/checkResults/release/bioc-LATEST/rifiComparative/

Perhaps, your push was to the devel version and resolved the error there?

Additionally, if you check the error, it is regarding package devtools'
(un)availability. Please note that using `devtools::load_all()` is not
recommended in the vignette. You should instead load your package by using
`library()` as anyone else (the end user) would do at their end.

Finally, you can always check whether your last commits were successfully
picked at two places: the build reports (links above) or also at
https://code.bioconductor.org/browse/

Hope this helps.

Best wishes,
  Sarvesh



On Sun, 21 May 2023 at 20:53, Loubna Youssar  wrote:

> Hello,
>
> I am the developer and maintainer of rifiComparative package. I was
> notified by an error and I fixed it then pushed three weeks ago.
> To my surprise I did get the same error with the last package version some
> days ago. This would mean the push did not work even I do remember no error
> was displayed. How can I be sure that my updated package with no error was
> successfully pushed? am I supposed to receive a confirmatory email?
>
> Here is the new version:
>
> Package: rifiComparative
> Title: 'rifiComparative' compares the output of rifi from two different
> conditions.
> Version: 1.1.1
>
> The error sent:
>
> Package: rifiComparative
> Version: 1.0.0
> Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check
> --install=check:rifiComparative.install-out.txt
> --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings
> rifiComparative_1.0.0.tar.gz
> StartedAt: 2023-05-20 00:15:11 -0400 (Sat, 20 May 2023)
> EndedAt: 2023-05-20 00:26:00 -0400 (Sat, 20 May 2023)
> EllapsedTime: 649.2 seconds
> RetCode: 1
> Status:   ERROR
> CheckDir: rifiComparative.Rcheck
> Warnings: NA
>
> Thanks in advance for your assistance
>
> Loubna
>
> [[alternative HTML version deleted]]
>
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-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

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[Bioc-devel] No vignette

2023-05-22 Thread Kristoffer Vitting-Seerup 
Hi

I finally have the devel version of my R package IsoformSwitchAnalyzeR
working (sorry I did not make it before the 1.17 release, but a new
dependency was only approved last second).

But now the devel version

does not seem to have a vignette. Does anybody have an idea why that is?
The vignette seems to be build and work during the automated checks.


Once that is fixed I'll push the devel changes into the main branch to have
IsoformSwitchAnalyzeR working again.

-- 
Cheers
Kristoffer

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