Re: [Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

[Rainer Johannes]

thanks to all for the explanations and feedback.

I'll reach out to the respective developers of these packages - hoping they 
respond and fix the issue timely.

cheers, jo

---
Johannes Rainer, PhD

Eurac Research
Institute for Biomedicine
Via A.-Volta 21, I-39100 Bolzano, Italy

email: johannes.rai...@eurac.edu
github: jorainer
mastodon: jorai...@fosstodon.org


Henrik Bengtsson wrote:


On Tue, Apr 4, 2023 at 2:44 AM Oleksii Nikolaienko
 wrote:
>
> Hi,
> maybe because BiocStyle is not listed as a dependency or suggested package
> in DESCRIPTION?
> More info here: 
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FBBS%2Fissues%2F248=05%7C01%7CJohannes.Rainer%40eurac.edu%7C7f8025a59146452919e608db352cd516%7C9251326703e3401a80d4c58ed6674e3b%7C0%7C0%7C638162238900423325%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=LSP5cavXgWpEbry0Azlho7aDmxSigh%2BtlvR2e95Q%2BtM%3D=0

Yes, this is why. The package needs 'BiocStyle' to build the vignette,
and therefore it needs to be declared. Some other packages forgot to
declare 'RUnit' needed for the unit tests. We'll also see packages
that rely on non-declared annotation packages. These new checks were
introduced for Bioc devel(*) checks and aligns with how this already
works on CRAN since a long time.

(*) I'm not 100% sure, but I believe the reason you only see it on the
Linux server is that that's the only one that runs 'R CMD check' on
vignettes. Checking vignettes takes time, so the decision was to do
that only one platform. Since 'BiocStyle' is only involved for
vignettes, this is why that particular package gets flagged only
there.  Packages that forgot to add 'RUnit' to suggests, will get an
error on all platforms.

Adding 'BiocStyle' to Suggests: in the package DESCRIPTION file solves
this problem.

/Henrik


>
> Best,
> Oleksii
>
> On Tue, 4 Apr 2023 at 11:22, Rainer Johannes 
> wrote:
>
> > Dear all,
> >
> > I'm continuing to see some strange dependency problems for packages on the
> > linux build system for Bioconductor 3.17. First time I've seen them where
> > on the build report for snapshot 2023-03-31, and they are still there for
> > snapshot date 2023-04-02 (build report from 2023-04-03). What I've seen so
> > far is that most are related to `BiocStyle` missing.
> >
> > Some examples are:
> > - ROC (missing BiocStyle)
> > - SCATE (missing BiocStyle)
> > - SC3 (missing BiocStyle)
> > - scTHI (missing BiocStyle)
> >
> > Since they are only present on the linux build system - maybe that's
> > something related to the setup on that particular server? Or the R version
> > used there does not properly get all dependencies of packages?
> >
> > cheers, jo
> >
> > ---
> > Johannes Rainer, PhD
> >
> > Eurac Research
> > Institute for Biomedicine
> > Via A.-Volta 21, I-39100 Bolzano, Italy
> >
> > email: johannes.rai...@eurac.edu
> > github: jorainer
> > mastodon: jorai...@fosstodon.org
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel=05%7C01%7CJohannes.Rainer%40eurac.edu%7C7f8025a59146452919e608db352cd516%7C9251326703e3401a80d4c58ed6674e3b%7C0%7C0%7C638162238900423325%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=D8tGLU94VNZPzgJXFAIX%2BGRNPbHJHDJVq%2FNn57Ts1vU%3D=0
> >
>
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Re: [Bioc-devel] EXTERNAL: Re: Bad description file

[matine rb]

Thank you all for the help. I corrected the DESCRIPTION file and bump the
version.

Thank you,
Matineh Rahmatbakhsh

On Tue, Apr 4, 2023 at 1:50 PM Ramos Perez, Marcel <
marcel.ramospe...@roswellpark.org> wrote:

> Thank you Martin for providing the link.
>
> I misread the changes on the release branch.
> It looks like the DESCRIPTION file should be modified by removing the
> merge commit tag and
> following the bug fix instructions here:
>
>
> https://contributions.bioconductor.org/git-version-control.html?q=bug#bug-fix-in-release-and-devel
>
> Marcel
>
> On 4/4/23 3:34 PM, Martin Morgan wrote:
>
> The release version DESCRIPTION file is malformed, because it contains a
> (partial) merge commit tag
>
> https://code.bioconductor.org/browse/HPiP/blob/RELEASE_3_16/DESCRIPTION#L69
>
> Martin
>
> From: Bioc-devel  bioc-devel-boun...@r-project.org> on behalf of matine rb <
> matinerb...@gmail.com>
> Date: Tuesday, April 4, 2023 at 3:00 PM
> To: bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> Subject: [Bioc-devel] Bad description file
> Dear Bioc team
>
> I am the maintainer of the HPiP package which is currently showing unknown
> on the build report on the landing page.
>
> I would appreciate it if you could please help with this matter.
>
> Thank you,
> Matineh Rahmatbakhsh
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>
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>
> ___
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>
>
> ---
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> 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
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Re: [Bioc-devel] EXTERNAL: Re: Bad description file

[Ramos Perez, Marcel]

Thank you Martin for providing the link.

I misread the changes on the release branch.
It looks like the DESCRIPTION file should be modified by removing the merge 
commit tag and
following the bug fix instructions here:

https://contributions.bioconductor.org/git-version-control.html?q=bug#bug-fix-in-release-and-devel

Marcel

On 4/4/23 3:34 PM, Martin Morgan wrote:

The release version DESCRIPTION file is malformed, because it contains a 
(partial) merge commit tag

https://code.bioconductor.org/browse/HPiP/blob/RELEASE_3_16/DESCRIPTION#L69

Martin

From: Bioc-devel 
 on 
behalf of matine rb 
Date: Tuesday, April 4, 2023 at 3:00 PM
To: bioc-devel@r-project.org 

Subject: [Bioc-devel] Bad description file
Dear Bioc team

I am the maintainer of the HPiP package which is currently showing unknown
on the build report on the landing page.

I would appreciate it if you could please help with this matter.

Thank you,
Matineh Rahmatbakhsh

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---
Marcel Ramos
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] Bad description file

[Martin Morgan]

The release version DESCRIPTION file is malformed, because it contains a 
(partial) merge commit tag

https://code.bioconductor.org/browse/HPiP/blob/RELEASE_3_16/DESCRIPTION#L69

Martin

From: Bioc-devel  on behalf of matine rb 

Date: Tuesday, April 4, 2023 at 3:00 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bad description file
Dear Bioc team

I am the maintainer of the HPiP package which is currently showing unknown
on the build report on the landing page.

I would appreciate it if you could please help with this matter.

Thank you,
Matineh Rahmatbakhsh

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Re: [Bioc-devel] EXTERNAL: Bad description file

[Ramos Perez, Marcel]

Hi Matineh,

It looks like there was some extra text in the DESCRIPTION at commit 83ab252 : 
>>> 509b8e4 (version bump)

The next build of the release branch will happen tomorrow. It should be cleared 
up by then based on the changes you've made.

Best regards,

Marcel

On 4/4/23 2:59 PM, matine rb wrote:

Dear Bioc team

I am the maintainer of the HPiP package which is currently showing unknown
on the build report on the landing page.

I would appreciate it if you could please help with this matter.

Thank you,
Matineh Rahmatbakhsh

[[alternative HTML version deleted]]

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


This email message may contain legally privileged and/or confidential 
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[Bioc-devel] Bad description file

[matine rb]

Dear Bioc team

I am the maintainer of the HPiP package which is currently showing unknown
on the build report on the landing page.

I would appreciate it if you could please help with this matter.

Thank you,
Matineh Rahmatbakhsh

[[alternative HTML version deleted]]

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[Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

[Aditya Bhagwat via Bioc-devel]

Dear BioC team,

I am having the same error as many others (the missing BiocStyle  
issue) and I wanted to fix it. But I somehow am not getting into  
git.bioconductor.org anymore :


$ git fetch --all
Fetching origin
Fetching upstream
ssh: connect to host git.bioconductor.org port 22: Connection timed out
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

I checked BiocCredentials and my public key is visible there.

What else could this be ? I changed institutes since my last push, in  
my current setup things go through a proxyserver, could that be the  
reason?


Thank you for feedback.

Aditya


--
Aditya Bhagwat
Statistics ∙ Bioinformatics ∙ Data Science
Translational Proteomics ∙ Philipps-University Marburg
Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
Tel.: +49 6421 28 27403

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Re: [Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

[Henrik Bengtsson]

On Tue, Apr 4, 2023 at 2:44 AM Oleksii Nikolaienko
 wrote:
>
> Hi,
> maybe because BiocStyle is not listed as a dependency or suggested package
> in DESCRIPTION?
> More info here: https://github.com/Bioconductor/BBS/issues/248

Yes, this is why. The package needs 'BiocStyle' to build the vignette,
and therefore it needs to be declared. Some other packages forgot to
declare 'RUnit' needed for the unit tests. We'll also see packages
that rely on non-declared annotation packages. These new checks were
introduced for Bioc devel(*) checks and aligns with how this already
works on CRAN since a long time.

(*) I'm not 100% sure, but I believe the reason you only see it on the
Linux server is that that's the only one that runs 'R CMD check' on
vignettes. Checking vignettes takes time, so the decision was to do
that only one platform. Since 'BiocStyle' is only involved for
vignettes, this is why that particular package gets flagged only
there.  Packages that forgot to add 'RUnit' to suggests, will get an
error on all platforms.

Adding 'BiocStyle' to Suggests: in the package DESCRIPTION file solves
this problem.

/Henrik


>
> Best,
> Oleksii
>
> On Tue, 4 Apr 2023 at 11:22, Rainer Johannes 
> wrote:
>
> > Dear all,
> >
> > I'm continuing to see some strange dependency problems for packages on the
> > linux build system for Bioconductor 3.17. First time I've seen them where
> > on the build report for snapshot 2023-03-31, and they are still there for
> > snapshot date 2023-04-02 (build report from 2023-04-03). What I've seen so
> > far is that most are related to `BiocStyle` missing.
> >
> > Some examples are:
> > - ROC (missing BiocStyle)
> > - SCATE (missing BiocStyle)
> > - SC3 (missing BiocStyle)
> > - scTHI (missing BiocStyle)
> >
> > Since they are only present on the linux build system - maybe that's
> > something related to the setup on that particular server? Or the R version
> > used there does not properly get all dependencies of packages?
> >
> > cheers, jo
> >
> > ---
> > Johannes Rainer, PhD
> >
> > Eurac Research
> > Institute for Biomedicine
> > Via A.-Volta 21, I-39100 Bolzano, Italy
> >
> > email: johannes.rai...@eurac.edu
> > github: jorainer
> > mastodon: jorai...@fosstodon.org
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] BIoconductor 3.16 Code Freeze

[Kern, Lori]

The Code Freeze for the current Bioconductor 3.16 Release is next Monday April 
10, 2023.  After this date there will be no changes to the code on this branch; 
this includes bug fixes or hot fixes.  If your package is failing on the 
release build report,  this weekend will be your last chance ever to update the 
code on RELEASE_3_16 branch of Bioconductor.

Software Report:
https://bioconductor.org/checkResults/3.16/bioc-LATEST/

Experiment Data Report:
https://bioconductor.org/checkResults/3.16/data-experiment-LATEST/

Workflow Report:
https://bioconductor.org/checkResults/3.16/workflows-LATEST/

We appreciate everyone's' continued contributions to Bioconductor.

For clarification: Everyone can still commit changes to the devel branch for 
the upcoming Bioconductor 3.17 release. This freeze only applies to the 
RELEASE_3_16 branch.  We ask that changes on the devel branch are limited to 
ERROR correction only; no API or major changes to packages as of today.  The 
master branch is now consider the release candidate branch for release 3.17.


Cheers,




Lori Shepherd - Kern

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 
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Re: [Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

[Oleksii Nikolaienko]

Hi,
maybe because BiocStyle is not listed as a dependency or suggested package
in DESCRIPTION?
More info here: https://github.com/Bioconductor/BBS/issues/248

Best,
Oleksii

On Tue, 4 Apr 2023 at 11:22, Rainer Johannes 
wrote:

> Dear all,
>
> I'm continuing to see some strange dependency problems for packages on the
> linux build system for Bioconductor 3.17. First time I've seen them where
> on the build report for snapshot 2023-03-31, and they are still there for
> snapshot date 2023-04-02 (build report from 2023-04-03). What I've seen so
> far is that most are related to `BiocStyle` missing.
>
> Some examples are:
> - ROC (missing BiocStyle)
> - SCATE (missing BiocStyle)
> - SC3 (missing BiocStyle)
> - scTHI (missing BiocStyle)
>
> Since they are only present on the linux build system - maybe that's
> something related to the setup on that particular server? Or the R version
> used there does not properly get all dependencies of packages?
>
> cheers, jo
>
> ---
> Johannes Rainer, PhD
>
> Eurac Research
> Institute for Biomedicine
> Via A.-Volta 21, I-39100 Bolzano, Italy
>
> email: johannes.rai...@eurac.edu
> github: jorainer
> mastodon: jorai...@fosstodon.org
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>

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[Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

[Rainer Johannes]

Dear all,

I'm continuing to see some strange dependency problems for packages on the 
linux build system for Bioconductor 3.17. First time I've seen them where on 
the build report for snapshot 2023-03-31, and they are still there for snapshot 
date 2023-04-02 (build report from 2023-04-03). What I've seen so far is that 
most are related to `BiocStyle` missing.

Some examples are:
- ROC (missing BiocStyle)
- SCATE (missing BiocStyle)
- SC3 (missing BiocStyle)
- scTHI (missing BiocStyle)

Since they are only present on the linux build system - maybe that's something 
related to the setup on that particular server? Or the R version used there 
does not properly get all dependencies of packages?

cheers, jo

---
Johannes Rainer, PhD

Eurac Research
Institute for Biomedicine
Via A.-Volta 21, I-39100 Bolzano, Italy

email: johannes.rai...@eurac.edu
github: jorainer
mastodon: jorai...@fosstodon.org


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