Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

[Martin Morgan]

It's likely failing because your package has C source code that accesses memory 
in an invalid way. Likely the bug is present on all platforms, but only 
apparent, for the tests you have written, on Windows. The right thing to do is 
to fix the bug, rather than avoid by not running on the troublesome platform.

Under Linux you'd likely have success with valgrind or UBSAN; if you were 
reasonably confident that the package occurred in unit tests, and you have a 
script to run the unit tests run_tests.R then something like

  R -d valgrind -f run_tests.R

may be productive. valgrind is slow so it pays to narrow the problem down as 
much as possible.

Maartin

On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" 
 wrote:


 I have a package which randomly segfaults when running my unit 
tests only on windows i386, but never on x64, or any other OS. I can't 
imagine there are many out there still running i386 systems are there? 
Is it possible to just disable the i386 build on bioconductor so that 
the tests are not run on that architecture?

 I have of course done my best to debug the issue, but all I get is 
an error in some nt dll file, with no useful message or location. I'm I 
Linux guy, I don't know how to do the in-depth debugging that would be 
required to track this bug down on windows. I tried disabling each test 
one by one to see which one caused the crash, but as is typical with 
segfaults, changing the setup can mask the bug even when the bad code is 
still be executed. Each test runs fine in isolation.

Thanks

Kevin

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[Bioc-devel] List of Deprecated Package Bioc 3.13

[Kern, Lori]

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. This is the current list 
of deprecated packages for Bioc 3.13 :

Maintainer requested deprecation:

Software:

BiocCaseStudies
RchyOptimyx
RNAither
SAGx
yaqcaffy

Experiment Data:

ceu1kg
ceu1kgv
ceuhm3
cgdv17
dsQTL
hmyriB36
yri1kgv


Workflow:

eQTL


Unresponsive/not-maintained packages:

Software:

AffyExpress
affyQCReport
ArrayTools
bigmemoryExtras
CexoR
CrossICC
CoRegFlux
DBChIP
dexus
EasyqpcR
EDDA
ELBOW
genoset
Imetagene
mdgsa
OutlierD
pcot2
Polyfit
POST
proFIA
RDAVIDWebService
RNAprobR
rnaSeqMap
samExploreR
seqplots
SSPA


Experiment Data:

facsDorit
gskb
JctSeqData
plasFIA

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

Previously listed as deprecated but have been undeprecated:

ExperimentData

DmelSGI
RNAinteractMAPK
sampleClassifierData

Software

APAlyzer
metagene2
sampleClassifier


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] is it possible to disable i386 builds on bioconductor

[Kevin Horan]

    I have a package which randomly segfaults when running my unit 
tests only on windows i386, but never on x64, or any other OS. I can't 
imagine there are many out there still running i386 systems are there? 
Is it possible to just disable the i386 build on bioconductor so that 
the tests are not run on that architecture?


    I have of course done my best to debug the issue, but all I get is 
an error in some nt dll file, with no useful message or location. I'm I 
Linux guy, I don't know how to do the in-depth debugging that would be 
required to track this bug down on windows. I tried disabling each test 
one by one to see which one caused the crash, but as is typical with 
segfaults, changing the setup can mask the bug even when the bad code is 
still be executed. Each test runs fine in isolation.


Thanks

Kevin

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Re: [Bioc-devel] Change maintainer email

[Jakob Willforss]

Hi,


I am the maintainer of the Bioconductor package NormalyzerDE.


My previous maintainer email (this one) will be inactivated in a month, and am 
thus changing the maintainer email to 'jakob.willfo...@hotmail.com'.


I am walking through the following four-step procedure as outlined by a 
previous post found when googling 
(https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015123.html):

* bioc-devel mailing list through
https://stat.ethz.ch/mailman/options/bioc-devel
* The BioC user support website through "edit my profile" (in my case
https://support.bioconductor.org/u/edit/6526/)
* a request to the bioc-devel for updating the maintainer email for
the related packages (for git?)
* updating the DESCRIPTION file in the release and devel branches of
all the packages the email is listed in

I am unsure about the third step - if needed, I would like to request the 
update of the maintainer emai.


Do I need to take any further actions to finalize updating the maintainer?


Thanks!


Best wishes,

Jakob Willforss


From: Jakob Willforss
Sent: Sunday, February 7, 2021 4:42:24 PM
To: maintai...@bioconductor.org
Cc: Fredrik Levander; jakob.willfo...@hotmail.com
Subject: Change maintainer email


Hi,


I am the maintainer of the Bioconductor package NormalyzerDE.


My previous maintainer email (this one) will be inactivated in a month, and am 
thus changing the maintainer email to 'jakob.willfo...@hotmail.com'.


I am walking through the following four-step procedure as outlined by a 
previous post found when googling 
(https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015123.html):

* bioc-devel mailing list through
https://stat.ethz.ch/mailman/options/bioc-devel
* The BioC user support website through "edit my profile" (in my case
https://support.bioconductor.org/u/edit/6526/)
* a request to the bioc-devel for updating the maintainer email for
the related packages (for git?)
* updating the DESCRIPTION file in the release and devel branches of
all the packages the email is listed in

I am unsure about the third step - if needed, I would like to request the 
update of the maintainer emai.


Do I need to take any further actions to finalize updating the maintainer?


Thanks!


Best wishes,

Jakob Willforss

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Re: [Bioc-devel] MOFA package deprecation

[Kern, Lori]

Yes. Im very sorry. I realized you requested this originally and I never 
changed the default message.  I just pushed up now and it should propagate on 
tomorrow's build.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Britta Velten 
Sent: Saturday, February 6, 2021 4:53 AM
To: Kern, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] MOFA package deprecation

Hi Lori,

a quick follow up question on the package depreciation of Mofa which you took 
care of a while ago. Would it be possible to also have the pointer to mofa2 on 
the landing page of the package instead of only in the startup message? There 
it simply reads
https://www.bioconductor.org/packages/release/bioc/html/MOFA.html
"This package is deprecated. It will probably be removed from Bioconductor.�

This has led to some confusion and it would be great to have the pointer to the 
new alternative package there.

Thanks and best regards
Britta

Kern, Lori 
mailto:lori.sheph...@roswellpark.org>> schrieb 
am Mi., 21. Okt. 2020, 13:42:
Thank you for letting us know.  Yes I can specialize the message to point users 
to MOFA2.  I will take care of this later today.

Does MOFA2 still use the accompanied data package MOFAdata or should that also 
be deprecated?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Britta Velten 
mailto:britta.vel...@gmail.com>>
Sent: Wednesday, October 21, 2020 7:01 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] MOFA package deprecation

Dear Bioconductor core team,

I would like to deprecate the MOFA package as it has been superseded by MOFA2.
Is it possible to add a note for users to turn to MOFA2 in the deprecation 
warning for MOFA?

Best,
Britta
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