[Bioc-devel] Single Package Builder for new Bioconductor Submissions

[Kern, Lori via Bioc-devel]

Over the next few days, we will be transitioning the single package builder for 
new Bioconductor submissions to use Bioconductor 3.20 rather than 3.19 
following the latest Bioconductor release on May 1.  This may result in 
downtime to the build on demand functionality.  We appreciate your 
understanding.

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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recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Ramos Perez, Marcel via Bioc-devel]

Hi Boyi,

This has been resolved in BiocCheck version 1.39.12.

https://github.com/Bioconductor/BiocCheck/issues/205

Best regards,

Marcel

On 1/10/24 2:53 PM, Boyi Guo wrote:

Hi,

I had the same problem (
https://bioconductor.org/spb_reports/tpSVG_buildreport_20240109095309.html).

* Checking for bioc-devel mailing list subscription...


  * ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel



In my experience, signing up the mailing list again, even though I
already signed up previously, resolved that error.
I am not sure if this practice should be advised, and I did receive an
auto email with subject line "Mailman privacy alert", telling me that
I've already signed up.

Thanks.

Best,

Boyi


On Mon, Jan 8, 2024 at 7:49 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> wrote:



I can confirm that this email is subscribed.  We can open an issue on
BiocCheck to investigate this more.  In the meantime I will comment on your
submission issue to ignore the error for now.



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 
<mailto:bioc-devel-boun...@r-project.org> on 
behalf of Richard
Heery <mailto:richardhe...@gmail.com>
Sent: Sunday, January 7, 2024 7:17 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
<mailto:bioc-devel@r-project.org>
Subject: [Bioc-devel] Single Package Builder failing to detect
subscription to the Bioc-devel mailing list

Hi all,

My package submission is repeatedly failing due to an error saying I am not
subscribed to the Bioc-devel mailing list, even though I am subscribed
using this email. This is the same email I have in the DESCRIPTION file and
also as my git user.email both globally and locally in the repository. Any
ideas what could be causing this?

Cheers,

Richard

[[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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recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Kern, Lori via Bioc-devel]

You shouldn't have to sign up again. There was a bug in the code that should be 
fixed in the latest push to BiocCheck version 1.39.12

https://github.com/Bioconductor/BiocCheck/issues/205
[https://opengraph.githubassets.com/ab6db7795256e2a9e1760a2a42b407dd2af58f3ce9960f3072377117a3801dae/Bioconductor/BiocCheck/issues/205]<https://github.com/Bioconductor/BiocCheck/issues/205>
bioc-devel mailing list check still not always accurate · Issue #205 · 
Bioconductor/BiocCheck<https://github.com/Bioconductor/BiocCheck/issues/205>
I can confirm the single package builder is using version 1.39.10 See mailing 
list https://stat.ethz.ch/pipermail/bioc-devel/2024-January/020119.html for 
email = "richardhe...@gmail.com". I can con...
github.com




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Boyi Guo 
Sent: Wednesday, January 10, 2024 2:53 PM
To: Kern, Lori 
Cc: Richard Heery ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Single Package Builder failing to detect subscription 
to the Bioc-devel mailing list

Hi,

I had the same problem 
(https://bioconductor.org/spb_reports/tpSVG_buildreport_20240109095309.html<https://secure-web.cisco.com/17WcfrGBiAYEYr5NOi5pUrQrU1hC_SXJiUwT-1FXzztXeAu4fuD0rYMmRGGJ3uisEslbV1knb6VpLqwBHcKE18ZozauDI7JQUUKX-Z9Mmzb1DVB7OxdfLPGBa2qC4rpFQeznZRc0JVS3-4rny_sZQWkVo896gpQXv4JTu-b8Kr3UTtH4dcL4yFdMNx5m4moYrm5nGJl3NKFBC54RPvOa0P2RGdOQb5S8R8WYYOHMFNmgr8aR7M14GKrPvcr5fGR0TsFpYn3i3F4v2Ox_3YH8mz_YcmlsEp8Y6f4TjWMDrwQYT5z34XnxOoUlviDMS4QNE/https%3A%2F%2Fbioconductor.org%2Fspb_reports%2FtpSVG_buildreport_20240109095309.html>).

* Checking for bioc-devel mailing list subscription...
  * ERROR: Subscribe to the Bioc-devel mailing list by going to 
https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://secure-web.cisco.com/1B-ujEW5G7_PxldFt9QOipEwKnjTDrDgnSdkN4Q0Sc7phvs4RaaxAscxtvbF3mu_Q1_bLUDDe8sO6EirtfSEDHkDIn0DCumfluJGJbW2q78hfXTxFyLvdlYMJYe4pAhxDzcpUOjhP9Z8jJnN6QQhgdl7NS00Zih7olJIjFRBsZBhSJcNuGjkR7MCB8Mk-JuZnJp3kJS0qjesg4CcGOsBFyt6y6KgSwSttx_6BFgO5vZnaBGSWTS61wDQssQqMvddMRoLpwyl7j92amaW91E-i2BB4ukcY26t8pLM1DyRDjJAiOFIYl83us7xf5tF0o1Z9/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel>

In my experience, signing up the mailing list again, even though I already 
signed up previously, resolved that error.
I am not sure if this practice should be advised, and I did receive an auto 
email with subject line "Mailman privacy alert", telling me that I've already 
signed up.


Thanks.


Best,

Boyi

On Mon, Jan 8, 2024 at 7:49 AM Kern, Lori via Bioc-devel 
mailto:bioc-devel@r-project.org>> wrote:
I can confirm that this email is subscribed.  We can open an issue on BiocCheck 
to investigate this more.  In the meantime I will comment on your submission 
issue to ignore the error for now.



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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Richard Heery mailto:richardhe...@gmail.com>>
Sent: Sunday, January 7, 2024 7:17 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Single Package Builder failing to detect subscription to 
the Bioc-devel mailing list

Hi all,

My package submission is repeatedly failing due to an error saying I am not
subscribed to the Bioc-devel mailing list, even though I am subscribed
using this email. This is the same email I have in the DESCRIPTION file and
also as my git user.email both globally and locally in the repository. Any
ideas what could be causing this?

Cheers,

Richard

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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this message in error, please notify the sender immediately by e-mail and 
del

Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Boyi Guo]

Hi,

I had the same problem (
https://bioconductor.org/spb_reports/tpSVG_buildreport_20240109095309.html).

* Checking for bioc-devel mailing list subscription...
>   * ERROR: Subscribe to the Bioc-devel mailing list by going to
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

In my experience, signing up the mailing list again, even though I
already signed up previously, resolved that error.
I am not sure if this practice should be advised, and I did receive an
auto email with subject line "Mailman privacy alert", telling me that
I've already signed up.

Thanks.

Best,

Boyi


On Mon, Jan 8, 2024 at 7:49 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> I can confirm that this email is subscribed.  We can open an issue on
> BiocCheck to investigate this more.  In the meantime I will comment on your
> submission issue to ignore the error for now.
>
>
>
> 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 Richard
> Heery 
> Sent: Sunday, January 7, 2024 7:17 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Single Package Builder failing to detect
> subscription to the Bioc-devel mailing list
>
> Hi all,
>
> My package submission is repeatedly failing due to an error saying I am not
> subscribed to the Bioc-devel mailing list, even though I am subscribed
> using this email. This is the same email I have in the DESCRIPTION file and
> also as my git user.email both globally and locally in the repository. Any
> ideas what could be causing this?
>
> Cheers,
>
> Richard
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
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>
>
>
> 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
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Kern, Lori via Bioc-devel]

I can confirm that this email is subscribed.  We can open an issue on BiocCheck 
to investigate this more.  In the meantime I will comment on your submission 
issue to ignore the error for now.



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 Richard Heery 

Sent: Sunday, January 7, 2024 7:17 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder failing to detect subscription to 
the Bioc-devel mailing list

Hi all,

My package submission is repeatedly failing due to an error saying I am not
subscribed to the Bioc-devel mailing list, even though I am subscribed
using this email. This is the same email I have in the DESCRIPTION file and
also as my git user.email both globally and locally in the repository. Any
ideas what could be causing this?

Cheers,

Richard

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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[Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Richard Heery]

Hi all,

My package submission is repeatedly failing due to an error saying I am not
subscribed to the Bioc-devel mailing list, even though I am subscribed
using this email. This is the same email I have in the DESCRIPTION file and
also as my git user.email both globally and locally in the repository. Any
ideas what could be causing this?

Cheers,

Richard

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[Bioc-devel] Single Package Builder for new submission

[Kern, Lori via Bioc-devel]

We will be updating the single package builder for new package submissions to 
run on the devel version of Bioconductor (3.19) and R (4.4).  During the update 
period there may be periods of intermittent downtime where build on demand is 
unavailable.  We appreciate your understanding during this time.


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 
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 e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Single Package Builder Maintenance

[Kern, Lori via Bioc-devel]

We will be performing maintenance on the single package builder for new 
submissions today.  There may be short intervals where the on-demand/build on 
version bump capabilities will not be accessible.  We appreciate your 
understanding.

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 
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 e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Single Package Builder and BiocCheck

[Kern, Lori]

There has been an issue identified that BiocCheck is currently broken.  We are 
investigating and will have it resolved soon.  Until it is resolved it will 
cause all packages to have an ERROR on the build report for new package 
submission.

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 
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 e-mail and 
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[Bioc-devel] Single Package Builder for New Submission

[Kern, Lori]

We will be updating the builder used for single package submission to our devel 
builders. There may be periods of time the build on demand feature for new 
package submissions is unavailable.  We appreciate your understanding.



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 
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 e-mail and 
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Re: [Bioc-devel] Single Package Builder package dependency issue

[Kern, Lori]

This issue should now be resolved.
Thank you for your patience

Cheers,


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 Kern, Lori 

Sent: Monday, March 20, 2023 2:00 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder package dependency issue

We recently updated R on the devel builders. Some of the recent updates have 
temporarily caused issues with finding package dependencies on the Single 
Package Builder for new submission.  We are aware of the issue and are working 
on a fix. We are sorry for the inconvenience and will have it remedied soon




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 
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 e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Single Package Builder package dependency issue

[Kern, Lori]

We recently updated R on the devel builders. Some of the recent updates have 
temporarily caused issues with finding package dependencies on the Single 
Package Builder for new submission.  We are aware of the issue and are working 
on a fix. We are sorry for the inconvenience and will have it remedied soon




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 
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 e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Single Package Builder for new submissions

[Kern, Lori]

We will be doing some testing on the single package builder for new submissions.
Autogeneration of build reports on version bumps may  be temporarily 
unavailable.
We hope to have minimal distruption.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Single Package Builder for New Package Submission

[Kern, Lori]

The updates are complete.  The Single Package Builder is now using Bioc 3.15 
and R 4.2 for new package submissions.

We have identified a bug in BiocCheck that will cause current packages to fail 
in BiocCheckGitClone on the Single Package Builder Report.  That looks similar 
to the following:


===

 BiocCheckGitClone('spbtest3')

===


/usr/bin/tar: 
/home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20211129101146/spbtest3: 
Cannot read: Is a directory /usr/bin/tar: At beginning of tape, quitting now 
/usr/bin/tar: Error is not recoverable: exiting now Warning in untar(pkgname, 
exdir = tmp_dir) :   /usr/bin/tar -xf 
'/home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20211129101146/spbtest3'
 -C '/tmp/RtmpTIAZO0/fileadac1b5fa962' returned error code 2 This is 
BiocCheckGitClone version 1.31.13. BiocCheckGitClone is a work in progress. 
Output and severity of issues may change. * Checking valid files... * Checking 
DESCRIPTION... * Checking if DESCRIPTION is well formatted... Warning in 
read.dcf(file.path(package_dir, "DESCRIPTION")) :   cannot open compressed file 
'/tmp/RtmpTIAZO0/fileadac1b5fa962/spbtest3/DESCRIPTION', probable reason 'No 
such file or directory' * ERROR: DESCRIPTION is malformed. cannot open 
the connection

We are working on the patch right now.  In the meantime you can ignore this 
ERROR.

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 Kern, Lori 

Sent: Monday, November 29, 2021 7:26 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder for New Package Submission

We will be making updates to the Single Package Builder for New Package 
Submissions throughout the morning.  This will cause some intermittent downtime 
on the build on commit feature of new submission review process.   We 
appreciate your patience while we update.


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] Single Package Builder for New Package Submission

[Kern, Lori]

We will be making updates to the Single Package Builder for New Package 
Submissions throughout the morning.  This will cause some intermittent downtime 
on the build on commit feature of new submission review process.   We 
appreciate your patience while we update.


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] Single Package Builder ERROR

[Kern, Lori]

We are currently seeing an ERROR on the Single Package Builder for new package 
submission for all packages.  It will appear something like the following:

Error in read.dcf(desc, fields = "Package") : cannot open the connection
Calls: BiocCheck -> .get_package_name -> read.dcf
Execution halted

This ERROR is on our end.  The Core Team is investigating and will have a 
resolution soon. Once the issue is resolved, we will manually kick off builds 
for affected packages.

We appreciate your patience and understanding.


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] Single Package Builder

[Kern, Lori]

We are making some updates to the single package builder.  While builds should 
not be affects, email notifications of events may be hindered.  The update 
should be complete within the next 30 minutes.

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] Single Package Builder Updates

[Kern, Lori]

Bioconductor Community,

We will be switching the single package builder for new package submissions to 
build off the devel Bioc 3.13 builders shortly.  During this time the single 
package builder will have intermittent connectivity and you will not receive 
automatic build reports on version bumps.  Once stable we will kick off any 
builds that failed to complete.
We appreciate your patience and understanding during this process.

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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Re: [Bioc-devel] Single Package Builder for New Package Submission

[Kern, Lori]

We believe this issue has now been resolved.  Thank you for your patience.


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 Kern, Lori 

Sent: Thursday, October 8, 2020 8:51 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder for New Package Submission

We are encountering ERRORs with the Single Package Builder used for new package 
submission.  Currently, build reports are not being produced on git push.  We 
are aware of the issue and are working to have it resolved as soon as possible. 
 We apologize for any inconvenience and will kick off manual builds for any new 
package submission that needs it when the issue is resolved.




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] Single Package Builder for New Package Submission

[Kern, Lori]

We are encountering ERRORs with the Single Package Builder used for new package 
submission.  Currently, build reports are not being produced on git push.  We 
are aware of the issue and are working to have it resolved as soon as possible. 
 We apologize for any inconvenience and will kick off manual builds for any new 
package submission that needs it when the issue is resolved.




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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Re: [Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

Updates are complete.  There should be no further interruption


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 Shepherd, Lori 

Sent: Wednesday, September 9, 2020 12:40 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder Updates

There have been some bugs reported for the MacOS Single Package Builder. We 
will begin running some tests and updates shortly which may result in some 
downtime or unexpected ERROR's when trying to trigger build reports.  We 
appreciate your understanding and hope to have the issue resolved shortly.

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] Single Package Builder Updates

[Shepherd, Lori]

There have been some bugs reported for the MacOS Single Package Builder. We 
will begin running some tests and updates shortly which may result in some 
downtime or unexpected ERROR's when trying to trigger build reports.  We 
appreciate your understanding and hope to have the issue resolved shortly.

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] single package builder updates

[Shepherd, Lori]

Hello,

We will be performing some updates on the single package builder for new 
submissions today June 30.  There will be a period of downtime while we run the 
updates.  During this time packages on the tracker will not receive automatic 
builds.  We apologize for any inconvenience and appreciate your patience.

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] Single Package Builder for New Package Submission

[Shepherd, Lori]

Hello all,

We will be updating the Single Package Builder to run on the devel version of 
Bioconductor 3.12 over the new few days. During the update the Single Package 
Builder may experience intermittent down time. We apologize for any 
inconvenience this may cause and hope to keep downtime to a minimum.

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] Single Package Builder for New Package Submissions

[Shepherd, Lori]

Hello all,

We will be updating the Single Package Builder to build on Bioc 3.11 and R 4.0 
later today and tomorrow.  You can expect some downtown and some periods of 
intermittent activity.  We appreciate your patience while we make the 
transition.

Thank you.


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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Re: [Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

The single package builder should be back online and available utilizing Bioc 
3.10 devel builders.

Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Tuesday, May 21, 2019 7:27:39 AM
To: bioc-devel
Subject: [Bioc-devel] Single Package Builder Updates

Hello maintainers,


Now that the devel builds have been stable for a few weeks we will transition 
the single package builder to also be building off Bioc 3.10.   The transition 
will begin this morning and hopefully only last a few hours. During this period 
the Single Package Builder will be offline.

Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

Hello maintainers,


Now that the devel builds have been stable for a few weeks we will transition 
the single package builder to also be building off Bioc 3.10.   The transition 
will begin this morning and hopefully only last a few hours. During this period 
the Single Package Builder will be offline.

Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Single Package Builder for New Submissions

[Shepherd, Lori]

The single package builder should now be fixed and produce build reports on 
version bumps.


Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, May 6, 2019 10:03:24 AM
To: bioc-devel
Subject: [Bioc-devel] Single Package Builder for New Submissions

We are experiencing some issues with the Single Package Builder relating to the 
release.  Currently builds may not be executing with versions bumps or you may 
get a report with a

Fatal error: cannot create 'R_TempDir'

We are working on a solution and hope to have it running as normal soon.


Thank you.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] Single Package Builder for New Submissions

[Shepherd, Lori]

We are experiencing some issues with the Single Package Builder relating to the 
release.  Currently builds may not be executing with versions bumps or you may 
get a report with a

Fatal error: cannot create 'R_TempDir'

We are working on a solution and hope to have it running as normal soon.


Thank you.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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] Single Package Builder

[Shepherd, Lori]

Sorry for the inconvenience.  The Single Package Builder should be up and 
running as normal now.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Martin Morgan 

Sent: Monday, February 18, 2019 12:30:37 PM
To: Felix Ernst; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Single Package Builder

Issues with the SPB may persist until Tuesday morning. Martin

On 2/18/19, 5:29 AM, "Bioc-devel on behalf of Felix Ernst" 
 wrote:

Hi,



I just wanted to ask, whether the SPB is under maintenance.



After a push, the bot reports the start of a build, but the build is not
started or at least the result is not reported back to the issue on GitHub.



I hope I didn�t miss something or is the info from the 29th of January still
valid?



Best regards,

Felix



---



Felix Ernst, PhD

Universit� Libre de Bruxelles

RNA MOLECULAR BIOLOGY

BIOPARK Charleroi Brussels-South CAMPUS

Rue Profs Jeener & Brachet, 12

B-6041 Charleroi - Gosselies

BELGIUM

+32(2)650 9774 (office phone)

 <mailto:felix.er...@ulb.ac.be> felix.er...@ulb.ac.be






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Re: [Bioc-devel] Single Package Builder

[Martin Morgan]

Issues with the SPB may persist until Tuesday morning. Martin

On 2/18/19, 5:29 AM, "Bioc-devel on behalf of Felix Ernst" 
 wrote:

Hi,

 

I just wanted to ask, whether the SPB is under maintenance.

 

After a push, the bot reports the start of a build, but the build is not
started or at least the result is not reported back to the issue on GitHub.

 

I hope I didn�t miss something or is the info from the 29th of January still
valid?

 

Best regards,

Felix

 

---



Felix Ernst, PhD

Universit� Libre de Bruxelles

RNA MOLECULAR BIOLOGY

BIOPARK Charleroi Brussels-South CAMPUS

Rue Profs Jeener & Brachet, 12

B-6041 Charleroi - Gosselies

BELGIUM

+32(2)650 9774 (office phone)

  felix.er...@ulb.ac.be

 

 


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[Bioc-devel] Single Package Builder

[Felix Ernst]

Hi,

 

I just wanted to ask, whether the SPB is under maintenance.

 

After a push, the bot reports the start of a build, but the build is not
started or at least the result is not reported back to the issue on GitHub.

 

I hope I didn�t miss something or is the info from the 29th of January still
valid?

 

Best regards,

Felix

 

---



Felix Ernst, PhD

Universit� Libre de Bruxelles

RNA MOLECULAR BIOLOGY

BIOPARK Charleroi Brussels-South CAMPUS

Rue Profs Jeener & Brachet, 12

B-6041 Charleroi - Gosselies

BELGIUM

+32(2)650 9774 (office phone)

  felix.er...@ulb.ac.be

 

 


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Re: [Bioc-devel] Single Package Builder for New Submissions

[Shepherd, Lori]

We are experience some intermittent drops in connectivity and are investigating 
this matter.  Thanks for pointing these out.  We hope to have to issue resolved 
shortly.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Ludwig 
Geistlinger 
Sent: Monday, January 28, 2019 7:53:05 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Single Package Builder for New Submissions

Dear Lori,

Is the update of the MAC SPB still ongoing?

Today, I managed to produce three different build reports - from "all-ok" to 
"timeout" and "errors" just
by documentation enhancements and version number bumps, ie no changes on the 
actual R stuff (code, vignette chunks, examples, etc):

http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128130552.html
http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128145534.html
http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128160110.html

Particularly, the mac builder doesn't seem to have an internet connection?

Thank you,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Tuesday, January 22, 2019 9:26 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Single Package Builder for New Submissions

During this week we will be updating the Single Package Builder to use a new 
MAC builder.  During this updating and testing,  the Single Package Builder may 
produce some sporadic ERRORs or experience intermittent periods of downtime.   
We will be as quick as possible and hope to keep the interruptions to a minimum.

We appreciate your understanding.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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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[Bioc-devel] Single Package Builder for New Submissions

[Ludwig Geistlinger]

Dear Lori,

Is the update of the MAC SPB still ongoing?

Today, I managed to produce three different build reports - from "all-ok" to 
"timeout" and "errors" just
by documentation enhancements and version number bumps, ie no changes on the 
actual R stuff (code, vignette chunks, examples, etc): 

http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128130552.html
http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128145534.html
http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128160110.html

Particularly, the mac builder doesn't seem to have an internet connection?

Thank you,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Tuesday, January 22, 2019 9:26 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Single Package Builder for New Submissions

During this week we will be updating the Single Package Builder to use a new 
MAC builder.  During this updating and testing,  the Single Package Builder may 
produce some sporadic ERRORs or experience intermittent periods of downtime.   
We will be as quick as possible and hope to keep the interruptions to a minimum.

We appreciate your understanding.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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, 
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[Bioc-devel] Single Package Builder for New Submissions

[Shepherd, Lori]

During this week we will be updating the Single Package Builder to use a new 
MAC builder.  During this updating and testing,  the Single Package Builder may 
produce some sporadic ERRORs or experience intermittent periods of downtime.   
We will be as quick as possible and hope to keep the interruptions to a minimum.

We appreciate your understanding.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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 
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[Bioc-devel] Single Package Builder for new package submission service Interruption

[Shepherd, Lori]

Hello all,


We will be working on converting the Single Package builder over to R 3.6 Bioc 
3.9.

During this time you may experience service downtime for the issue tracker and 
automatic builds during the submission review process.  We hope the 
inconvenience will be minimal and thank you for your understanding.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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 
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[Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

We will be updating the Single Package Builder for new package submissions this 
morning.  While the updates are occurring there will be a temporary downtime 
for submitting new packages and receiving the automatically generated build 
reports for existing submissions.  We will announce when it is back up and 
running.


Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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 
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Re: [Bioc-devel] Single Package Builder temporarily down

[Shepherd, Lori]

The single package builder is back on line.   Submissions and versions bumps to 
new packages submissions should now build and result in a report. We apologize 
for the inconvenience.


Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori 
<lori.sheph...@roswellpark.org>
Sent: Saturday, March 3, 2018 8:44:58 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Single Package Builder temporarily down

There have been some updates to the builders and will require some additional 
updates to the single package builder.  While this is occurring the single 
package builder for new package submissions will temporarily be down.  We will 
notify when the updates are complete and the single package builder back online.


Thank you for your patience


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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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[Bioc-devel] Single Package Builder temporarily down

[Shepherd, Lori]

There have been some updates to the builders and will require some additional 
updates to the single package builder.  While this is occurring the single 
package builder for new package submissions will temporarily be down.  We will 
notify when the updates are complete and the single package builder back online.


Thank you for your patience


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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 
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Re: [Bioc-devel] Single Package Builder Updates and Testing

[Shepherd, Lori]

Testing is complete.  The single package builder should be functioning normally


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori 
<lori.sheph...@roswellpark.org>
Sent: Monday, December 11, 2017 9:14:41 AM
To: Martin Morgan
Subject: [Bioc-devel] Single Package Builder Updates and Testing

The Single Package Builder will be undergoing some updating and testing over 
the next few days.  While it will still be active and generating reports, there 
may be intermittent periods of inactivity.  We hope this will be to a minimum 
and will notify when testing is complete.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

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 
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[Bioc-devel] Single Package Builder Updates and Testing

[Shepherd, Lori]

The Single Package Builder will be undergoing some updating and testing over 
the next few days.  While it will still be active and generating reports, there 
may be intermittent periods of inactivity.  We hope this will be to a minimum 
and will notify when testing is complete.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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] Single Package Builder / Package Submission

[Shepherd, Lori]

Thank you.  Our transitions are complete. New packages will now be built agains 
R 3.5 and Bioc 3.7.


Until the CRAN binaries are available for windows we will temporarily not be 
building on windows

See related post:

https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012265.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori 
<lori.sheph...@roswellpark.org>
Sent: Tuesday, November 14, 2017 8:08:06 AM
To: Martin Morgan
Subject: [Bioc-devel] Single Package Builder / Package Submission

We will begin to update the single package builders used to build and check new 
package submission to R 3.5 Bioc 3.7 today.  While this is occurring the single 
package builder will be off line and there will be no builds for newly 
submitted packages.


Thank you for your patience and understanding.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] Single Package Builder / Package Submission

[Shepherd, Lori]

We will begin to update the single package builders used to build and check new 
package submission to R 3.5 Bioc 3.7 today.  While this is occurring the single 
package builder will be off line and there will be no builds for newly 
submitted packages.


Thank you for your patience and understanding.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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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[Bioc-devel] Single Package Builder

[Shepherd, Lori]

Over the next week,  we will be transitioning the Single Package Builder to the 
latest versions of R and Bioc 3.6. The single package builder is used when new 
packages are submitted to:  https://github.com/Bioconductor/Contributions .  
Please be advised that there may be intermittent periods where the single 
package builder is offline during this process.

Thank you for your understanding.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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] Single Package Builder

[Shepherd, Lori]

The Single Package Builder is now online.  Thank you for your patience.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori 
<lori.sheph...@roswellpark.org>
Sent: Monday, February 27, 2017 9:14:45 AM
To: Martin Morgan
Subject: [Bioc-devel] Single Package Builder

The Single Package Builder is currently offline.  We are working on restoring 
and will update when it is back online.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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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[Bioc-devel] Single Package Builder

[Shepherd, Lori]

The Single Package Builder is currently offline.  We are working on restoring 
and will update when it is back online.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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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[Bioc-devel] single package builder

[Shepherd, Lori]

Hello


We will be attempting to update the single package builder to bioc 3.5 with R 
3.4 over the next few days.  Please note that there may be some disruption and 
the builders may not be available for packages that make updates during this 
time.  We hope this transition will go quickly and smoothly. Thank you for your 
understanding.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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