[Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

I have a loop in a function of my R package which by default uses bpparam() to 
set the framework used for parallelisation. On Windows, I see the error

Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: object 'selParams' not found

This error does not happen on the Linux or MacOS operating systems. It happens 
using both R 3.6 and the upcoming version 4. The error can be reproduced 
running the examples of runTests function in ClassifyR.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Bioc-devel] BiocParallel Variable Not Found

[Martin Morgan]

Windows uses separate processes that do not share memory (SnowParam()), whereas 
linux / mac by default use forked processes that share the original memory 
(MulticoreParam()). So

> y = 1
> param = MulticoreParam()
> res = bplapply(1:2, function(x) y, BPPARAM=param)

works because the function can 'see' y, whereas

> param = SnowParam()
> res = bplapply(1:2, function(x) y, BPPARAM=param)
Error: BiocParallel errors
  element index: 1, 2
  first error: object 'y' not found

fails because the new processes cannot see y. The robust way to implement this 
makes the FUN in bplapply truly functional, depending only on variables 
received as arguments

> res = bplapply(1:2, function(x, y) y, y = 1, BPPARAM=param)
>

The situation is more complicated in package code in particular and in general, 
because R sends not just FUN to the workers, but also the environment (up to 
but not including the global environment) in which the function applies. So

doit <- function() {
y = 1
bplapply(1:2, function(x) y, BPPARAM = SnowParam(2))
}

also works

> res = doit()
>

Note that

fun = function(x) y

doit = function() {
y = 1
bplapply(1:2, fun, BPPARAM = SnowParam(2))
}

fails, because y is not defined in the environment in which fun is defined 
(it's defined in the calling environment, which is different).

The most robust advice is to develop you code with the most conservative 
assumptions (e.g., register(SnowParam())) and to write functional functions 
where all variables are passed as arguments.

Martin

On 3/17/20, 6:00 AM, "Bioc-devel on behalf of Dario Strbenac" 
 
wrote:

Good day,

I have a loop in a function of my R package which by default uses bpparam() 
to set the framework used for parallelisation. On Windows, I see the error

Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: object 'selParams' not found

This error does not happen on the Linux or MacOS operating systems. It 
happens using both R 3.6 and the upcoming version 4. The error can be 
reproduced running the examples of runTests function in ClassifyR.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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[Bioc-devel] Fw: Bioconductor package SIM

[r.menezes]

l.s.


I cannot seem to be able to activate my account on the bioconductor git. I get 
a message saying my email address (the same one on the package help file) is 
not associated with a maintainer of a Bioconductor package. The email address 
is write simply is


r.xavierdemene...@vumc.nl


as stated in the SIM package page.


I tried this on both firefox and chrome, and get the same error each time.


Is there anything I could be doing wrong?


Thanks in advance,

Renee



From: Shepherd, Lori 
Sent: 16 March 2020 15:47
To: Menezes, R. (Ren�e)
Cc: Ren�e Menezes
Subject: Re: Bioconductor package SIM

Please be aware your package is still failing.  This is very problematic.  The
next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
your quick response in this matter. If your package remains broken we will begin
the deprecation process to remove the package from Bioconductor.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shepherd, Lori 
Sent: Thursday, February 27, 2020 12:08 PM
To: Menezes, R. (Ren�e) 
Cc: r.mene...@nki.nl 
Subject: Re: Bioconductor package SIM

Thank you! Please remember to update your email address in the DESCRIPTION of 
the package when you make changes too.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Menezes, R. (Ren�e) 
Sent: Thursday, February 27, 2020 12:07 PM
To: Shepherd, Lori 
Cc: r.mene...@nki.nl 
Subject: Re: Bioconductor package SIM

Dear Lori,

Thanks for your email. I saw the previous email but have not had the time to 
look at the problem. I have recently changed jobs (my new email address is in 
cc) and it has been really busy in the last few weeks.

I will look at the issue ASAP.

Kind regards,
Renee

Renee X. de Menezes
Lecturer, Dept. Epidemiology and Biostatistics, VUmc
r.mene...@vumc.nl
http://www.bigstatistics.nl/renee





Van: Shepherd, Lori 
Verzonden: donderdag 27 februari 2020 17:36
Aan: Menezes, R. (Ren�e) 
Onderwerp: Bioconductor package SIM

Dear Package Maintainer,

We would like to bring to your attention that your package is failing to 
build/check on our devel build machines:

http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
mailing list if you have any question or need help.

While the development branch is a place to develop new features and we expect 
packages to occasionally break,  they should not remain broken for an extended 
period of time.   If no action is taken over the next few weeks we will begin 
the deprecation process for your package.  The package has been failing since 
at least 01/24/20.  Thank you for your time and effort.

We notified you of your package failure in a group message entitled 
"Bioconductor Package Needs Update"  back on 01/27/20.

Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html

Information can also be found on the troubleshooting build page of the website:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/



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] Change associated email/github

[Russell Bainer]

I'd like to change the email address associated with my
Bioconductor account, and also update the ownership of my packages to my
personal Github account (I originally registered both of these with my
employer, and I have since left the company). Could you please direct me to
documentation that will help me do this?

Thanks very much

-R

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[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Charles Warden]

Hi,

I recently received error messages for 2 packages.  As a worst-case-scenario, 
it is acceptable if the sRAP package had to be removed.  However, I need to 
resolve the issue for the COHCAP package.

This is odd because I don’t think I have updated either package in the last 
year or so.  In fact, if I check the CHANGES file in the COHCAP package, the 
last change I manually noted was v1.29.3, which I can see was added to the 
GitHub version of the code on 3/2/2019:

https://github.com/cwarden45/COHCAP/commits/master/CHANGES

I can successfully install the package, with either the GitHub or Bioconductor 
instructions.  However, I want to correct the error because I don’t want the 
Bioconductor package to be removed.

I had some dependency issues on some systems related to the PDF generation 
(which I would usually ignore).  However, if I run “R CMD build” on an Ubuntu 
system where I have all dependencies installed, I don’t get any error message:

$ R CMD build COHCAP
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* preparing ‘COHCAP’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘COHCAP.Rnw’, ‘COHCAP.pdf’, ‘COHCAP.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘COHCAP_1.33.0.tar.gz’

I am using the development version, which I thought should match what was being 
tested for the BioC 3.11 error message.

Can you please either tell me what I need to do to reproduce (and then correct) 
this error, or confirm that it is OK to ignore the e-mails that I have received 
recently?

Thank You,
Charles

Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375
Work-From-Home Cell: 404-316-0012

--

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Re: [Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

Thanks for the examples which demonstrate the issue. Do you have other 
recommendations if, inside the loop, another function in the package is being 
called and the variable being passed is the ellipsis? There are only a couple 
of variables which might be provided by the user collected in the ellipsis, so 
the functional approach might still be the best in that case.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] BiocParallel Variable Not Found

[Martin Morgan]

The question is a bit abstract for me to understand and it might be better to 
point to actual code in a git repository or similar... 

Inside a package, something like

fun = function(x, y, ...) {
c(x, y, length(as.list(...)))
}

user_visible <- function(x, ...) {
y = 1
internal_function(x, y, ...)
}

internal_function <- function(x, y, ...) {
bplapply(1:5, fun, x, y, ...)
}

I think would 'work'.

Martin

On 3/17/20, 4:00 PM, "Bioc-devel on behalf of Dario Strbenac" 
 
wrote:

Good day,

Thanks for the examples which demonstrate the issue. Do you have other 
recommendations if, inside the loop, another function in the package is being 
called and the variable being passed is the ellipsis? There are only a couple 
of variables which might be provided by the user collected in the ellipsis, so 
the functional approach might still be the best in that case.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] Change associated email/github

[Turaga, Nitesh]

Hi,

There are a couple of things you'd have to do,

1. In the BiocCredentials app, you'd have to change your email address 
registered. And update your SSH keys if needed, add your personal Github ID as 
well.

2. In the DESCRIPTION file of the package, you'd have to change your email 
address to reflect where you'll be able to receive emails as a maintainer. 

3. Update your email address on Bioc-devel mailing list if it is not already 
registered. 

Best,

Nitesh 

> On Mar 17, 2020, at 1:34 PM, Russell Bainer  wrote:
> 
> I'd like to change the email address associated with my
> Bioconductor account, and also update the ownership of my packages to my
> personal Github account (I originally registered both of these with my
> employer, and I have since left the company). Could you please direct me to
> documentation that will help me do this?
> 
> Thanks very much
> 
> -R
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] Fw: Bioconductor package SIM

[Turaga, Nitesh]

The SIM package is registered to mboetze...@hotmail.com.

You can change the email on BiocCredentials app yourself.

Best,

Nitesh 

> On Mar 17, 2020, at 11:52 AM, r.mene...@nki.nl wrote:
> 
> l.s.
> 
> 
> I cannot seem to be able to activate my account on the bioconductor git. I 
> get a message saying my email address (the same one on the package help file) 
> is not associated with a maintainer of a Bioconductor package. The email 
> address is write simply is
> 
> 
> r.xavierdemene...@vumc.nl
> 
> 
> as stated in the SIM package page.
> 
> 
> I tried this on both firefox and chrome, and get the same error each time.
> 
> 
> Is there anything I could be doing wrong?
> 
> 
> Thanks in advance,
> 
> Renee
> 
> 
> 
> From: Shepherd, Lori 
> Sent: 16 March 2020 15:47
> To: Menezes, R. (Ren�e)
> Cc: Ren�e Menezes
> Subject: Re: Bioconductor package SIM
> 
> Please be aware your package is still failing.  This is very problematic.  The
> next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
> your quick response in this matter. If your package remains broken we will 
> begin
> the deprecation process to remove the package from Bioconductor.
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Shepherd, Lori 
> Sent: Thursday, February 27, 2020 12:08 PM
> To: Menezes, R. (Ren�e) 
> Cc: r.mene...@nki.nl 
> Subject: Re: Bioconductor package SIM
> 
> Thank you! Please remember to update your email address in the DESCRIPTION of 
> the package when you make changes too.
> 
> Cheers,
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Menezes, R. (Ren�e) 
> Sent: Thursday, February 27, 2020 12:07 PM
> To: Shepherd, Lori 
> Cc: r.mene...@nki.nl 
> Subject: Re: Bioconductor package SIM
> 
> Dear Lori,
> 
> Thanks for your email. I saw the previous email but have not had the time to 
> look at the problem. I have recently changed jobs (my new email address is in 
> cc) and it has been really busy in the last few weeks.
> 
> I will look at the issue ASAP.
> 
> Kind regards,
> Renee
> 
> Renee X. de Menezes
> Lecturer, Dept. Epidemiology and Biostatistics, VUmc
> r.mene...@vumc.nl
> http://www.bigstatistics.nl/renee
> 
> 
> 
> 
> 
> Van: Shepherd, Lori 
> Verzonden: donderdag 27 februari 2020 17:36
> Aan: Menezes, R. (Ren�e) 
> Onderwerp: Bioconductor package SIM
> 
> Dear Package Maintainer,
> 
> We would like to bring to your attention that your package is failing to 
> build/check on our devel build machines:
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM
> 
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if you have any question or need help.
> 
> While the development branch is a place to develop new features and we expect 
> packages to occasionally break,  they should not remain broken for an 
> extended period of time.   If no action is taken over the next few weeks we 
> will begin the deprecation process for your package.  The package has been 
> failing since at least 01/24/20.  Thank you for your time and effort.
> 
> We notified you of your package failure in a group message entitled 
> "Bioconductor Package Needs Update"  back on 01/27/20.
> 
> Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html
> 
> Information can also be found on the troubleshooting build page of the 
> website:
> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
> 
> 
> 
> Lori Shepherd
> 
> 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.
> __
> VUmc disclaimer : www.vumc.nl/disclaimer
> AMC disclaimer : www.amc.nl/disclaimer
> 
> 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

Re: [Bioc-devel] Fw: Bioconductor package SIM

[Turaga, Nitesh]

You'll have to activate your account first, 

https://git.bioconductor.org/BiocCredentials/account_activation/



> On Mar 17, 2020, at 5:11 PM, ni41435_ca  wrote:
> 
> The SIM package is registered to mboetze...@hotmail.com.
> 
> You can change the email on BiocCredentials app yourself.
> 
> Best,
> 
> Nitesh 
> 
>> On Mar 17, 2020, at 11:52 AM, r.mene...@nki.nl wrote:
>> 
>> l.s.
>> 
>> 
>> I cannot seem to be able to activate my account on the bioconductor git. I 
>> get a message saying my email address (the same one on the package help 
>> file) is not associated with a maintainer of a Bioconductor package. The 
>> email address is write simply is
>> 
>> 
>> r.xavierdemene...@vumc.nl
>> 
>> 
>> as stated in the SIM package page.
>> 
>> 
>> I tried this on both firefox and chrome, and get the same error each time.
>> 
>> 
>> Is there anything I could be doing wrong?
>> 
>> 
>> Thanks in advance,
>> 
>> Renee
>> 
>> 
>> 
>> From: Shepherd, Lori 
>> Sent: 16 March 2020 15:47
>> To: Menezes, R. (Ren�e)
>> Cc: Ren�e Menezes
>> Subject: Re: Bioconductor package SIM
>> 
>> Please be aware your package is still failing.  This is very problematic.  
>> The
>> next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
>> your quick response in this matter. If your package remains broken we will 
>> begin
>> the deprecation process to remove the package from Bioconductor.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> From: Shepherd, Lori 
>> Sent: Thursday, February 27, 2020 12:08 PM
>> To: Menezes, R. (Ren�e) 
>> Cc: r.mene...@nki.nl 
>> Subject: Re: Bioconductor package SIM
>> 
>> Thank you! Please remember to update your email address in the DESCRIPTION 
>> of the package when you make changes too.
>> 
>> Cheers,
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> From: Menezes, R. (Ren�e) 
>> Sent: Thursday, February 27, 2020 12:07 PM
>> To: Shepherd, Lori 
>> Cc: r.mene...@nki.nl 
>> Subject: Re: Bioconductor package SIM
>> 
>> Dear Lori,
>> 
>> Thanks for your email. I saw the previous email but have not had the time to 
>> look at the problem. I have recently changed jobs (my new email address is 
>> in cc) and it has been really busy in the last few weeks.
>> 
>> I will look at the issue ASAP.
>> 
>> Kind regards,
>> Renee
>> 
>> Renee X. de Menezes
>> Lecturer, Dept. Epidemiology and Biostatistics, VUmc
>> r.mene...@vumc.nl
>> http://www.bigstatistics.nl/renee
>> 
>> 
>> 
>> 
>> 
>> Van: Shepherd, Lori 
>> Verzonden: donderdag 27 februari 2020 17:36
>> Aan: Menezes, R. (Ren�e) 
>> Onderwerp: Bioconductor package SIM
>> 
>> Dear Package Maintainer,
>> 
>> We would like to bring to your attention that your package is failing to 
>> build/check on our devel build machines:
>> 
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM
>> 
>> Would you mind taking a look at this? Don't hesitate to ask on the 
>> bioc-devel mailing list if you have any question or need help.
>> 
>> While the development branch is a place to develop new features and we 
>> expect packages to occasionally break,  they should not remain broken for an 
>> extended period of time.   If no action is taken over the next few weeks we 
>> will begin the deprecation process for your package.  The package has been 
>> failing since at least 01/24/20.  Thank you for your time and effort.
>> 
>> We notified you of your package failure in a group message entitled 
>> "Bioconductor Package Needs Update"  back on 01/27/20.
>> 
>> Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html
>> 
>> Information can also be found on the troubleshooting build page of the 
>> website:
>> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> 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

Re: [Bioc-devel] Change associated email/github

[Russell Bainer]

Thanks very much for the response. Can you recommend a way to do password
recovery? I no longer have access to the registered email address, and I'm
afraid that I registered long enough ago that I don't have the password
that I used.


On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> There are a couple of things you'd have to do,
>
> 1. In the BiocCredentials app, you'd have to change your email address
> registered. And update your SSH keys if needed, add your personal Github ID
> as well.
>
> 2. In the DESCRIPTION file of the package, you'd have to change your email
> address to reflect where you'll be able to receive emails as a maintainer.
>
> 3. Update your email address on Bioc-devel mailing list if it is not
> already registered.
>
> Best,
>
> Nitesh
>
> > On Mar 17, 2020, at 1:34 PM, Russell Bainer 
> wrote:
> >
> > I'd like to change the email address associated with my
> > Bioconductor account, and also update the ownership of my packages to my
> > personal Github account (I originally registered both of these with my
> > employer, and I have since left the company). Could you please direct me
> to
> > documentation that will help me do this?
> >
> > Thanks very much
> >
> > -R
> >
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[Bioc-devel] regionReport error: leads to potential disk space issues for ImageMagick

[Leonardo Collado Torres]

Hi BioC-devel,

I spent some time yesterday getting my Windows laptop ready to debug a
Windows OS-only issue in regionReport (bioc-release 3.10), but
ultimately I couldn't reproduce it. Since the error seems to be some
type of cache, I bumped the version number but it still failed today
and it then also failed on bioc-devel (3.11) on Linux (as well as
Windows).

## Bioc-release (3.10) Windows is the only that fails

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
--- failed re-building ‘regionReport.Rmd’

similarly

Quitting from lines 224-229 (basicExploration.Rmd)
Error in magick_image_trim(image, fuzz) :
  R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
Calls: render ...  -> assert_image ->  ->
magick_image_trim


## Bioc-devel (3.11) Linux and Windows fails

http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html

However, I see at
http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/malbec2-buildsrc.html
that the error appeared today also on the Linux bioc-devel builder.

## Google

Searching for the error message led me to
https://github.com/phw/peek/issues/112 which talks about disk space
running out for ImageMagick. Do you think that this is something that
is affecting the builders too? Do you have any suggestions I could
try?

Best,
Leo

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Re: [Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

I am not sure how to fix my package properly, even with the good example. A 
link to the specific part of my function is 
https://github.com/DarioS/ClassifyR/blob/e35899caceb401691990136387a517f4c3b57d5e/R/runTests.R#L567
 and the example in the help page of runTestsEasyHard function triggers the 
error shown in Bioconductor's daily build.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Bioc-devel] Push the updated package to Bioconductor

[Ruijia Wang]

Hi BioC-devel,

I am the author of the Bioconductor package APAlyzer (
https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). We are
trying to push our updated package (version 1.1.1) to Bioconductor.
However, the git tutorial seems doesn't work in my case, here's what I've
done:

$ git remote -v
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (fetch)
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (push)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (fetch)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (push)

$ git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

$ git push upstream master
Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 4 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 299 bytes | 74.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
To git.bioconductor.org:packages/APAlyzer.git
   4f098be..d2ad6cb  master -> master

I didn't get any notice and find any changes on the Bioconductor website
(both the development version and stable version). Did I miss anything?
Could you help me to figure out how to fix this?  Thank you in advance!

Best,
Ray

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Re: [Bioc-devel] Push the updated package to Bioconductor

[Shepherd, Lori]

Please see the top portion of this page 
http://bioconductor.org/developers/how-to/troubleshoot-build-report/.  Updates 
are not instantaneous; it can take 24-48 hours to appear, and will only appear 
on the landing page if the build and check completed without Error.

Get Outlook for Android


From: Bioc-devel  on behalf of Ruijia Wang 

Sent: Tuesday, March 17, 2020 8:43:35 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Push the updated package to Bioconductor

Hi BioC-devel,

I am the author of the Bioconductor package APAlyzer (
https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). We are
trying to push our updated package (version 1.1.1) to Bioconductor.
However, the git tutorial seems doesn't work in my case, here's what I've
done:

$ git remote -v
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (fetch)
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (push)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (fetch)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (push)

$ git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

$ git push upstream master
Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 4 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 299 bytes | 74.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
To git.bioconductor.org:packages/APAlyzer.git
   4f098be..d2ad6cb  master -> master

I didn't get any notice and find any changes on the Bioconductor website
(both the development version and stable version). Did I miss anything?
Could you help me to figure out how to fix this?  Thank you in advance!

Best,
Ray

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[Bioc-devel] Deploy a critical patch

[Julian Flesch]

Hi Bioc team,


I am the maintainer of the package /waddR/.

We have had built issues on the active branch recently, due a dependency
being unavailable. After pushing a patch, the issues were resolved on
the devel branch.

Is it possible to merge these critical changes (version 1.1.4) to the
active branch of Bioconductor?


Best,

Julian


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