Re: [Bioc-devel] Use set.seed inside function

[Meng, Chen]

Thanks, and good to know the with_seed function.

best,
Chen

On 29.11.21 22:43, Henrik Bengtsson wrote:

The easiest is to use withr::with_seed(), e.g.


withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))

[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"

withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))

[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"

It works by undoing globalenv()$.Random.seed after the random number
generator has updated.  If you want to roll your own version of this,
you need to make sure to handle the special case when there is no
pre-existing .Random.seed in globalenv().

Regarding packages and functions changing the random seed via a
set.seed() [without undoing it]: this should *never* be done, because
it will wreak havoc on a analyses and studies that rely on random
numbers.  My rule of thumb: only the end-user should be allowed to use
set.seed(), which should typically be done at the top of their R
scripts.

/Henrik

On Mon, Nov 29, 2021 at 1:23 PM Meng Chen  wrote:

Thanks. I think it may work in theory, generating "enough" distinct colors
is fairly easy. Then the problem will be how to find a subset of colors of
size n, and the selected colors are still most distinguishable. I think I
will do this with my eyes if no other methods, a tedious job.
But at least for my curiosity, I still want to know if there are other ways
to achieve this. I feel like 80% of people who use the distinctColorPallete
function actually don't need the "random" feature :) Thanks.

On Mon, Nov 29, 2021 at 9:39 PM James W. MacDonald  wrote:


It appears that you don't actually want random colors, but instead you
want the same colors each time. Why not just generate the vector of 'random
distinct colors' one time and save the vector of colors?

-Original Message-
From: Bioc-devel  On Behalf Of Meng Chen
Sent: Monday, November 29, 2021 3:21 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Use set.seed inside function

Dear BioC team and developers,

I am using BiocCheck to check my package, it returns a warning:
" Remove set.seed usage in R code"

I am using "set.seed" inside my functions, before calling function
distinctColorPalette (randomcoloR package) in order to generate
reproducible "random distinct colors". So what would be the best practice
to solve this warning? I think 1. use set.seed and don't change anything.
2. use the set.seed function, but include something like below inside the
function *gl.seed <- .Random.seed* *on.exit(assign(".Random.seed", gl.seed,
envir = .GlobalEnv))* 3. use some other functions for the purpose

Any suggestions will be appreciated. Thanks.
--
Best Regards,
Chen

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Chen

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Re: [Bioc-devel] [External] Memory error from sesame build

[Zhou, Wanding]

Thanks Herve. That's super helpful. I will use your trick!

Best,

Wanding

> On Nov 29, 2021, at 5:51 PM, Hervé Pagès  wrote:
> 
> On 29/11/2021 09:25, Zhou, Wanding wrote:
>> Thanks for the input Herve. I saw your post but can you help me confirm that 
>> mine is on the 32-bit windows since it says mingw32 (64-bit)?
>> Windows Server 2012 R2 Standard / x64
>> * using platform: x86_64-w64-mingw32 (64-bit)
> 
> This shows the Windows arch that R uses by default on Windows. But we use 
> --force-multiarch when running 'R CMD check' on our Windows builders to force 
> 'R CMD check' to run all the examples, unit tests, and vignettes in the two 
> supported Windows archs: 32-bit and 64-bit.
> 
> The error was happening during the following step:
> 
>  ** running examples for arch 'i386'
> 
> and not during the following step:
> 
>  ** running examples for arch 'x64'
> 
> So yes, this is a Windows 32-bit only error.
> 
>> http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html
>>  
>> 
>> Does that mean all the examples added together cannot use over 3G memory?
> 
> Yes.
> 
>> I still don't think I am using that much but I will remove some examples and 
>> see that solves the problem
> 
> Here is one way to see how much memory 'R CMD check' consumes when running 
> the examples:
> 
> 1. Run 'R CMD check' on the package. This collates all the examples in 
> sesame.Rcheck/sesame-Ex.R.
> 
> 2. Comment out the last line (quit('no')) in sesame.Rcheck/sesame-Ex.R.
> 
> 3. From R do: source("sesame.Rcheck/sesame-Ex.R", echo=TRUE). At the same 
> time, monitor memory usage in another terminal e.g. by running 'top' on 
> Linux/macOS.
> 
> 4.Once all the examples have finished, do gc().
> 
> This is what I get on my laptop when doing the above with sesame 1.13.3:
> 
> > gc()
> 
>used   (Mb) gc trigger   (Mb)  max used   (Mb)
> 
> Ncells  15062911  804.5   24349446 1300.5  24349446 1300.5
> 
> Vcells 278380669 2123.9  473158124 3610.0 473157073 3610.0
> 
> 
> That's a memory consumption of 4.9G which is confirmed by the 'top' command I 
> was running in another terminal.
> 
> It would be awesome if 'R CMD check' could do the above for us i.e. report 
> the amount of memory used by the examples. Any volunteer to request this 
> feature on the R-devel mailing list?
> 
> Hope this helps,
> H.
> 
>> Very best,
>> Wanding
>>> On Nov 29, 2021, at 12:15 PM, Hervé Pagès >> > wrote:
>>> 
>>> Hi Wanding,
>>> 
>>> A process cannot allocate more than 3Gb of memory on 32-bit Windows. See my 
>>> other post on this list for more information about this:
>>> 
>>> https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html 
>>> 
>>> 
>>> Cheers,
>>> H.
>>> 
>>> 
>>> On 22/11/2021 05:17, Zhou, Wanding wrote:
 Hi,
 Recently we are experience some memory issue on both development and 
 release (mostly Windows) that causes the sesame package build to fail. We 
 are trying to address it but it seems to run fine locally on our side.
 This is the error on the development branch
 Setting options('download.file.method.GEOquery'='auto')
 Setting options('GEOquery.inmemory.gpl'=FALSE)
 Error: processing vignette 'sesame.Rmd' failed with diagnostics:
 C stack usage  7977908 is too close to the limit
 And this is the error on the release branch
> data = data.frame(estimate=c(runif(10, 0, 10)))
> plotLollipop(data)
 Error in grid.newpage() :
   'Calloc' could not allocate memory (27541715 of 1 bytes)
 Calls:  -> print.ggplot -> grid.newpage
 Let me know if you are aware of something or have a clue. Any insight will 
 be super helpful!
 Thanks!
 Zoom link: https://us02web.zoom.us/j/4248839577 
 
 
 Wanding Zhou, Ph.D.
 Assistant Professor
 Office: CTRB 9050
 3501 Civic Center Blvd
 Philadelphia, PA 19104
 Lab: https://zhou-lab.github.io/ 
 Phone (o):  (215) 590-0473
 [[alternative HTML version deleted]]
 ___
 Bioc-devel@r-project.org  mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel 
 
>>> 
>>> -- 
>>> Hervé Pagès
>>> 
>>> Bioconductor Core Team
>>> hpages.on.git...@gmail.com 
> 
> -- 
> Hervé Pagès
> 
> Bioconductor Core Team
> hpages.on.git...@gmail.com

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Re: [Bioc-devel] [External] Memory error from sesame build

[Hervé Pagès]

On 29/11/2021 09:25, Zhou, Wanding wrote:
Thanks for the input Herve. I saw your post but can you help me confirm 
that mine is on the 32-bit windows since it says mingw32 (64-bit)?


Windows Server 2012 R2 Standard / x64

* using platform: x86_64-w64-mingw32 (64-bit)


This shows the Windows arch that R uses by default on Windows. But we 
use --force-multiarch when running 'R CMD check' on our Windows builders 
to force 'R CMD check' to run all the examples, unit tests, and 
vignettes in the two supported Windows archs: 32-bit and 64-bit.


The error was happening during the following step:

  ** running examples for arch 'i386'

and not during the following step:

  ** running examples for arch 'x64'

So yes, this is a Windows 32-bit only error.



http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html 



Does that mean all the examples added together cannot use over 3G 
memory?


Yes.

I still don't think I am using that much but I will remove some 
examples and see that solves the problem


Here is one way to see how much memory 'R CMD check' consumes when 
running the examples:


1. Run 'R CMD check' on the package. This collates all the examples in 
sesame.Rcheck/sesame-Ex.R.


2. Comment out the last line (quit('no')) in sesame.Rcheck/sesame-Ex.R.

3. From R do: source("sesame.Rcheck/sesame-Ex.R", echo=TRUE). At the 
same time, monitor memory usage in another terminal e.g. by running 
'top' on Linux/macOS.


4.Once all the examples have finished, do gc().

This is what I get on my laptop when doing the above with sesame 1.13.3:

> gc()

used   (Mb) gc trigger   (Mb)  max used   (Mb)

Ncells  15062911  804.5   24349446 1300.5  24349446 1300.5

Vcells 278380669 2123.9  473158124 3610.0 473157073 3610.0


That's a memory consumption of 4.9G which is confirmed by the 'top' 
command I was running in another terminal.


It would be awesome if 'R CMD check' could do the above for us i.e. 
report the amount of memory used by the examples. Any volunteer to 
request this feature on the R-devel mailing list?


Hope this helps,
H.



Very best,

Wanding


On Nov 29, 2021, at 12:15 PM, Hervé Pagès > wrote:


Hi Wanding,

A process cannot allocate more than 3Gb of memory on 32-bit Windows. 
See my other post on this list for more information about this:


https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html 



Cheers,
H.


On 22/11/2021 05:17, Zhou, Wanding wrote:

Hi,
Recently we are experience some memory issue on both development and 
release (mostly Windows) that causes the sesame package build to 
fail. We are trying to address it but it seems to run fine locally on 
our side.

This is the error on the development branch
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'sesame.Rmd' failed with diagnostics:
C stack usage  7977908 is too close to the limit
And this is the error on the release branch

data = data.frame(estimate=c(runif(10, 0, 10)))
plotLollipop(data)

Error in grid.newpage() :
  'Calloc' could not allocate memory (27541715 of 1 bytes)
Calls:  -> print.ggplot -> grid.newpage
Let me know if you are aware of something or have a clue. Any insight 
will be super helpful!

Thanks!
Zoom link: https://us02web.zoom.us/j/4248839577 



Wanding Zhou, Ph.D.
Assistant Professor
Office: CTRB 9050
3501 Civic Center Blvd
Philadelphia, PA 19104
Lab: https://zhou-lab.github.io/ 
Phone (o):  (215) 590-0473
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--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com 




--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Use set.seed inside function

[Henrik Bengtsson]

The easiest is to use withr::with_seed(), e.g.

> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"
> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"

It works by undoing globalenv()$.Random.seed after the random number
generator has updated.  If you want to roll your own version of this,
you need to make sure to handle the special case when there is no
pre-existing .Random.seed in globalenv().

Regarding packages and functions changing the random seed via a
set.seed() [without undoing it]: this should *never* be done, because
it will wreak havoc on a analyses and studies that rely on random
numbers.  My rule of thumb: only the end-user should be allowed to use
set.seed(), which should typically be done at the top of their R
scripts.

/Henrik

On Mon, Nov 29, 2021 at 1:23 PM Meng Chen  wrote:
>
> Thanks. I think it may work in theory, generating "enough" distinct colors
> is fairly easy. Then the problem will be how to find a subset of colors of
> size n, and the selected colors are still most distinguishable. I think I
> will do this with my eyes if no other methods, a tedious job.
> But at least for my curiosity, I still want to know if there are other ways
> to achieve this. I feel like 80% of people who use the distinctColorPallete
> function actually don't need the "random" feature :) Thanks.
>
> On Mon, Nov 29, 2021 at 9:39 PM James W. MacDonald  wrote:
>
> > It appears that you don't actually want random colors, but instead you
> > want the same colors each time. Why not just generate the vector of 'random
> > distinct colors' one time and save the vector of colors?
> >
> > -Original Message-
> > From: Bioc-devel  On Behalf Of Meng Chen
> > Sent: Monday, November 29, 2021 3:21 PM
> > To: bioc-devel@r-project.org
> > Subject: [Bioc-devel] Use set.seed inside function
> >
> > Dear BioC team and developers,
> >
> > I am using BiocCheck to check my package, it returns a warning:
> > " Remove set.seed usage in R code"
> >
> > I am using "set.seed" inside my functions, before calling function
> > distinctColorPalette (randomcoloR package) in order to generate
> > reproducible "random distinct colors". So what would be the best practice
> > to solve this warning? I think 1. use set.seed and don't change anything.
> > 2. use the set.seed function, but include something like below inside the
> > function *gl.seed <- .Random.seed* *on.exit(assign(".Random.seed", gl.seed,
> > envir = .GlobalEnv))* 3. use some other functions for the purpose
> >
> > Any suggestions will be appreciated. Thanks.
> > --
> > Best Regards,
> > Chen
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
> --
> Best Regards,
> Chen
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Use set.seed inside function

[Meng Chen]

Thanks. I think it may work in theory, generating "enough" distinct colors
is fairly easy. Then the problem will be how to find a subset of colors of
size n, and the selected colors are still most distinguishable. I think I
will do this with my eyes if no other methods, a tedious job.
But at least for my curiosity, I still want to know if there are other ways
to achieve this. I feel like 80% of people who use the distinctColorPallete
function actually don't need the "random" feature :) Thanks.

On Mon, Nov 29, 2021 at 9:39 PM James W. MacDonald  wrote:

> It appears that you don't actually want random colors, but instead you
> want the same colors each time. Why not just generate the vector of 'random
> distinct colors' one time and save the vector of colors?
>
> -Original Message-
> From: Bioc-devel  On Behalf Of Meng Chen
> Sent: Monday, November 29, 2021 3:21 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Use set.seed inside function
>
> Dear BioC team and developers,
>
> I am using BiocCheck to check my package, it returns a warning:
> " Remove set.seed usage in R code"
>
> I am using "set.seed" inside my functions, before calling function
> distinctColorPalette (randomcoloR package) in order to generate
> reproducible "random distinct colors". So what would be the best practice
> to solve this warning? I think 1. use set.seed and don't change anything.
> 2. use the set.seed function, but include something like below inside the
> function *gl.seed <- .Random.seed* *on.exit(assign(".Random.seed", gl.seed,
> envir = .GlobalEnv))* 3. use some other functions for the purpose
>
> Any suggestions will be appreciated. Thanks.
> --
> Best Regards,
> Chen
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best Regards,
Chen

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[Bioc-devel] Change bioconductor maintainer

[Li, Ziyi]

Hello,

I recently changed my institution and my email address. Could you update the 
maintainer email address of TOAST 
(https://bioconductor.org/packages/release/bioc/html/TOAST.html) to 
zl...@mdanderson.org?


Thank you!

Ziyi

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Re: [Bioc-devel] Use set.seed inside function

[James W. MacDonald]

It appears that you don't actually want random colors, but instead you want the 
same colors each time. Why not just generate the vector of 'random distinct 
colors' one time and save the vector of colors?

-Original Message-
From: Bioc-devel  On Behalf Of Meng Chen
Sent: Monday, November 29, 2021 3:21 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Use set.seed inside function

Dear BioC team and developers,

I am using BiocCheck to check my package, it returns a warning:
" Remove set.seed usage in R code"

I am using "set.seed" inside my functions, before calling function 
distinctColorPalette (randomcoloR package) in order to generate reproducible 
"random distinct colors". So what would be the best practice to solve this 
warning? I think 1. use set.seed and don't change anything.
2. use the set.seed function, but include something like below inside the 
function *gl.seed <- .Random.seed* *on.exit(assign(".Random.seed", gl.seed, 
envir = .GlobalEnv))* 3. use some other functions for the purpose

Any suggestions will be appreciated. Thanks.
--
Best Regards,
Chen

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[Bioc-devel] Use set.seed inside function

[Meng Chen]

Dear BioC team and developers,

I am using BiocCheck to check my package, it returns a warning:
" Remove set.seed usage in R code"

I am using "set.seed" inside my functions, before calling function
distinctColorPalette (randomcoloR package) in order to generate
reproducible "random distinct colors". So what would be the best practice
to solve this warning? I think
1. use set.seed and don't change anything.
2. use the set.seed function, but include something like below inside the
function
*gl.seed <- .Random.seed*
*on.exit(assign(".Random.seed", gl.seed, envir = .GlobalEnv))*
3. use some other functions for the purpose

Any suggestions will be appreciated. Thanks.
-- 
Best Regards,
Chen

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Re: [Bioc-devel] bpparam Non-deterministic Default

[Kasper Daniel Hansen]

This should be solved by the vignette appropriately calling set.seed and
explaining why they set the seed and why it is not done automatically. In a
visible code chunk.

On Sat, Nov 27, 2021 at 7:31 AM Spencer Nystrom 
wrote:

> This GitHub issue, although lengthy, discusses some of the technical
> difficulties associated with pulling from the random stream. I've linked to
> a comment from Martin that discusses this in particular, but there's other
> good stuff in the rest of the issue.
>
>
> https://github.com/Bioconductor/BiocParallel/pull/140#issuecomment-921627153
>
>-Spencer
>
>
> On Fri, Nov 26, 2021, 10:41 PM Ellis Patrick 
> wrote:
>
> > Hi All,
> >
> > Sorry I'm not an advanced user. What is the disadvantage of pulling the
> > default from .Random.seed? As a non-advanced user it took me way too long
> > to figure out that set.seed() doesn't work.
> >
> > Thanks,
> > Ellis
> >
> > -Original Message-
> > From: Bioc-devel  On Behalf Of Spencer
> > Nystrom
> > Sent: Saturday, 27 November 2021 2:15 PM
> > To: Dario Strbenac 
> > Cc: bioc-devel@r-project.org
> > Subject: Re: [Bioc-devel] bpparam Non-deterministic Default
> >
> > I agree with Martin. I think it is worse for beginners to falsely believe
> > their results are deterministic when they are not. This sounds like a
> > problem that should be solved with documentation and maybe even examples
> of
> > setting the RNG seed manually.
> >
> > I also worry about advanced users and pollution of RNG seed global state
> > by having packages assign their own seed. Just sounds like a mess for
> > little gain.
> >
> >   -Spencer
> >
> >
> > On Fri, Nov 26, 2021, 7:00 PM Dario Strbenac via Bioc-devel <
> > bioc-devel@r-project.org> wrote:
> >
> > > Hello,
> > >
> > > Might it instead made possible to set an RNGseed value by specifying
> > > one to bpparam but still get the automated back-end selection, so that
> > > it could easily be set to a particular value in an R package?
> > >
> > > --
> > > Dario Strbenac
> > > University of Sydney
> > > Camperdown NSW 2050
> > > Australia
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel.
> > > ethz.ch
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
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> >
> >
>
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>
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Re: [Bioc-devel] [External] Memory error from sesame build

[Zhou, Wanding]

Thanks for the input Herve. I saw your post but can you help me confirm that 
mine is on the 32-bit windows since it says mingw32 (64-bit)?

Windows Server 2012 R2 Standard / x64

* using platform: x86_64-w64-mingw32 (64-bit)


http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html

Does that mean all the examples added together cannot use over 3G memory? I 
still don't think I am using that much but I will remove some examples and see 
that solves the problem

Very best,

Wanding


On Nov 29, 2021, at 12:15 PM, Hervé Pagès 
mailto:hpages.on.git...@gmail.com>> wrote:

Hi Wanding,

A process cannot allocate more than 3Gb of memory on 32-bit Windows. See my 
other post on this list for more information about this:

 https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html

Cheers,
H.


On 22/11/2021 05:17, Zhou, Wanding wrote:
Hi,
Recently we are experience some memory issue on both development and release 
(mostly Windows) that causes the sesame package build to fail. We are trying to 
address it but it seems to run fine locally on our side.
This is the error on the development branch
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'sesame.Rmd' failed with diagnostics:
C stack usage  7977908 is too close to the limit
And this is the error on the release branch
data = data.frame(estimate=c(runif(10, 0, 10)))
plotLollipop(data)
Error in grid.newpage() :
  'Calloc' could not allocate memory (27541715 of 1 bytes)
Calls:  -> print.ggplot -> grid.newpage
Let me know if you are aware of something or have a clue. Any insight will be 
super helpful!
Thanks!
Zoom link: https://us02web.zoom.us/j/4248839577

Wanding Zhou, Ph.D.
Assistant Professor
Office: CTRB 9050
3501 Civic Center Blvd
Philadelphia, PA 19104
Lab:  https://zhou-lab.github.io/
Phone (o):  (215) 590-0473
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Bioconductor Core Team
hpages.on.git...@gmail.com


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Re: [Bioc-devel] Memory error from sesame build

[Hervé Pagès]

Hi Wanding,

A process cannot allocate more than 3Gb of memory on 32-bit Windows. See 
my other post on this list for more information about this:


  https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html

Cheers,
H.


On 22/11/2021 05:17, Zhou, Wanding wrote:

Hi,
Recently we are experience some memory issue on both development and release 
(mostly Windows) that causes the sesame package build to fail. We are trying to 
address it but it seems to run fine locally on our side.

This is the error on the development branch

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'sesame.Rmd' failed with diagnostics:
C stack usage  7977908 is too close to the limit

And this is the error on the release branch



data = data.frame(estimate=c(runif(10, 0, 10)))
plotLollipop(data)

Error in grid.newpage() :
   'Calloc' could not allocate memory (27541715 of 1 bytes)
Calls:  -> print.ggplot -> grid.newpage

Let me know if you are aware of something or have a clue. Any insight will be 
super helpful!

Thanks!


Zoom link: https://us02web.zoom.us/j/4248839577


Wanding Zhou, Ph.D.
Assistant Professor

Office: CTRB 9050
3501 Civic Center Blvd
Philadelphia, PA 19104
Lab:  https://zhou-lab.github.io/
Phone (o):  (215) 590-0473

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--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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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


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Landing page build status different from the build report

[Kern, Lori]

The builds reports are not all OK.  There is still an ERROR on the windows 
riesling1 on devel and windows tokay2 in release. Until all are OK it will 
default to ERROR because there is an ERROR in at least one platform:

http://bioconductor.org/checkResults/release/bioc-LATEST/bambu/

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




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 CHEN Ying 

Sent: Wednesday, November 24, 2021 10:25 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Landing page build status different from the build report

Hi,

I have recently pushed a change to fix the build error reported previously due 
to dependency packages' updates for bambu. Now the build report is all ok, but 
the landing page still shows error. Any suggestions to fix this?

Thank you,
Regards,
Ying
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