Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

[Chau, Reina]

Hi Martin,

That would be very helpful. Thanks so much! Right now, it is failing in one of 
the unit test cases. In particular, our core function, CaDrA::CaDrA, which is 
used to run permutation-based tests to determine whether the strength of the 
association between the set of features and the observed input scores (e.g., 
pathway activity, drug sensitivity, etc.) is greater than it would be expected 
by chance.

Here is a snippet of where the test failed in Mac and Linux ARM64 machine:

# R library
library(CaDrA)
library(testthat)

data("sim_FS”)
data("sim_Scores")

# Set seed
set.seed(21)

# ks_score
result <- CaDrA::CaDrA(
FS = sim_FS,
input_score = sim_Scores,
method = "ks_score",
weights = NULL,
alternative = "less",
top_N = 1,
search_start = NULL,
search_method = "both",
max_size = 7,
n_perm = 10,
plot = FALSE,
smooth = TRUE,
obs_best_score = NULL,
ncores = 1,
cache = FALSE,
cache_path = NULL
)

testthat::expect_length(result, 4L)
testthat::expect_type(result, "list")
testthat::expect_named(result,
 
c("key","perm_best_scores","obs_best_score","perm_pval"))
testthat::expect_type(result$key, "list")
testthat::expect_length(result$key, 11L)
testthat::expect_named(result$key,
 c("FS", "input_score", "method", "custom_function",
   "custom_parameters", "alternative", "weights", 
"top_N",
   "search_start", "search_method", "max_size"))
testthat::expect_type(result$key$FS, "double")

testthat::expect_equal(round(result$perm_best_scores[1:10], 5),
 c('TP_8'=0.34,
   'TP_10'=0.54,
   'TP_9'=0.37,
   'TP_6'=0.40,
   'TP_9'=0.38,
   'TP_9'=0.52,
   'TP_2'=0.44,
   'TP_2'=0.40,
   'TP_4'=0.44,
   'TP_9'=0.49))

testthat::expect_equal(round(result$obs_best_score, 2), c("TP_9"=0.66))

# A smooth factor of 1
c <- 1

# Add a smoothing factor of 1
# This is just to not return a p-value of 0
testthat::expect_equal(
round((sum(result$perm_best_scores[1:10] > 
result$obs_best_score)+c)/(10+c), 6),
c(0.090909)
)

Any helps or directions on how to resolve this problem would be be greatly 
appreciated!

Best,

Reina C.


On Oct 18, 2023, at 4:35 PM, Martin Grigorov  wrote:



On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina 
mailto:rcha...@bu.edu>> wrote:
Thank you both! I will look thru the links and see if I can implement a fix.

I'd be happy to test any patches if it will be easier for you !

Martin



Best,

Reina C.

On Oct 18, 2023, at 4:03 PM, Martin Grigorov 
mailto:martin.grigo...@gmail.com>> wrote:

Hi,

On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès 
mailto:hpages.on.git...@gmail.com>> wrote:
Hi Reina,

Note that CaDrA results on Mac ARM64 are also affected:
https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/

See Martin Grigorov's blog post here
https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
for how to debug Linux ARM64 related issues on a x86_64 host.

Note that different architectures use slightly different floating point
arithmetic with slightly different precision. This can affect the
results of your numerical calculations. The degree to which they are
affected will vary greatly depending on what calculations you perform
and how you perform them. So it's important to implement things in a way
that tries to minimize the impact of these variations as much as possible.

See https://go.dev/ref/spec#Floating_point_operators for some further 
explanation of the problem and possible fix by explicit rounding (in Golang, 
but I guess something similar happens in R)


Best,

H.


On 10/18/23 10:46, Chau, Reina wrote:
> Hi Bioconductor Core Team,
>
> I’m the maintainer of CaDrA package, and recently, I notice that my package 
> built successfully for all platforms except on Kunpeng2 Linux machine 
> (seehttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/
>   
> andhttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html)
>
> I did try to figure out what is causing the different results using this 
> particular platform compare with others but with no resolves.
>
> Hope you can give me some guidance or feedback of why the build is failing 
> for this particular case.
>
> Thanks so much!
>
> Best,
>
> Reina C.
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

--
Hervé Pagès

Bioconductor Core Team

Re: [Bioc-devel] groHMM package error

[Kern, Lori via Bioc-devel]

There is no RELEASE_3_18 branch until the release next week (created 
automatically by the core team on release day) .  All updates should be pushed 
to the devel branch.




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 Tulip Nandu 

Sent: Wednesday, October 18, 2023 4:30 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] groHMM package error

Hi,

I just got an email from the Bioconductor stating,

According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$


I feel it's the version issue 3.17 to 3.18 and I need to release the package to 
3.18 too. But moment I try to update it throws up a error message:

git checkout RELEASE_3_18
error: pathspec 'RELEASE_3_18' did not match any file(s) known to git

Can anyone help me with this update and error.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

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Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

[Martin Grigorov]

On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina  wrote:

> Thank you both! I will look thru the links and see if I can implement a
> fix.
>

I'd be happy to test any patches if it will be easier for you !

Martin



>
> Best,
>
> Reina C.
>
> On Oct 18, 2023, at 4:03 PM, Martin Grigorov 
> wrote:
>
> Hi,
>
> On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès 
> wrote:
>
>> Hi Reina,
>>
>> Note that CaDrA results on Mac ARM64 are also affected:
>> https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/
>>
>> See Martin Grigorov's blog post here
>>
>> https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
>>
>> for how to debug Linux ARM64 related issues on a x86_64 host.
>>
>> Note that different architectures use slightly different floating point
>> arithmetic with slightly different precision. This can affect the
>> results of your numerical calculations. The degree to which they are
>> affected will vary greatly depending on what calculations you perform
>> and how you perform them. So it's important to implement things in a way
>> that tries to minimize the impact of these variations as much as possible.
>>
>
> See https://go.dev/ref/spec#Floating_point_operators for some further
> explanation of the problem and possible fix by explicit rounding (in
> Golang, but I guess something similar happens in R)
>
>
>>
>> Best,
>>
>> H.
>>
>>
>> On 10/18/23 10:46, Chau, Reina wrote:
>> > Hi Bioconductor Core Team,
>> >
>> > I’m the maintainer of CaDrA package, and recently, I notice that my
>> package built successfully for all platforms except on Kunpeng2 Linux
>> machine (seehttps://
>> bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/  andhttps://
>> bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html
>> )
>> >
>> > I did try to figure out what is causing the different results using
>> this particular platform compare with others but with no resolves.
>> >
>> > Hope you can give me some guidance or feedback of why the build is
>> failing for this particular case.
>> >
>> > Thanks so much!
>> >
>> > Best,
>> >
>> > Reina C.
>> >
>> >   [[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
>>
>> [[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] groHMM package error

[Martin Grigorov]

Hi,

On Wed, Oct 18, 2023 at 11:31 PM Tulip Nandu 
wrote:

> Hi,
>
> I just got an email from the Bioconductor stating,
>
> According to the Multiple platform build/check report for BioC 3.18,
> the groHMM package has the following problem(s):
>
>  o ERROR for 'R CMD build' on nebbiolo2. See the details here:
>
> https://urldefense.com/v3/__https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$
>
>
> I feel it's the version issue 3.17 to 3.18 and I need to release the
> package to 3.18 too. But moment I try to update it throws up a error
> message:
>
> git checkout RELEASE_3_18
> error: pathspec 'RELEASE_3_18' did not match any file(s) known to git
>

Use "devel" instead of "RELEASE_3_18".
3.18 is not released yet.

Martin


> Can anyone help me with this update and error.
>
> Regards,
>
> Tulip.
>
>
> 
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
>
> [[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] groHMM package error

[Tulip Nandu]

Is this error to be neglected then?

Package: groHMM
Version: 1.35.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs 
--no-resave-data groHMM
StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 112.0 seconds
RetCode: 1
Status:   ERROR
PackageFile: None
PackageFileSize: NA


According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$

Let me know.

Thank you so much.

Regards,

Tulip.



From: Kern, Lori 
Sent: Wednesday, October 18, 2023 3:36 PM
To: Tulip Nandu ; bioc-devel@r-project.org 

Subject: Re: groHMM package error


EXTERNAL MAIL

There is no RELEASE_3_18 branch until the release next week (created 
automatically by the core team on release day) .  All updates should be pushed 
to the devel branch.




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 Tulip Nandu 

Sent: Wednesday, October 18, 2023 4:30 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] groHMM package error

Hi,

I just got an email from the Bioconductor stating,

According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$


I feel it's the version issue 3.17 to 3.18 and I need to release the package to 
3.18 too. But moment I try to update it throws up a error message:

git checkout RELEASE_3_18
error: pathspec 'RELEASE_3_18' did not match any file(s) known to git

Can anyone help me with this update and error.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list

[Bioc-devel] groHMM package error

[Tulip Nandu]

Hi,

I just got an email from the Bioconductor stating,

According to the Multiple platform build/check report for BioC 3.18,
the groHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
 
https://urldefense.com/v3/__https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$


I feel it's the version issue 3.17 to 3.18 and I need to release the package to 
3.18 too. But moment I try to update it throws up a error message:

git checkout RELEASE_3_18
error: pathspec 'RELEASE_3_18' did not match any file(s) known to git

Can anyone help me with this update and error.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

[Chau, Reina]

Thank you both! I will look thru the links and see if I can implement a fix.

Best,

Reina C.

On Oct 18, 2023, at 4:03 PM, Martin Grigorov  wrote:

Hi,

On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès 
mailto:hpages.on.git...@gmail.com>> wrote:
Hi Reina,

Note that CaDrA results on Mac ARM64 are also affected:
https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/

See Martin Grigorov's blog post here
https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
for how to debug Linux ARM64 related issues on a x86_64 host.

Note that different architectures use slightly different floating point
arithmetic with slightly different precision. This can affect the
results of your numerical calculations. The degree to which they are
affected will vary greatly depending on what calculations you perform
and how you perform them. So it's important to implement things in a way
that tries to minimize the impact of these variations as much as possible.

See https://go.dev/ref/spec#Floating_point_operators for some further 
explanation of the problem and possible fix by explicit rounding (in Golang, 
but I guess something similar happens in R)


Best,

H.


On 10/18/23 10:46, Chau, Reina wrote:
> Hi Bioconductor Core Team,
>
> I’m the maintainer of CaDrA package, and recently, I notice that my package 
> built successfully for all platforms except on Kunpeng2 Linux machine 
> (seehttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/
>   
> andhttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html)
>
> I did try to figure out what is causing the different results using this 
> particular platform compare with others but with no resolves.
>
> Hope you can give me some guidance or feedback of why the build is failing 
> for this particular case.
>
> Thanks so much!
>
> Best,
>
> Reina C.
>
>   [[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

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

[Martin Grigorov]

Hi,

On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès 
wrote:

> Hi Reina,
>
> Note that CaDrA results on Mac ARM64 are also affected:
> https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/
>
> See Martin Grigorov's blog post here
> https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
> for how to debug Linux ARM64 related issues on a x86_64 host.
>
> Note that different architectures use slightly different floating point
> arithmetic with slightly different precision. This can affect the
> results of your numerical calculations. The degree to which they are
> affected will vary greatly depending on what calculations you perform
> and how you perform them. So it's important to implement things in a way
> that tries to minimize the impact of these variations as much as possible.
>

See https://go.dev/ref/spec#Floating_point_operators for some further
explanation of the problem and possible fix by explicit rounding (in
Golang, but I guess something similar happens in R)


>
> Best,
>
> H.
>
>
> On 10/18/23 10:46, Chau, Reina wrote:
> > Hi Bioconductor Core Team,
> >
> > I’m the maintainer of CaDrA package, and recently, I notice that my
> package built successfully for all platforms except on Kunpeng2 Linux
> machine (seehttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/
> andhttps://
> bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html
> )
> >
> > I did try to figure out what is causing the different results using this
> particular platform compare with others but with no resolves.
> >
> > Hope you can give me some guidance or feedback of why the build is
> failing for this particular case.
> >
> > Thanks so much!
> >
> > Best,
> >
> > Reina C.
> >
> >   [[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
>
> [[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] Build error for CaDrA package on kunpeng2 Linux machine

[Hervé Pagès]

Hi Reina,

Note that CaDrA results on Mac ARM64 are also affected: 
https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/

See Martin Grigorov's blog post here 
https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/ 
for how to debug Linux ARM64 related issues on a x86_64 host.

Note that different architectures use slightly different floating point 
arithmetic with slightly different precision. This can affect the 
results of your numerical calculations. The degree to which they are 
affected will vary greatly depending on what calculations you perform 
and how you perform them. So it's important to implement things in a way 
that tries to minimize the impact of these variations as much as possible.

Best,

H.


On 10/18/23 10:46, Chau, Reina wrote:
> Hi Bioconductor Core Team,
>
> I’m the maintainer of CaDrA package, and recently, I notice that my package 
> built successfully for all platforms except on Kunpeng2 Linux machine 
> (seehttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/  
> andhttps://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html)
>
> I did try to figure out what is causing the different results using this 
> particular platform compare with others but with no resolves.
>
> Hope you can give me some guidance or feedback of why the build is failing 
> for this particular case.
>
> Thanks so much!
>
> Best,
>
> Reina C.
>
>   [[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

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[Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

[Chau, Reina]

Hi Bioconductor Core Team,

I’m the maintainer of CaDrA package, and recently, I notice that my package 
built successfully for all platforms except on Kunpeng2 Linux machine (see 
https://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/ and 
https://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html)

I did try to figure out what is causing the different results using this 
particular platform compare with others but with no resolves.

Hope you can give me some guidance or feedback of why the build is failing for 
this particular case.

Thanks so much!

Best,

Reina C.

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Re: [Bioc-devel] Push update to an existing remote branch

[Jennifer Wokaty]

Hi Carlotta,

The branch is named devel on git.bioconductor.org. If you want to push from 
your local main branch to your repo on git.bioconductor.org, you should do

git push upstream main:devel

See https://contributions.bioconductor.org/git-version-control.html for more 
details.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team

From: Bioc-devel  on behalf of Carlotta 
Meyring 
Sent: Wednesday, October 18, 2023 9:26 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Push update to an existing remote branch

* This email originates from a sender outside of CUNY. Verify the sender before 
replying or clicking on links and attachments. *

Hi all,



I have a package in review on 
g...@git.bioconductor.org and I have added a 
remote named upstream pointing to my package there. I want to push an updated 
version and



$ git push origin main



Works well, however



$ git push upstream main


Doesn't work with the error message being:

error: cannot spawn 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys__%3B!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C2fde39c6fc9c42077c1c08dbcfddf81f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638332324514380110%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ONFWPeZ%2Fbv%2BprbBfT7sdnkCb%2BUvhp74JHSfq0vnctZQ%3D=0
 : No such file or directory
error: cannot spawn 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys__%3B!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C2fde39c6fc9c42077c1c08dbcfddf81f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638332324514380110%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ONFWPeZ%2Fbv%2BprbBfT7sdnkCb%2BUvhp74JHSfq0vnctZQ%3D=0
 : No such file or directory
fatal: unable to fork


I already checked that the key is connected with my github account.
Any help would be appreciated!

Thanks in advance!

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Push update to an existing remote branch

[Kern, Lori via Bioc-devel]

Bioconductor does not have a main branch.  The default branch on BIoconductor 
is devel.  If your local or github branch is called main, you need to map the 
main branch to the devel branch of Bioconductor.

git push upstream main:devel



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 Carlotta 
Meyring 
Sent: Wednesday, October 18, 2023 9:26 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Push update to an existing remote branch

Hi all,



I have a package in review on 
g...@git.bioconductor.org and I have added a 
remote named upstream pointing to my package there. I want to push an updated 
version and



$ git push origin main



Works well, however



$ git push upstream main


Doesn't work with the error message being:

error: cannot spawn 
https://secure-web.cisco.com/1nxrZJ2rsPTsMHIsPIoKr6ovQYHV0EbhTufEE3HI_Ppt02VU4RFHpyCVxvQEMB8naZDNQ8JS6sIeVIPvbbbffs3TI_jVWbuX5W1tDSvaijeo_QuHKVJjACBvfhMpVUFih_smzyq0d5qMQrSgecAns9ZKmEfFvLZAJDpkSMS9YdGp-ReIim6rfLyXcdjlhPmcZvoUpqfmjlROrOiS0ccjtLxrpVqym5nlaUWaofmVZew_b-2kHDiLQBy8_ybI2bG7huBOqYgM2n379_a3oUBtQ_I4JBgQHvyEuW1C3drXgA1r5A3NfL0BifhlpvX9ncxDo/https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys%3A
 No such file or directory
error: cannot spawn 
https://secure-web.cisco.com/1nxrZJ2rsPTsMHIsPIoKr6ovQYHV0EbhTufEE3HI_Ppt02VU4RFHpyCVxvQEMB8naZDNQ8JS6sIeVIPvbbbffs3TI_jVWbuX5W1tDSvaijeo_QuHKVJjACBvfhMpVUFih_smzyq0d5qMQrSgecAns9ZKmEfFvLZAJDpkSMS9YdGp-ReIim6rfLyXcdjlhPmcZvoUpqfmjlROrOiS0ccjtLxrpVqym5nlaUWaofmVZew_b-2kHDiLQBy8_ybI2bG7huBOqYgM2n379_a3oUBtQ_I4JBgQHvyEuW1C3drXgA1r5A3NfL0BifhlpvX9ncxDo/https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys%3A
 No such file or directory
fatal: unable to fork


I already checked that the key is connected with my github account.
Any help would be appreciated!

Thanks in advance!

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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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] Hub access temporarily unavailable

[Kern, Lori via Bioc-devel]

Hello Bioconductor,

We are experiencing temporary downtime of the experimenthub and annotationhub. 
We are working on a resolution as soon as possible. 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 
delete this email message from your computer. Thank you.
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[Bioc-devel] Push update to an existing remote branch

[Carlotta Meyring]

Hi all,



I have a package in review on 
g...@git.bioconductor.org and I have added a 
remote named upstream pointing to my package there. I want to push an updated 
version and



$ git push origin main



Works well, however



$ git push upstream main


Doesn't work with the error message being:

error: cannot spawn https://github.com/myowngithubname.keys: No such file or 
directory
error: cannot spawn https://github.com/myowngithubname.keys: No such file or 
directory
fatal: unable to fork


I already checked that the key is connected with my github account.
Any help would be appreciated!

Thanks in advance!

[[alternative HTML version deleted]]

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