[Bioc-devel] skipped, ERROR

2020-10-29 Thread ???? 
Dear Devel team��


My package encountered an error "ERROR: this R is version 4.0.3, package 
'RLassoCox' requires R = 4.1".


I don't know if it is because I added Depends: R (= 4.1) in the DESCRIPTION 
file as suggested by BiocCheck. How to fix this error?
===  R CMD BUILD === * 
checking for file RLassoCox/DESCRIPTION ... OK * preparing RLassoCox: * 
checking DESCRIPTION meta-information ... OK * installing the package to 
process help pages   --- ERROR: this R is 
version 4.0.3, package 'RLassoCox' requires R = 4.1
Best regards,Wei Liu
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Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Damian Szklarczyk 
Dear Herve,

Thank you for the feedback. The IP is indeed correct.
I’ll write if it again starts being recurring issue on one platform.

Thanks and all the best,
Damian.

--
Damian Szklarczyk, PhD
Bioinformatics / Systems Biology Group

SIB | Swiss Institute of Bioinformatics
UZH, Institute of Molecular Life Sciences
Winterthurerstrasse 190
8057 Zurich, Switzerland

Mobile: +41 788 3232 97
Office:   +41 446 3531 49

> On 29 Oct 2020, at 22:39, Pages, Herve  wrote:
> 
> Hi Damian,
> 
> Looks like today the problem went away and that STRINGdb 2.2.0 is now 
> available on all platforms. We should still keep an eye on this for a 
> few more days though so we get an idea of whether this is intermittent 
> or gone for good.
> 
> Cheers,
> H.
> 
> 
> On 10/28/20 23:45, Pages, Herve wrote:
>> Hi Damian,
>> 
>> stringdb-static.org resolves to 185.111.60.15 on malbec1 like on
>> nebbiolo1 and merida1.
>> 
>> Also the following code runs with no problem in an interactive session
>> on malbec1:
>> 
>>> tmp <- tempfile()
>>> 
>> download.file("https://urldefense.proofpoint.com/v2/url?u=https-3A__stringdb-2Dstatic.org_download_protein.links.v11.0_9606.protein.links.v11.0.txt.gz=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=NwTs0bD-eq0uQyUXca_bcbP1ir-B0xVXgIMxsAUsiDQ=5q0wAWGX7D7LgDIC36EhG47PWjTLd5JSqOKodh1FTy8=
>>  ",
>> tmp)
>> trying URL
>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__stringdb-2Dstatic.org_download_protein.links.v11.0_9606.protein.links.v11.0.txt.gz=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=NwTs0bD-eq0uQyUXca_bcbP1ir-B0xVXgIMxsAUsiDQ=5q0wAWGX7D7LgDIC36EhG47PWjTLd5JSqOKodh1FTy8='
>> Content type 'application/x-gzip' length 71241372 bytes (67.9 MB)
>> ==
>> downloaded 67.9 MB
>> 
>> I'm not sure why this fails in the context of the nightly builds. Let's
>> hope it's just an intermittent connectivity issue between malbec1 and
>> stringdb-static.org. We'll keep an eye on this.
>> 
>> Best,
>> H.
>> 
>> 
>> On 10/27/20 02:15, Damian Szklarczyk wrote:
>>> Dear Devel team,
>>> 
>>> My package is failing on one of the platforms (malbec1) and I can’t 
>>> reproduce the problem.
>>> 
>>> It’s a simple timeout on file download.
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_STRINGdb_malbec1-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=5sxGQVYMTq8docWLZxPmXrvnPYISVOIT90tYs-Q4pcw=
>>> 
>>> We have been recently DDoS’ed and in response we have changed the 
>>> infrastructure a bit.
>>> Long story short, I think melbec1 didn’t update the DNS, and still points 
>>> to the attacked IP which is bandwidth limited due to the attack.
>>> 
>>> It’s just guess, but before the DNS switch (about two weeks ago) the other 
>>> platforms were also failing in similar manner.
>>> Is it possible to confirm that resolved IP for the failing address is the 
>>> same on Malbec1 as on the other platforms?
>>> 
>>> Best regards,
>>> Damian.
>>> 
>>> 
>>> —
>>> Damian Szklarczyk, PhD
>>> Bioinformatics / Systems Biology Group
>>> 
>>> SIB | Swiss Institute of Bioinformatics
>>> UZH, Institute of Molecular Life Sciences
>>> Winterthurerstrasse 190
>>> 8057 Zurich, Switzerland
>>> 
>>> Mobile: +41 788 3232 97
>>> Office:   +41 446 3531 49
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=GtVR-YCXpuQmZBpaD5xQdIaA2_QWeUcomsphmCyEzYg=
>>> 
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319


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Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Pages, Herve 
Hi Damian,

Looks like today the problem went away and that STRINGdb 2.2.0 is now 
available on all platforms. We should still keep an eye on this for a 
few more days though so we get an idea of whether this is intermittent 
or gone for good.

Cheers,
H.


On 10/28/20 23:45, Pages, Herve wrote:
> Hi Damian,
> 
> stringdb-static.org resolves to 185.111.60.15 on malbec1 like on
> nebbiolo1 and merida1.
> 
> Also the following code runs with no problem in an interactive session
> on malbec1:
> 
>   > tmp <- tempfile()
>   >
> download.file("https://urldefense.proofpoint.com/v2/url?u=https-3A__stringdb-2Dstatic.org_download_protein.links.v11.0_9606.protein.links.v11.0.txt.gz=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=NwTs0bD-eq0uQyUXca_bcbP1ir-B0xVXgIMxsAUsiDQ=5q0wAWGX7D7LgDIC36EhG47PWjTLd5JSqOKodh1FTy8=
>  ",
> tmp)
> trying URL
> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__stringdb-2Dstatic.org_download_protein.links.v11.0_9606.protein.links.v11.0.txt.gz=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=NwTs0bD-eq0uQyUXca_bcbP1ir-B0xVXgIMxsAUsiDQ=5q0wAWGX7D7LgDIC36EhG47PWjTLd5JSqOKodh1FTy8='
> Content type 'application/x-gzip' length 71241372 bytes (67.9 MB)
> ==
> downloaded 67.9 MB
> 
> I'm not sure why this fails in the context of the nightly builds. Let's
> hope it's just an intermittent connectivity issue between malbec1 and
> stringdb-static.org. We'll keep an eye on this.
> 
> Best,
> H.
> 
> 
> On 10/27/20 02:15, Damian Szklarczyk wrote:
>> Dear Devel team,
>>
>> My package is failing on one of the platforms (malbec1) and I can’t 
>> reproduce the problem.
>>
>> It’s a simple timeout on file download.
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_STRINGdb_malbec1-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=5sxGQVYMTq8docWLZxPmXrvnPYISVOIT90tYs-Q4pcw=
>>
>> We have been recently DDoS’ed and in response we have changed the 
>> infrastructure a bit.
>> Long story short, I think melbec1 didn’t update the DNS, and still points to 
>> the attacked IP which is bandwidth limited due to the attack.
>>
>> It’s just guess, but before the DNS switch (about two weeks ago) the other 
>> platforms were also failing in similar manner.
>> Is it possible to confirm that resolved IP for the failing address is the 
>> same on Malbec1 as on the other platforms?
>>
>> Best regards,
>> Damian.
>>
>>
>> —
>> Damian Szklarczyk, PhD
>> Bioinformatics / Systems Biology Group
>>
>> SIB | Swiss Institute of Bioinformatics
>> UZH, Institute of Molecular Life Sciences
>> Winterthurerstrasse 190
>> 8057 Zurich, Switzerland
>>
>> Mobile: +41 788 3232 97
>> Office:   +41 446 3531 49
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=GtVR-YCXpuQmZBpaD5xQdIaA2_QWeUcomsphmCyEzYg=
>>
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Bioconductor Git Credentials

2020-10-29 Thread Turaga, Nitesh 
Hi,

It seems you’ve never activated your account. Please try 
https://git.bioconductor.org/BiocCredentials/account_activation first and then 
add an SSH key.

Nitesh

On Oct 28, 2020, at 2:48 PM, Wubing Zhang 
mailto:watson5bzh...@gmail.com>> wrote:

Hi Nitesh,

As you suggested, I tried the password reset option, but I didn't get any 
email. So I can't add a new SSH key to my account. Could you help me with that?

Thanks
Wubing Zhang
CLS11025, 3 Blackfan Circle, Boston 02115
Department of Data Sciences
Dana-Farber Cancer Institute
Phone: +1 617 319 5887


On Mon, Oct 26, 2020 at 1:29 PM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi,

1. You can use the password reset link 
https://git.bioconductor.org/BiocCredentials/password_reset/
 and add a new SSH key to your account which is also on your new machine.

2. You cannot update the RELEASE_3_11 branch anymore. The Bioc 3.12 release 
happens in a couple of days. Check the 
http://bioconductor.org/developers/release-schedule/

Best,

Nitesh

On Oct 26, 2020, at 1:27 PM, Wubing Zhang 
mailto:watson5bzh...@gmail.com>> wrote:

Hi,

I'm the maintainer of the package "MAGeCKFlute" and I got two problems on the 
maintenance of the package.
1. I want to use a different machine in the future to maintain the package, but 
I can't log in to the git credentials website 
(https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/)
 anymore.
2. I tried to update the package on the RELEASE_3_11 branch and got a fatal 
error (hook declined to update refs/heads/RELEASE_3_11).
Could you please help me to fix the two problems? Thanks in advance!

Best,
Wubing Zhang
CLS11025, 3 Blackfan Circle, Boston 02115
Department of Data Sciences
Dana-Farber Cancer Institute
Phone: +1 617 319 5887


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Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Pages, Herve 
Hi Damian,

stringdb-static.org resolves to 185.111.60.15 on malbec1 like on 
nebbiolo1 and merida1.

Also the following code runs with no problem in an interactive session 
on malbec1:

 > tmp <- tempfile()
 > 
download.file("https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz;,
 
tmp)
trying URL 
'https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/x-gzip' length 71241372 bytes (67.9 MB)
==
downloaded 67.9 MB

I'm not sure why this fails in the context of the nightly builds. Let's 
hope it's just an intermittent connectivity issue between malbec1 and 
stringdb-static.org. We'll keep an eye on this.

Best,
H.


On 10/27/20 02:15, Damian Szklarczyk wrote:
> Dear Devel team,
> 
> My package is failing on one of the platforms (malbec1) and I can’t reproduce 
> the problem.
> 
> It’s a simple timeout on file download.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_STRINGdb_malbec1-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=5sxGQVYMTq8docWLZxPmXrvnPYISVOIT90tYs-Q4pcw=
> 
> We have been recently DDoS’ed and in response we have changed the 
> infrastructure a bit.
> Long story short, I think melbec1 didn’t update the DNS, and still points to 
> the attacked IP which is bandwidth limited due to the attack.
> 
> It’s just guess, but before the DNS switch (about two weeks ago) the other 
> platforms were also failing in similar manner.
> Is it possible to confirm that resolved IP for the failing address is the 
> same on Malbec1 as on the other platforms?
> 
> Best regards,
> Damian.
> 
> 
> —
> Damian Szklarczyk, PhD
> Bioinformatics / Systems Biology Group
> 
> SIB | Swiss Institute of Bioinformatics
> UZH, Institute of Molecular Life Sciences
> Winterthurerstrasse 190
> 8057 Zurich, Switzerland
> 
> Mobile: +41 788 3232 97
> Office:   +41 446 3531 49
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VCJIZLg4z8KBx_40fL6k8tTqA1sdrezVR9o9tjHz11Y=GtVR-YCXpuQmZBpaD5xQdIaA2_QWeUcomsphmCyEzYg=
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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