Re: [Bioc-devel] Querying web resources slow in Windows

[Richard Virgen-Slane]

I had a similar issue in the past. It was during vignette builiding. I
fixed it by adding the argument “result=FALSE” in the r code.

On Mon, Sep 30, 2019 at 9:25 AM Alberto Valdeolivas 
wrote:

> Dear Bioc-Team,
>
> I am submitting the following new package to Bioconductor:
>
> https://github.com/Bioconductor/Contributions/issues/1263
>
> R CMD check results in a TIMEOUT when running in Windows server, whereas it
> runs much faster in Linux and MAC:
>
>
> http://bioconductor.org/spb_reports/OmnipathR_buildreport_20190930111332.html
>
> <
> http://bioconductor.org/spb_reports/OmnipathR_buildreport_20190925041516.html
> >I
> am querying web resources following the template function suggested in the
> Bioconductor "How to". However, it seems that my queries work much faster
> in Unix and MAC than in Windows.
>
> Is this a common issue? Where are these different between OS coming from?
> Any clue on how to improve the performance in Windows?
>
> Many thanks and best regards,
> Alberto.
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] Large file problem in git

[Turaga, Nitesh]

Try BFG cleaner https://rtyley.github.io/bfg-repo-cleaner/

But I agree with what Herve says. You may use this on your own github repo if 
you'd like. But leaving it as is, is a good option. 

On 9/30/19, 10:57 PM, "Bioc-devel on behalf of Pages, Herve" 
 wrote:

Hi Jelena,

The .Rproj.user/ folder and the .git/ folder are 2 different things. Not 
sure exactly which one is causing you problem but they shouldn't.

The .Rproj.user/ folder is an RStudio thing that should not be added to 
git so make sure it's listed in your .gitignore file.

The .git folder is a place where the git client stores information about 
your local git clone. What is stored there is really git internal 
business and you should never touch or try to alter the content of this 
folder. Note that there is no need to list this one on your .gitignore 
file because the git client already knows about this folder and will 
ignore it. Nothing in this folder will ever get staged, committed, or 
pushed so having files larger than 5MB there should not be an issue.

H.

On 9/30/19 07:35, Cuklina  Jelena wrote:
> Dear all,
> 
> I have a WARNING, caused by the file larger than 5 MB:
> 
>  From the file name,
> .Rproj.user/4185876F/ctx/ctx-17050/environment
>
.git/objects/pack/pack-88dfd7e4c8ad695717e8d77594e9c340fabcc39f.pack
> 
> it looks like it’s an R project environment file which was out of 
gitignore at some point, so should be safe to get rid of it. I have quite 
limited experience with git to judge that fully, so I have two questions:
> 1) How do I make sure nothing valuable is in this pack?
> 2) How do I remove it safely?
> 
> Best regards,
> Jelena.
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> 
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> 

-- 
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] Large file problem in git

[Pages, Herve]

Hi Jelena,

The .Rproj.user/ folder and the .git/ folder are 2 different things. Not 
sure exactly which one is causing you problem but they shouldn't.

The .Rproj.user/ folder is an RStudio thing that should not be added to 
git so make sure it's listed in your .gitignore file.

The .git folder is a place where the git client stores information about 
your local git clone. What is stored there is really git internal 
business and you should never touch or try to alter the content of this 
folder. Note that there is no need to list this one on your .gitignore 
file because the git client already knows about this folder and will 
ignore it. Nothing in this folder will ever get staged, committed, or 
pushed so having files larger than 5MB there should not be an issue.

H.

On 9/30/19 07:35, Cuklina  Jelena wrote:
> Dear all,
> 
> I have a WARNING, caused by the file larger than 5 MB:
> 
>  From the file name,
> .Rproj.user/4185876F/ctx/ctx-17050/environment
>.git/objects/pack/pack-88dfd7e4c8ad695717e8d77594e9c340fabcc39f.pack
> 
> it looks like it’s an R project environment file which was out of gitignore 
> at some point, so should be safe to get rid of it. I have quite limited 
> experience with git to judge that fully, so I have two questions:
> 1) How do I make sure nothing valuable is in this pack?
> 2) How do I remove it safely?
> 
> Best regards,
> Jelena.
> 
>   [[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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V8sRletkOxpgakacSWr3_gWgGBFN_uoociRf-EQwOI4=DQsva-NURI04uxAPZlf1hU-5gOnuV-HxfUdYk60APc4=
> 

-- 
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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[Bioc-devel] Querying web resources slow in Windows

[Alberto Valdeolivas]

Dear Bioc-Team,

I am submitting the following new package to Bioconductor:

https://github.com/Bioconductor/Contributions/issues/1263

R CMD check results in a TIMEOUT when running in Windows server, whereas it
runs much faster in Linux and MAC:

http://bioconductor.org/spb_reports/OmnipathR_buildreport_20190930111332.html

I
am querying web resources following the template function suggested in the
Bioconductor "How to". However, it seems that my queries work much faster
in Unix and MAC than in Windows.

Is this a common issue? Where are these different between OS coming from?
Any clue on how to improve the performance in Windows?

Many thanks and best regards,
Alberto.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] pwrEWAS - checkResults error

[Shepherd, Lori]

There is a separate Experiment data package pwrEWAS.data correct?

I think this is our mistake and it wasn't added to the experiment data package 
manifest.  We will correct on our end.  The next Data Experiment package builds 
will happen Tuesday so the software package will not clear up until later in 
the week.



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 Graw, Stefan H 

Sent: Monday, September 30, 2019 10:26 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] pwrEWAS - checkResults error

Dear Bioc-Team,

A packages (pwrEWAS) I submitted caused an error in checkResults:

https://bioconductor.org/checkResults/3.10/bioc-LATEST/pwrEWAS/malbec1-install.html

ERROR: dependency 'pwrEWAS.data' is not available for package 'pwrEWAS'

The error was caused by failing to load the related ExperimentHub package 
(pwrEWAS.data).
How do I address this issue?

Thank you,
Stefan




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Re: [Bioc-devel] pwrEWAS - checkResults error

[Graw, Stefan H]

Hey Lori,

Yes, pwrEWAS.data is a separate ExperimentHub package to cache the data.
The package was originally submitted as pwrEWAS_data and subsequently changed 
to pwrEWAS.data. Maybe that cause the error.

Thank you for looking into this.
Stefan

From: Shepherd, Lori 
Sent: Monday, September 30, 2019 9:40 AM
To: Graw, Stefan H ; bioc-devel@r-project.org
Subject: Re: pwrEWAS - checkResults error

There is a separate Experiment data package pwrEWAS.data correct?

I think this is our mistake and it wasn't added to the experiment data package 
manifest.  We will correct on our end.  The next Data Experiment package builds 
will happen Tuesday so the software package will not clear up until later in 
the week.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Graw, Stefan H mailto:shg...@uams.edu>>
Sent: Monday, September 30, 2019 10:26 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] pwrEWAS - checkResults error

Dear Bioc-Team,

A packages (pwrEWAS) I submitted caused an error in checkResults:

https://bioconductor.org/checkResults/3.10/bioc-LATEST/pwrEWAS/malbec1-install.html

ERROR: dependency 'pwrEWAS.data' is not available for package 'pwrEWAS'

The error was caused by failing to load the related ExperimentHub package 
(pwrEWAS.data).
How do I address this issue?

Thank you,
Stefan




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[Bioc-devel] Large file problem in git

[Cuklina Jelena]

Dear all,

I have a WARNING, caused by the file larger than 5 MB:

From the file name,
.Rproj.user/4185876F/ctx/ctx-17050/environment
  .git/objects/pack/pack-88dfd7e4c8ad695717e8d77594e9c340fabcc39f.pack

it looks like it’s an R project environment file which was out of gitignore at 
some point, so should be safe to get rid of it. I have quite limited experience 
with git to judge that fully, so I have two questions:
1) How do I make sure nothing valuable is in this pack?
2) How do I remove it safely?

Best regards,
Jelena.

[[alternative HTML version deleted]]

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[Bioc-devel] pwrEWAS - checkResults error

[Graw, Stefan H]

Dear Bioc-Team,

A packages (pwrEWAS) I submitted caused an error in checkResults:

https://bioconductor.org/checkResults/3.10/bioc-LATEST/pwrEWAS/malbec1-install.html

ERROR: dependency 'pwrEWAS.data' is not available for package 'pwrEWAS'

The error was caused by failing to load the related ExperimentHub package 
(pwrEWAS.data).
How do I address this issue?

Thank you,
Stefan




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[Bioc-devel] Deadline for commits to current Release 3.9 Branch and Devel 3.10

[Shepherd, Lori]

The deadline for commits to the current release 3.9 branch is Monday October 
14th. At this time the release 3.9 branch will be frozen and no longer accept 
any commits. If your package is having TIMEOUT, ERROR, or WARNINGS - it will 
forever be frozen in this state. This is in preparation for the Wednesday 
October 30th 3.10 release. We encourage last submits to this branch to be 
Friday October 25th so that any changes will be reflected in a build report 
before the branch is frozen and branched. October 28th is the deadline for 
devel packages to be building without TIMEOUT/ERROR/WARNING.

Thank you


Please keep an eye on other important release deadlines:
http://bioconductor.org/developers/release-schedule/
Bioconductor - Release: 
Schedule
Bioconductor 3.10 Release Schedule. This release will use the latest R-3.6.1 
(�Action of the Toes�). The official release date is schedule for Wednsday 
October 30th.
bioconductor.org




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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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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