Re: [Bioc-devel] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

[Turaga, Nitesh]

I've changed your email address. Please activate your account and access your 
git repository. 

You'd need to activate and add your SSH credentials to the BiocCredentials 
account. https://git.bioconductor.org/BiocCredentials/account_activation/

Nitesh 

> On Jan 24, 2020, at 10:19 AM, Tim Beissbarth 
>  wrote:
> 
> 
> Your email listed is beissba...@wehi.edu.au
> No, it is not. Might have been in some earlier version of the package, but 
> has been at least for the last ten years 
> "tim.beissba...@ams.med.uni-goettingen.de". I don't have any access to the 15 
> year old email address any more. Also the password from the old SVN does not 
> seem to work for the GIT. 
> 
> Best,
> Tim
> 
> 
> 



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Re: [Bioc-devel] TensorFlow installations

[Simon Dirmeier]

Hi Lori,


that's great news! Thanks for the info. And cool to have TF Probability,
too.


Cheers,

Simon


On 23.01.20 18:45, Shepherd, Lori wrote:
> Hello Simon,
>
> The devel builders for tokay2 (windows) and malbec2 (linux) have
> tensorflow 2.x
> tensorflow � � � � � � 2.0.0
> tensorflow-estimator � 2.0.1
> tensorflow-probability 0.7.0
>
>
> For the release builders
> We have tensorflow 1.x installed on malbec1 (linux)
> tensorflow (1.14.0)
> tensorflow-estimator (1.14.0)
> tensorflow-probability (0.7.0)
>
> We have not updated tokay1 (windows) with python3 and python2 does not
> support tensorflow
> We plan to update tokay1 and malbec1 when we do the next Bioconductor
> release in the spring following the principle that new and updated
> software should be introduced on the development branch and to keep
> the release branch as stable as possible.
>
> Are current mac builders use El Capitan and because of constraints
> beyond our control we can not switch from El Capitan at this time.
> Tensorflow does not support El Capitan.� �We have tried different work
> around but have been unsuccessful.
>
> 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
> Simon Dirmeier 
> *Sent:* Thursday, January 23, 2020 5:01 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] TensorFlow installations
> Dear all,
>
> I wanted to ask if there are any news regarding TensorFlow installations
> on /tokay1/ and /merida1. /Is it already possible to use TF on these
> servers? If not, can I maybe help out?
>
> Thanks a lot.
>
> Cheers,
>
> Simon
>
>
> ��� [[alternative HTML version deleted]]
>
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>
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> 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,
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Re: [Bioc-devel] New setting on devel builders will cause some new package failures

[Henrik Bengtsson]

This is great news.  For those who wish to reproduce this locally when
running R CMD check, I suggest creating '~/.R/check.Renviron' with:

## Check for bugs like if (c(TRUE, FALSE)) ... Supported since R 3.4.0
_R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,verbose

## Check for bugs like c(TRUE, FALSE) && TRUE. Supported since R 3.6.0
_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,verbose

These environment variables will be applied only when running 'R CMD
check'.  The 'package:_R_CHECK_PACKAGE_NAME_' part makes sure these
bugs trigger check ERRORs only on the package being tested, i.e. you
can check for these bugs in your package also when one of your
dependencies have this bug.

If you want to detect these errors when you run R in general, e.g. in
your analysis, you can add:

_R_CHECK_LENGTH_1_CONDITION_=${_R_CHECK_LENGTH_1_CONDITION_-verbose}
_R_CHECK_LENGTH_1_LOGIC2_=${_R_CHECK_LENGTH_1_LOGIC2_-verbose}

to your ~/.Renviron.  This will trigger a run-time error whenever and
wherever this bug occurs.  If you prefer to get warnings instead of
errors, use 'warn,verbose' instead of 'verbose'.  If you find these
mistakes in other packages, please consider taking the time to report
the maintainer.

/Henrik

On Fri, Jan 24, 2020 at 6:07 AM Shepherd, Lori
 wrote:
>
> Hello developers,
>
> As a heads up notification,  we have enabled the check setting for 
> _R_CHECK_LENGTH_1_LOGIC2_  on the main daily builders (this setting was 
> already active for incoming submissions on the single package builder).  New 
> ERROR's relating to this setting should be seen on the daily build reports 
> either today or tomorrow.  Your packages may need adjustment to account for 
> this setting.  This setting will catch logic ERROR similar to the following:
>
> > Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_`="true")
> > c(TRUE, TRUE) && TRUE
> Error in c(TRUE, TRUE) && TRUE :
>   'length(x) = 2 > 1' in coercion to 'logical(1)'
>
> Note:  The syntax ERROR in this case is using && which anticipates scalar 
> comparison vs a vector comparison   (similar for ||  vs | )
>
> > c(TRUE, TRUE) & TRUE
> [1] TRUE TRUE
>
>
> Also Note:
>
> The logic check for conditionals greater than length one has been implemented 
> since the beginning of the last release so the following are also caught but 
> with _R_CHECK_LENGTH_1_CONDITION_  so technically the above solution would 
> also be an ERROR if it was in a conditional.
> > Sys.setenv(`_R_CHECK_LENGTH_1_CONDITION_`="true")
> > Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_`="true")
> > if( c(TRUE, TRUE) && TRUE ) "yes"
> Error in c(TRUE, TRUE) && TRUE :
>   'length(x) = 2 > 1' in coercion to 'logical(1)'
>
> > if( c(TRUE, TRUE) & TRUE ) "yes"
> Error in if (c(TRUE, TRUE) & TRUE) "yes" : the condition has length > 1
>
> # any and all could be useful in these cases
> > if( all(c(TRUE, TRUE)) & TRUE ) "yes"
> [1] "yes"
>
>
> We made these changes as we have been notified by the R development team that 
> the goal is to make these setting default in a near future version of 
> R-devel.  We therefore are implementing now to allow maintainers to have as 
> much notice as possible.
>
>
> Cheers,
>
>
> 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.
> [[alternative HTML version deleted]]
>
> ___
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Re: [Bioc-devel] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

[Tim Beissbarth]

> Your email listed is beissba...@wehi.edu.au

No, it is not. Might have been in some earlier version of the package, but
has been at least for the last ten years "
tim.beissba...@ams.med.uni-goettingen.de". I don't have any access to the
15 year old email address any more. Also the password from the old SVN does
not seem to work for the GIT.

Best,
Tim

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Re: [Bioc-devel] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

[Turaga, Nitesh]

Your email listed is beissba...@wehi.edu.au

Best,

Nitesh 

> On Jan 24, 2020, at 8:04 AM, Tim Beissbarth 
>  wrote:
> 
>> Firstly you will probably have to log into the git credentials app to load
>> a ssh key
>> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
>> 
> Can't. When I go to activate account I always get a message like:
> 
> tim.beissba...@ams.med.uni-goettingen.de is not associated with a
>> maintainer of a Bioconductor package. Please check the spelling or contact
>> bioc-devel@r-project.org for help
>> 
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] New setting on devel builders will cause some new package failures

[Shepherd, Lori]

Hello developers,

As a heads up notification,  we have enabled the check setting for 
_R_CHECK_LENGTH_1_LOGIC2_  on the main daily builders (this setting was already 
active for incoming submissions on the single package builder).  New ERROR's 
relating to this setting should be seen on the daily build reports either today 
or tomorrow.  Your packages may need adjustment to account for this setting.  
This setting will catch logic ERROR similar to the following:

> Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_`="true")
> c(TRUE, TRUE) && TRUE
Error in c(TRUE, TRUE) && TRUE :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

Note:  The syntax ERROR in this case is using && which anticipates scalar 
comparison vs a vector comparison   (similar for ||  vs | )

> c(TRUE, TRUE) & TRUE
[1] TRUE TRUE


Also Note:

The logic check for conditionals greater than length one has been implemented 
since the beginning of the last release so the following are also caught but 
with _R_CHECK_LENGTH_1_CONDITION_  so technically the above solution would also 
be an ERROR if it was in a conditional.
> Sys.setenv(`_R_CHECK_LENGTH_1_CONDITION_`="true")
> Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_`="true")
> if( c(TRUE, TRUE) && TRUE ) "yes"
Error in c(TRUE, TRUE) && TRUE :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

> if( c(TRUE, TRUE) & TRUE ) "yes"
Error in if (c(TRUE, TRUE) & TRUE) "yes" : the condition has length > 1

# any and all could be useful in these cases
> if( all(c(TRUE, TRUE)) & TRUE ) "yes"
[1] "yes"


We made these changes as we have been notified by the R development team that 
the goal is to make these setting default in a near future version of R-devel.  
We therefore are implementing now to allow maintainers to have as much notice 
as possible.


Cheers,


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] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

[Tim Beissbarth]

> Firstly you will probably have to log into the git credentials app to load
> a ssh key
> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
>
Can't. When I go to activate account I always get a message like:

tim.beissba...@ams.med.uni-goettingen.de is not associated with a
> maintainer of a Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help
>

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Re: [Bioc-devel] Problem with uncompressing files on tokay1?

[Shepherd, Lori]

With some additional investigation this appears to be a firewall issue as the 
error was reproducible on other machines.  Work is being done to rectify the 
issue.

Get Outlook for Android


From: Bioc-devel  on behalf of Nicolas 
Delhomme 
Sent: Monday, January 20, 2020 4:43:11 AM
To: Martin Morgan 
Cc: Dan Tenenbaum 
Subject: Re: [Bioc-devel] Problem with uncompressing files on tokay1?

Hej Martin and Dan!

First of all, I wish you both a happy new year!

I have made the move to the BiocFileCache, but the build report (3.10 for 
easyRNASeq) fails as follows:

* creating vignettes ... ERROR
--- re-building ‘simpleRNASeq.Rmd’ using rmarkdown
Quitting from lines 40-41 (./Chapters/01-Introduction.Rmd)
Quitting from lines NA-42 (./Chapters/01-Introduction.Rmd)
Error: processing vignette 'simpleRNASeq.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()

I can’t reproduce it, so it seems to be related to the build system at Bioc?

Thanks,

Nico

> On 25 Nov 2019, at 15:39, Martin Morgan  wrote:
>
> Thanks this seems like a problem with large file size on Windows, probably in 
> Rhtslib.
>
> It might be better practice and more reliable to use BiocFileCache for 
> downloads, e.g.,
>
> url = 
> "ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/data/star/unitTest/213.1_subset_sortmerna_trimmomatic_sorted.bam.bai;
> BiocFileCache::bfcrpath(rnames = url)
>
> which downloads (once) and returns the path to the cached file.
>
> Martin
>
> On 11/25/19, 8:24 AM, "Bioc-devel on behalf of Nicolas Delhomme" 
>  wrote:
>
>Hej!
>
>The easyRNASeq package is not building on tokay1, with what seems to be a 
> file decompression issue?
>
>
> https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/easyRNASeq/tokay1-buildsrc.html
>
>It works fine on the other OSs.
>
>The error is triggered while downloading a small dataset during the 
> vignette creation. I use `download.file` as the function to fetch the data, 
> so it should be cross-platform compatible. I have no easy access to a windows 
> machine, so I can’t easily reproduce the problem. Any insight into what could 
> be the reason would be much appreciated :-)
>
>The easy solution would be to turn off the evaluation of that section of 
> the vignette, but I’d rather not as it is a good test of the complete 
> functionality of the package (something that would feel ill-fitted as a unit 
> test).
>
>Thanks in advance,
>
>Nico
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Re: [Bioc-devel] DeMixT issue

[Martin Morgan]

Just as before 
(https://github.com/Bioconductor/Contributions/issues/853#issuecomment-496776719),
 you pushed your changes AFTER the nightly build started. Compare the 'Snapshot 
Date: 2020-01-22 16:45:20 -0500 (Wed, 22 Jan 2020)' with the date of your commit

DeMixT RELEASE_3_10$ git log
commit e4e3f547d28e1e23015715f5c417de3cc8a0a37d (HEAD -> RELEASE_3_10, 
origin/RELEASE_3_10)
Merge: 5e4f45c b3e094b
Author: pengyang0411 
Date:   Wed Jan 22 21:24:07 2020 -0600
...

ALSO REMEMBER (as mentioned in 
https://github.com/Bioconductor/Contributions/issues/1343#issuecomment-574858510)
 THAT THE RELEASE BRANCH IS MEANT FOR BUG FIXES ONLY, so that your users have a 
consistent experience. You made major changes in the devel branch, and then 
ported those major changes to the release branch, ruining any of your users' 
existing work flows and reproducible research. It is 'too late' to reverse 
this; in the future only incorporate bug fixes in the release branch.

Martin Morgan
Bioconductor

On 1/23/20, 11:09 PM, "py11"  wrote:

Hi Lori,

I just pushed my new updated package into RELEASE_3_10 with version  
1.2.3(old one was 1.2.1); however, I didn't see the change in release  
version as well as no build report update in the following link,

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

may I know how should address this issue? In the mean time, I  
successfully pushed version 1.3.3 into devel branch and has built  
successfully.

Thanks,
Peng


Quoting "Shepherd, Lori" :

> We noticed the build report has not been updated since Fri Jan 17th.  
>   We have corrected the issue and there should be a new report today  
> or tomorrow.
>
> 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  
> Shepherd, Lori 
> Sent: Tuesday, January 21, 2020 9:06 AM
> To: py11 ; Martin Morgan 
> Cc: bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] DeMixT issue
>
> The current version on devel is 1.3.2 which is what is consistent  
> with what is in
> g...@git.bioconductor.org:packages/DeMixT.git
>
> If you would like updates you need to update your version to 1.3.3   
> in the next round of changes.
>
>
> As Martin said previously,  the landing page will not update until  
> you have a successful build.  You can see from the build report,   
> the package is still timing out using version 1.3.2
> http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
> Therefore the landing page remains at 1.3.1
>
> 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  
> py11 
> Sent: Monday, January 20, 2020 3:11 PM
> To: Martin Morgan 
> Cc: bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] DeMixT issue
>
> Hello,
>
> I pushed my updated package into biconductor master branch on Jan
> 18th; however, I still didn't see the version change in devel branch
> as follow:
>
> https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>
> May I ask where can I find the build report for the latest update?
>
> Thanks,
> Peng
>
> Quoting Martin Morgan :
>
>> The package is always built from the current git repository,
>> regardless of version. So your package will build.
>>
>> A successfully built package (passing install / build / check) is
>> only 'pushed' to the public repository if the version is different
>> (higher) than the current published repository. Your original 1.3.2
>> version has not built successfully, it has not been pushed. If your
>> new 1.3.2 version builds successfully, it will be pushed.
>>
>> BUT the best practice is simply to increment the version, so that
>> there is no confusion -- in the previous paragraph I had to say
>> 'your original 1.3.2 version' and 'your new 1.3.2 version', but it
>> would have been much clearer to say version 1.3.2 and 1.3.3.
>>
>> Martin
>>
>> On 1/18/20, 5:39 PM, "py11"  wrote:
>>
>> Hi Martin,
>>
>> Thank you very much for the detailed report. I have noticed in  
>> the report
>>
>> https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
>>
>> the build failed due to check out of time. I re-arrange the examples
>>