date:20200320

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

2020-03-20 Thread Charles Warden

Hi Martin,

That is probably what happened.

Thank you again for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan  
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden ; Alexey Sergushichev 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, 
'1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin


On 3/20/20, 4:28 PM, "Charles Warden"  wrote:

Hi Martin,

I am currently having difficulty reproducing my earlier error (which I 
think didn’t even get to the step of testing the demo code).  So, I think the 
short answer is that I should just use version 1.33.1.

In my search history, I can tell that I Googled "R Malformed package 
version," so I think that was part of the earlier message that I got.

For what is worth, I think this is what gave me the idea to change the 
version numbering system:


https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$
 

However, if I am not currently getting an error message, then I won't worry 
about it.

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan  
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev 

Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions 
in R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD 
build”, I had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, 
and that was OK.

However, when I am working on merging the GitHub and Bioconductor 
branches, I get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is 
only a NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; 
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error 
Message

I think one of the major changes recently is setting stringsAsFactors 
option to FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error 
message.

I will work in figuring out why the code works with R-3.6 but not 
R-4.0, but it seems like this might affect other packages as well (since I 
received error messages for 2 out of 2 of the Bioconductor packages that I 
contributed to).

Do you have any general suggestions of what types of new errors might 
be encountered from using R-4.0?

Thanks Again,
Charles

From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles 
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message

Yes that is the correct version of R to use. Thank you for taking the 
time to make sure everything is correct to debug. We appreciate your effort and 
contributors to bioconductor.
Get Outlook for 
Android


From: Charles Warden

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

2020-03-20 Thread Martin Morgan

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, 
'1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin


On 3/20/20, 4:28 PM, "Charles Warden"  wrote:

Hi Martin,

I am currently having difficulty reproducing my earlier error (which I 
think didn’t even get to the step of testing the demo code).  So, I think the 
short answer is that I should just use version 1.33.1.

In my search history, I can tell that I Googled "R Malformed package 
version," so I think that was part of the earlier message that I got.

For what is worth, I think this is what gave me the idea to change the 
version numbering system:


https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file

However, if I am not currently getting an error message, then I won't worry 
about it.

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan  
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev 

Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions 
in R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD 
build”, I had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, 
and that was OK.

However, when I am working on merging the GitHub and Bioconductor 
branches, I get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is 
only a NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; 
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error 
Message

I think one of the major changes recently is setting stringsAsFactors 
option to FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error 
message.

I will work in figuring out why the code works with R-3.6 but not 
R-4.0, but it seems like this might affect other packages as well (since I 
received error messages for 2 out of 2 of the Bioconductor packages that I 
contributed to).

Do you have any general suggestions of what types of new errors might 
be encountered from using R-4.0?

Thanks Again,
Charles

From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles 
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message

Yes that is the correct version of R to use. Thank you for taking the 
time to make sure everything is correct to debug. We appreciate your effort and 
contributors to bioconductor.
Get Outlook for 
Android


From: Charles Warden 
mailto:cwar...@coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>;
 
bioc-devel@r-project.org>
 
mailto:bioc-devel@r-project.org>>>
Subject: RE: Issue Reproducing

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

2020-03-20 Thread Charles Warden

Hi Martin,

I am currently having difficulty reproducing my earlier error (which I think 
didn’t even get to the step of testing the demo code).  So, I think the short 
answer is that I should just use version 1.33.1.

In my search history, I can tell that I Googled "R Malformed package version," 
so I think that was part of the earlier message that I got.

For what is worth, I think this is what gave me the idea to change the version 
numbering system:

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file

However, if I am not currently getting an error message, then I won't worry 
about it.

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan  
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions in 
R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD 
build”, I had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, and 
that was OK.

However, when I am working on merging the GitHub and Bioconductor branches, 
I get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is 
only a NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

I think one of the major changes recently is setting stringsAsFactors 
option to FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.

I will work in figuring out why the code works with R-3.6 but not R-4.0, 
but it seems like this might affect other packages as well (since I received 
error messages for 2 out of 2 of the Bioconductor packages that I contributed 
to).

Do you have any general suggestions of what types of new errors might be 
encountered from using R-4.0?

Thanks Again,
Charles

From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles 
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message

Yes that is the correct version of R to use. Thank you for taking the time 
to make sure everything is correct to debug. We appreciate your effort and 
contributors to bioconductor.
Get Outlook for 
Android


From: Charles Warden 
mailto:cwar...@coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>;
 
bioc-devel@r-project.org>
 
mailto:bioc-devel@r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message


Hi Lori,



Thank you very much for your response.



I was testing building the Bioconductor development branch, but I was using 
R-3.6.



On the Ubuntu server where I have all the necessary dependencies 
configured, I tested compiling R-devel but it didn't exactly say R-4.0.



So, in order to see if I can reproduce the error, I want to make sure I am 
using the same version of R:



On the R website, it says "R version 4.0.0 (Arbor Day) prerelease 
versions
 will appear

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

2020-03-20 Thread Martin Morgan

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions in 
R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD 
build”, I had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, and 
that was OK.

However, when I am working on merging the GitHub and Bioconductor branches, 
I get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is 
only a NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

I think one of the major changes recently is setting stringsAsFactors 
option to FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.

I will work in figuring out why the code works with R-3.6 but not R-4.0, 
but it seems like this might affect other packages as well (since I received 
error messages for 2 out of 2 of the Bioconductor packages that I contributed 
to).

Do you have any general suggestions of what types of new errors might be 
encountered from using R-4.0?

Thanks Again,
Charles

From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles 
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message

Yes that is the correct version of R to use. Thank you for taking the time 
to make sure everything is correct to debug. We appreciate your effort and 
contributors to bioconductor.
Get Outlook for 
Android


From: Charles Warden 
mailto:cwar...@coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>;
 
bioc-devel@r-project.org>
 
mailto:bioc-devel@r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message


Hi Lori,



Thank you very much for your response.



I was testing building the Bioconductor development branch, but I was using 
R-3.6.



On the Ubuntu server where I have all the necessary dependencies 
configured, I tested compiling R-devel but it didn't exactly say R-4.0.



So, in order to see if I can reproduce the error, I want to make sure I am 
using the same version of R:



On the R website, it says "R version 4.0.0 (Arbor Day) prerelease 
versions
 will appear starting Tuesday 2020-03-24. Final release is scheduled for Friday 
2020-04-24.", but I can download prerelease files from the following page:




https://cran.r-project.org/src/base-prerelease/



I tested compiling the R-devel.tar.gz file.  I think that completed without 
errors, but the version of R is reported as "R Under development (unstable) 
(2020-03-18 r78002)".  So, I am not sure if this is correct.



Is this the correct version of R to try and reproduce the error on my own 
computer?  If not, can you please describe which file I should be using?

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

2020-03-20 Thread Charles Warden

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions in 
R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD build”, I 
had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, and that 
was OK.

However, when I am working on merging the GitHub and Bioconductor branches, I 
get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is only a 
NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

I think one of the major changes recently is setting stringsAsFactors option to 
FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.

I will work in figuring out why the code works with R-3.6 but not R-4.0, but it 
seems like this might affect other packages as well (since I received error 
messages for 2 out of 2 of the Bioconductor packages that I contributed to).

Do you have any general suggestions of what types of new errors might be 
encountered from using R-4.0?

Thanks Again,
Charles

From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles Warden 
mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message

Yes that is the correct version of R to use. Thank you for taking the time to 
make sure everything is correct to debug. We appreciate your effort and 
contributors to bioconductor.
Get Outlook for 
Android


From: Charles Warden 
mailto:cwar...@coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>;
 
bioc-devel@r-project.org>
 
mailto:bioc-devel@r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message


Hi Lori,



Thank you very much for your response.



I was testing building the Bioconductor development branch, but I was using 
R-3.6.



On the Ubuntu server where I have all the necessary dependencies configured, I 
tested compiling R-devel but it didn't exactly say R-4.0.



So, in order to see if I can reproduce the error, I want to make sure I am 
using the same version of R:



On the R website, it says "R version 4.0.0 (Arbor Day) prerelease 
versions
 will appear starting Tuesday 2020-03-24. Final release is scheduled for Friday 
2020-04-24.", but I can download prerelease files from the following page:



https://cran.r-project.org/src/base-prerelease/



I tested compiling the R-devel.tar.gz file.  I think that completed without 
errors, but the version of R is reported as "R Under development (unstable) 
(2020-03-18 r78002)".  So, I am not sure if this is correct.



Is this the correct version of R to try and reproduce the error on my own 
computer?  If not, can you please describe which file I should be using?  I 
would like to install this separately from R 3.6 (in case the version of R 
affects other packages as well).



Thank You,

Charles



From: Shepherd, Lori 
[mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 10:48 AM
To: Charles Warden 
mailto:cwar...@coh.org>>>;
 
bioc-devel@r-project.org>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message



It is not okay to ignore the emails you are getting.  You need to investigate 
to find out if the ERROR is from your

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

2020-03-20 Thread Laurent Gatto

FYI - I can reproduce this on linux with R Under development (unstable) 
(2020-03-19 r78011)



From: Bioc-devel  on behalf of Vincent Carey 

Sent: 16 March 2020 23:52
To: bioc-devel
Subject: [Bioc-devel] proper way to define an S4 method for 'plot'

I just updated my R and I am getting into trouble with MLInterfaces
maintenance.

> BiocManager::install("MLInterfaces")

*Bioconductor version 3.11 (BiocManager 1.30.10), R Under development
(unstable)*

*  (2020-03-15 r77975)*

*Installing package(s) 'MLInterfaces'*

*Warning: unable to access index for repository
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615sdata=7Pq9i9bWYWJ3AaK%2FnGWpAZuvOa0RFGoXLg3cY6XY660%3Dreserved=0
:*

*  cannot open URL
'https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0%2FPACKAGESdata=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615sdata=BWqDMETTVk7AEYIj1gpfTYDzjsHADvqmqfD6RloDaK4%3Dreserved=0
'*


  There is a binary version available but the source version is later:

 binary source needs_compilation

MLInterfaces 1.67.2 1.67.5 FALSE


*installing the source package ‘MLInterfaces’*


*trying URL
'https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fsrc%2Fcontrib%2FMLInterfaces_1.67.5.tar.gzdata=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615sdata=yWBq%2BjSD4xvRKkWUKkjoFXuG074hlVcsLSPRiPc5YAc%3Dreserved=0
'*

*Content type 'application/x-gzip' length 1071876 bytes (1.0 MB)*

*==*

*downloaded 1.0 MB*


* installing *source* package ‘MLInterfaces’ ...

** using staged installation

** R

** inst

** byte-compile and prepare package for lazy loading

Error in getGeneric(f, TRUE, envir, package) :

  no generic function found for ‘plot’

Calls:  ... namespaceImportFrom -> .mergeImportMethods ->
 -> getGeneric

recover called non-interactively; frames dumped, use debugger() to view

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded from temporary location

Error: package or namespace load failed for ‘MLInterfaces’ in getGeneric(f,
TRUE, envir, package):

 no generic function found for ‘plot’


...


> sessionInfo()

R Under development (unstable) (2020-03-15 r77975)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Mojave 10.14.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] rmarkdown_2.1


loaded via a namespace (and not attached):

 [1] BiocManager_1.30.10 compiler_4.0.0  startup_0.14.0

 [4] tools_4.0.0 htmltools_0.4.0 Rcpp_1.0.3

 [7] codetools_0.2-16knitr_1.28  xfun_0.12

[10] digest_0.6.25   rlang_0.4.5 evaluate_0.14

--
The information in this e-mail is intended only for the ...{{dropped:10}}

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[Bioc-devel] INSPEcT vignette building issue

2020-03-20 Thread Mattia Furlan

Hello,

I am one of the maintainers of the INSPEcT package.

I noticed that the vignette building on tokay2 resulted in a timeout.
So, I tried to build the document on a Windows 10 64 bit machine with the 
development version of Bioconductor and R4.0.
In this configuration, everything run smoothly with a reasonable computational 
time (few minutes).

Could you please help me to fix the issue?

Thank you,


Mattia Furlan

[[alternative HTML version deleted]]

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Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

2020-03-20 Thread Shepherd, Lori

We appreciate your effort and contributions to Bioconductor.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: L Rutter 
Sent: Friday, March 20, 2020 4:04 AM
To: Shepherd, Lori 
Cc: Turaga, Nitesh ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Dear Lori and Nitesh:

Thank you so much for your help. I was able to make the changes and fix the 
error. It seems my release version is also now building without 
error. Your 
feedback has helped me a lot and allowed me to get this right finally. I think 
I have a better understanding of how to maintain these branches in the future 
now. Thank you very much again for all your patience and support!

Sincerely,
Lindsay


2020年3月16日(月) 20:07 Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>:
If you can make the changes just to fix the error in release than nitesh is 
right and it would be better to do that and follow his commands he sent earlier.

Get Outlook for Android


From: L Rutter mailto:lindsayannerut...@gmail.com>>
Sent: Sunday, March 15, 2020 11:03:42 PM
To: Shepherd, Lori 
Cc: Turaga, Nitesh ; 
bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Dear Lori and Nitesh:

Thank you both for your support. I should clarify that the changes in the devel 
branch (unfortunately) do include new features in addition to correcting the 
original source of failure. This happened inadvertently due to me still 
building my git skills and also me adding features requested while an 
associated paper was under peer review.

I am hesitant to attempt commands without consulting first as I am still 
improving these skillsets. Thank you again for sharing your expertise.

Sincerely,
Lindsay


2020年3月16日(月) 6:50 Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>:
Lindsay, please wait for niteshs response as there could be intracacies with 
the versioning git hook that I'm not aware of.

Get Outlook for Android


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Shepherd, Lori 
Sent: Sunday, March 15, 2020 4:59:14 PM
To: Turaga, Nitesh ; L Rutter 
mailto:lindsayannerut...@gmail.com>>
Cc: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Hello,

Nitesh I disagree.  Given this is a bug correction and the release version is 
failing it is perfectly reasonable for them to merge the master branch in the 
RELEASE_3_10 branch as long as they change the version number before committing 
to the git.biconductor.org  branch; The changes in 
the devel branch as far as I am aware were to correct the failure occurring and 
not introducing any new features.  Ideally it would have been better to do the 
correction on the RELEASE_3_10 and then have merged into master but as far as I 
am aware as long as the version number is corrected before the push they should 
be okay.

Lindsay  then the last two steps are not correct . You should not pull and push 
to master as you are working on the RELEASE_3_10 branch

1) git fetch --all (get any updated branches)
2) git checkout RELEASE_3_10  upstream/RELEASE_3_10   (checkout branch)
3) git pull upstream RELEASE_3_10(pull before any changes are made)
4) git merge master
5) Change the version number in DESCRIPTION to 1.2.1   (DO NOT FORGET THIS 
STEP)
6) git add DESCRIPTION
7) git commit -m 
8) git push upstream RELEASE_3_10


Nitesh can you verify these steps?
And Nitesh is right in the sense that in the future bug corrections should be 
done on the release branch and merged into the master branch as it is cleaner.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Turaga, Nitesh 
Sent: Sunday, March 15, 2020 3:31 PM
To: L Rutter mailto:lindsayannerut...@gmail.com>>; 
Shepherd, Lori 
Cc: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

You cannot merge your master branch into the RELEASE_3_10 branch.

The version number will not match, and all the devel changes will go into the 
release.

Instead,

1) git checkout RELEASE_3_10
2) Make the changes again in the RELEASE_3_10 branch.
3) git add 
4) git commit -m ""
5) git push upstream RELEASE_3_10


Best,

Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

2020-03-20 Thread L Rutter

Dear Lori and Nitesh:

Thank you so much for your help. I was able to make the changes and fix the
error. It seems my release version is also now building without error
. Your
feedback has helped me a lot and allowed me to get this right finally. I
think I have a better understanding of how to maintain these branches in
the future now. Thank you very much again for all your patience and support!

Sincerely,
Lindsay


2020年3月16日(月) 20:07 Shepherd, Lori :

> If you can make the changes just to fix the error in release than nitesh
> is right and it would be better to do that and follow his commands he sent
> earlier.
>
> Get Outlook for Android 
>
> --
> *From:* L Rutter 
> *Sent:* Sunday, March 15, 2020 11:03:42 PM
> *To:* Shepherd, Lori 
> *Cc:* Turaga, Nitesh ;
> bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Dear Lori and Nitesh:
>
> Thank you both for your support. I should clarify that the changes in the
> devel branch (unfortunately) do include new features in addition to
> correcting the original source of failure. This happened inadvertently due
> to me still building my git skills and also me adding features requested
> while an associated paper was under peer review.
>
> I am hesitant to attempt commands without consulting first as I am still
> improving these skillsets. Thank you again for sharing your expertise.
>
> Sincerely,
> Lindsay
>
>
> 2020年3月16日(月) 6:50 Shepherd, Lori :
>
> Lindsay, please wait for niteshs response as there could be intracacies
> with the versioning git hook that I'm not aware of.
>
> Get Outlook for Android 
>
> --
> *From:* Bioc-devel  on behalf of
> Shepherd, Lori 
> *Sent:* Sunday, March 15, 2020 4:59:14 PM
> *To:* Turaga, Nitesh ; L Rutter <
> lindsayannerut...@gmail.com>
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Hello,
>
> Nitesh I disagree.  Given this is a bug correction and the release version
> is failing it is perfectly reasonable for them to merge the master branch
> in the RELEASE_3_10 branch as long as they change the version number before
> committing to the git.biconductor.org  branch; The changes in the devel
> branch as far as I am aware were to correct the failure occurring and not
> introducing any new features.  Ideally it would have been better to do the
> correction on the RELEASE_3_10 and then have merged into master but as far
> as I am aware as long as the version number is corrected before the push
> they should be okay.
>
> Lindsay  then the last two steps are not correct . You should not pull and
> push to master as you are working on the RELEASE_3_10 branch
>
> 1) git fetch --all (get any updated branches)
> 2) git checkout RELEASE_3_10  upstream/RELEASE_3_10   (checkout branch)
> 3) git pull upstream RELEASE_3_10(pull before any changes are made)
> 4) git merge master
> 5) Change the version number in DESCRIPTION to 1.2.1   (DO NOT FORGET
> THIS STEP)
> 6) git add DESCRIPTION
> 7) git commit -m 
> 8) git push upstream RELEASE_3_10
>
>
> Nitesh can you verify these steps?
> And Nitesh is right in the sense that in the future bug corrections should
> be done on the release branch and merged into the master branch as it is
> cleaner.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Turaga, Nitesh 
> Sent: Sunday, March 15, 2020 3:31 PM
> To: L Rutter ; Shepherd, Lori
> 
> Cc: bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> You cannot merge your master branch into the RELEASE_3_10 branch.
>
> The version number will not match, and all the devel changes will go into
> the release.
>
> Instead,
>
> 1) git checkout RELEASE_3_10
> 2) Make the changes again in the RELEASE_3_10 branch.
> 3) git add 
> 4) git commit -m ""
> 5) git push upstream RELEASE_3_10
>
>
> Best,
>
> Nitesh
>
> On 3/15/20, 12:01 PM, "Bioc-devel on behalf of L Rutter" <
> bioc-devel-boun...@r-project.org on behalf of lindsayannerut...@gmail.com>
> wrote:
>
> Dear Lori:
>
> Thank you for all your help. I am happy to say that the landing
> development
> page is now building without errors
> . I
> believe
> my GitHub master branch (1.3.3) and Bioconductor development branch
> are now
> the same.
>
> I am hoping to now likewise push what is on my GitHub master branch
> (1.3.3)
> to the release branch of Bioconductor, which is still currently failing
> (1.2.0) <
>

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