[Bioc-devel] Docker images for RELEASE_3_11 and devel on R-4.0.0

2020-05-07 Thread Nitesh Turaga 
Dear Maintainers,

The latest set of docker images on R-4.0.0 are now available on docker hub. You 
can access the latest images with,

docker pull bioconductor/bioconductor_docker:devel 

docker pull bioconductor/bioconductor_docker:RELEASE_3_11

docker pull bioconductor/bioconductor_docker:latest


Note: The "latest" tag now points to the RELEASE_3_11 version of Bioconductor.

Details:

- The new set of docker images inherit from the latest stack of images produced 
by rocker (https://github.com/rocker-org/rocker-versioned2). It has taken some 
time to produce the new images because the rocker images have been developed on 
Ubuntu 18.04 base images, as opposed to Debian. 

- With the new 'bioconductor/bioconductor_docker' images being available on 
Ubuntu 18.04, we move closer to mimicking the Bioconductor linux build machine.

- Both images which are produced now, build almost all the packages in 
Bioconductor. RStudio is also available as in previous versions. 

Best regards,

Nitesh Turaga
Bioconductor Core Team
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Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

2020-05-07 Thread Shepherd, Lori 
We have encountered some problems with the build report since last Friday as 
reported here
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016766.html

It is possibly related to that.  We are hopeful we have resolved the builder 
issues and once it returns to a normal state we are hopeful this will resolve 
on its own.

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 Arman Shahrisa 

Sent: Thursday, May 7, 2020 11:57 AM
To: bioc-devel 
Subject: [Bioc-devel] The new version of the package 'cbaf' is not downloadable 
for BioC 3.11

Hi to all,

I�m maintainer of the package  �cbaf�. I have pushed changes to both devel and 
stable branches almost two days ago. The package check has only been carried 
out for the stable release so far. There has been only one error on macOS 
server as a result of the version of Java used on the server. Despite this, the 
older version is listed on the cbaf web page for BioC 3.11.

https://secure-web.cisco.com/1AcNMU_2RNz5_Rl5kl5xdhVk-0dJ3GrNdCoaa0t9UvVAwqP1jwApZvMJU39pBinP7RLEwOVIXgEJ0fksXR71QrWGvgNIRShgiAr8vEMy_-cFP5OT9HuE64Zo9VVb_yGj25LBrvlDkKsiKMGRGFjNg-xR5Enmjh2beUBIjAw5VRKDQOMkeJSFugsX35HqpQbP8JIBsQS6A0XAR4WjRNaJ98S222iajXeLA7oZ09CWR1YkSr3NHHzC-iWlgjUjjl9n9BIu2Yfj20eEXTvf-KqUsT8Fuypye82cyupnJYXv6FcFJDdzHurdvlA6xy0JV7RGmcqIqmXdsKoCl8T7sKorSiVvncBM80T2JrBe2gJFvsso/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fcbaf.html

Am I missing something?

Best regards,
Arman


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[Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

2020-05-07 Thread Arman Shahrisa 
Hi to all,

I�m maintainer of the package  �cbaf�. I have pushed changes to both devel and 
stable branches almost two days ago. The package check has only been carried 
out for the stable release so far. There has been only one error on macOS 
server as a result of the version of Java used on the server. Despite this, the 
older version is listed on the cbaf web page for BioC 3.11.

https://bioconductor.org/packages/release/bioc/html/cbaf.html

Am I missing something?

Best regards,
Arman


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Re: [Bioc-devel] Failing Travis build on bioc-devel

2020-05-07 Thread Waldir Leoncio Netto 
Thank you Charlotte, that was it!

On Thu, 2020-05-07 at 11:39 +0200, Charlotte Soneson wrote:

Hi Waldir,


try to delete the travis cache (under More Options - Caches) and restart the 
build. That helped for me.


Best,

Charlotte


On 7 May 2020, at 11:33, Waldir Leoncio Netto 
mailto:w.l.ne...@medisin.uio.no>> wrote:


Dear fellow developers,


I have a package which has been failing on Travis CI's bioc-devel build since 
the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still 
working fine.


The error happens when installing the SummarizedExperiment dependency (or, 
apparently, when installing its dependency, GenomicRanges). Here is the 
relevant part of the log:


* installing *source* package ‘SummarizedExperiment’ ...

** using staged installation

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for ‘GenomicRanges’:

.onLoad failed in loadNamespace() for 'XVector', details:

 call: NULL

 error: (converted from warning) undefined slot classes in definition of 
"XRaw": elementMetadata(class "DataTable_OR_NULL")

Error: package ‘GenomicRanges’ could not be loaded

Execution halted

ERROR: lazy loading failed for package ‘SummarizedExperiment’

* removing ‘/home/travis/R/Library/SummarizedExperiment’

* restoring previous ‘/home/travis/R/Library/SummarizedExperiment’

Error in i.p(...) :

 (converted from warning) installation of package ‘SummarizedExperiment’ had 
non-zero exit status

Calls:  ... with_rprofile_user -> with_envvar -> force -> force -> 
i.p

Execution halted

travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=

The command "Rscript -e 'deps <- 
remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies 
= TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: 
", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status 
= 1, save = "no")}'" failed and exited with 1 during .


Your build has been stopped.


I was wondering if anyone else went through this or can offer a solution.


Best regards,

Waldir


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Re: [Bioc-devel] annotationhub troubleshooting

2020-05-07 Thread Shepherd, Lori 
This is a known reported issue.  See open issue:

https://github.com/Bioconductor/AnnotationHub/issues/10


It actually is not coming from AnnotationHub but from interactiveDisplayBase 
package.  I have reported the issue to those maintainers who have yet to make a 
fix.

In the meantime there is a user interface at 
https://annotationhub.bioconductor.org ; it is not quite as convenient as doing 
it directly in R and having the shiny app but a temporary solution until the 
underlying functionality is fixed.


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 Pierre Germon 

Sent: Thursday, May 7, 2020 3:09 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] annotationhub troubleshooting

Dear Bioconductor Support Site,

I have loaded AnnotatioHub in R( ver 4.0) using Rstudio (1.2.5042) under macosx 
(10.15.3) and I am currently trying to retrive bos taurus annotations.
I run the following script :
> ah <- AnnotationHub(localHub=FALSE)
snapshotDate(): 2020-04-27
> display(ah)

And I get the following pop-up window:

DataTables warning: table id=DataTables_Table_0 - Requested unknown parameter 
'6' for row 0. For more information about this error, please see 
http://secure-web.cisco.com/1y7T8RYvRdXaKEroMp5RqE-W864wx8bA4RqkxtLVhjHdp2KhK4jzqnGIjdtPnnntfnGaEUiXB24miZ-yVdBx4cqj4fTKNow4ylp8VUlPvPUst3PRsACcgmlEHNkGpZyUUpu0jwqIxdQYY90Ph7OVnHBvS-lzLk_ENuooraLRDLcCQTxuKkGKBt5ZaNx1m3QdEbA8fJU2Kl9akLfsl0KHwOwWSXvnSYipRyVShT3IgCtmE89qMinNP4O05DidJ-zZS4ME7_4nobqStsCWnBjxZiHclEEn6aOmBtfFS2wDbjDBlTfbEjF_noFMZ1EnEXUCY0hHKBP18NxbJhxFp-ZCmlg/http%3A%2F%2Fdatatables.net%2Ftn%2F4


The same script used to work 6 month ago. Is there anything I can do to correct 
this issue ?

Thanks very much in advance,

Pierre

INRAE

Pierre GERMON
UMR 1282 ISP - Infectiologie et Sant� Publique
INRAE Centre Val de Loire - b�timent 311
Route de Crotelles
37380 Nouzilly

T�l. : +33 2 47 42 78 86
T�l. IP : 74 78 86
pierre.ger...@inrae.fr

val-de-loire.inrae.fr/infectiologie-santepublique




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Re: [Bioc-devel] Failing Travis build on bioc-devel

2020-05-07 Thread Charlotte Soneson 
Hi Waldir,

try to delete the travis cache (under More Options - Caches) and restart the 
build. That helped for me.

Best,
Charlotte

> On 7 May 2020, at 11:33, Waldir Leoncio Netto  
> wrote:
> 
> Dear fellow developers,
> 
> I have a package which has been failing on Travis CI's bioc-devel build since 
> the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still 
> working fine.
> 
> The error happens when installing the SummarizedExperiment dependency (or, 
> apparently, when installing its dependency, GenomicRanges). Here is the 
> relevant part of the log:
> 
> * installing *source* package ‘SummarizedExperiment’ ...
> ** using staged installation
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Error: package or namespace load failed for ‘GenomicRanges’:
> .onLoad failed in loadNamespace() for 'XVector', details:
>  call: NULL
>  error: (converted from warning) undefined slot classes in definition of 
> "XRaw": elementMetadata(class "DataTable_OR_NULL")
> Error: package ‘GenomicRanges’ could not be loaded
> Execution halted
> ERROR: lazy loading failed for package ‘SummarizedExperiment’
> * removing ‘/home/travis/R/Library/SummarizedExperiment’
> * restoring previous ‘/home/travis/R/Library/SummarizedExperiment’
> Error in i.p(...) :
>  (converted from warning) installation of package ‘SummarizedExperiment’ had 
> non-zero exit status
> Calls:  ... with_rprofile_user -> with_envvar -> force -> force -> 
> i.p
> Execution halted
> travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=
> The command "Rscript -e 'deps <- 
> remotes::dev_package_deps(dependencies = 
> NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% 
> installed.packages())) { message("missing: ", paste(setdiff(deps$package, 
> installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed 
> and exited with 1 during .
> 
> Your build has been stopped.
> 
> I was wondering if anyone else went through this or can offer a solution.
> 
> Best regards,
> Waldir
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Failing Travis build on bioc-devel

2020-05-07 Thread Waldir Leoncio Netto 
Dear fellow developers,

I have a package which has been failing on Travis CI's bioc-devel build since 
the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still 
working fine.

The error happens when installing the SummarizedExperiment dependency (or, 
apparently, when installing its dependency, GenomicRanges). Here is the 
relevant part of the log:

* installing *source* package ‘SummarizedExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘GenomicRanges’:
 .onLoad failed in loadNamespace() for 'XVector', details:
  call: NULL
  error: (converted from warning) undefined slot classes in definition of 
"XRaw": elementMetadata(class "DataTable_OR_NULL")
Error: package ‘GenomicRanges’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘SummarizedExperiment’
* removing ‘/home/travis/R/Library/SummarizedExperiment’
* restoring previous ‘/home/travis/R/Library/SummarizedExperiment’
Error in i.p(...) :
  (converted from warning) installation of package ‘SummarizedExperiment’ had 
non-zero exit status
Calls:  ... with_rprofile_user -> with_envvar -> force -> force -> 
i.p
Execution halted
travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=
The command "Rscript -e 'deps <- 
remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies 
= TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: 
", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status 
= 1, save = "no")}'" failed and exited with 1 during .

Your build has been stopped.

I was wondering if anyone else went through this or can offer a solution.

Best regards,
Waldir

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[Bioc-devel] annotationhub troubleshooting

2020-05-07 Thread Pierre Germon 
Dear Bioconductor Support Site,

I have loaded AnnotatioHub in R( ver 4.0) using Rstudio (1.2.5042) under macosx 
(10.15.3) and I am currently trying to retrive bos taurus annotations.
I run the following script :
> ah <- AnnotationHub(localHub=FALSE)
snapshotDate(): 2020-04-27
> display(ah)

And I get the following pop-up window:

DataTables warning: table id=DataTables_Table_0 - Requested unknown parameter 
'6' for row 0. For more information about this error, please see 
http://datatables.net/tn/4


The same script used to work 6 month ago. Is there anything I can do to correct 
this issue ?

Thanks very much in advance,

Pierre

INRAE

Pierre GERMON
UMR 1282 ISP - Infectiologie et Santé Publique
INRAE Centre Val de Loire - bâtiment 311
Route de Crotelles
37380 Nouzilly

Tél. : +33 2 47 42 78 86
Tél. IP : 74 78 86
pierre.ger...@inrae.fr

val-de-loire.inrae.fr/infectiologie-santepublique




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