Re: [Bioc-devel] To Push or Not To Push?

[Hervé Pagès]

Hi Chris,

That is the question :-)

The last run of the builds got delayed (that's because we updated R to 
final 4.0.0 on all build machines on Friday) so we weren't able to 
update the report in time today with the results of the builds. Today's 
builds have started already and I see that CoreGx is on the build 
machines. So if everything goes as expected it should show up on 
tomorrow's report.


I would say push your updates to PharmacoGx. HOWEVER, it's important 
that you run R CMD build/check on PharmacoGx before you do so. Make sure 
you use R 4.0.0 when you do this, that all your packages are up-to-date 
(BiocManager::valid() will tell you that), and that you are using the 
same version of CoreGx that is currently on the build machines (which is 
the one at 'git clone https://git.bioconductor.org/packages/CoreGx'). If 
every looks good then you can push with confidence.


Since today's builds have already started they won't pick up your 
changes to PharmacoGx. But tomorrow's builds will. This means that you 
won't be able to see the full picture before Monday's report. So yes, 
that's kind of last minute but, again, if you're cautious before 
pushing, everything should be fine ;-)


Cheers,
H.


On 4/25/20 17:27, Chris Eeles wrote:

Hello Bioc-Devel community,

We recently submitted CoreGx to Bioconductor and am happy to announce it was 
accepted. However, the package has not yet made it into the 3.11 build and we 
are concerned it may not make the release.

Our existing Bioconductor package, PharmacoGx, has significant updates which 
depend on CoreGx; thus we are hesitant to push our updates without CoreGx being 
available in 3.11.

I wonder if anyone can provide guidance on how best to move forward? We would 
very much like to get the updated PharmacoGx into this release, but don't want 
to risk releasing a package without a dependency. Should we push and hope for 
the best or wait until tomorrow to see if we make the final build?

Any advice would be appreciated.

Thanks for your support.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network



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

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[Bioc-devel] To Push or Not To Push?

[Chris Eeles]

Hello Bioc-Devel community,

We recently submitted CoreGx to Bioconductor and am happy to announce it was 
accepted. However, the package has not yet made it into the 3.11 build and we 
are concerned it may not make the release.

Our existing Bioconductor package, PharmacoGx, has significant updates which 
depend on CoreGx; thus we are hesitant to push our updates without CoreGx being 
available in 3.11.

I wonder if anyone can provide guidance on how best to move forward? We would 
very much like to get the updated PharmacoGx into this release, but don't want 
to risk releasing a package without a dependency. Should we push and hope for 
the best or wait until tomorrow to see if we make the final build?

Any advice would be appreciated.

Thanks for your support.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network



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[Bioc-devel] TxDb.Hsapiens.UCSC.hg19.knownGene fails to install unless you manually install GenomeInfoDbData first

[Leonardo Collado Torres]

Hi Bioc-devel,

Similar to the message I just sent about GenomicFeatures and
TxDb.Hsapiens.UCSC.hg19.knownGene, I found that
TxDb.Hsapiens.UCSC.hg19.knownGene will fail to install on both macOS
and Windows with a fresh R 4.0 and BioC 3.11 installation unless
GenomeInfoDbData is installed manually before.

At 
https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1192
you can see how it failed.

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
1193** using staged installation
1194** R
1195** inst
1196** byte-compile and prepare package for lazy loading
1197##[error]Error: package or namespace load failed for
'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]):
1198ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
1199* removing 'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
1200 there is no package called 'GenomeInfoDbData'
1201##[error]Error: package 'GenomeInfoDb' could not be loaded

Immediately afterwards GenomeInfoDbData does get installed
https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1203
(tibble gets installed just after GenomeInfoDbData).

If you install GenomeInfoDbData prior to attempting to install
TxDb.Hsapiens.UCSC.hg19.knownGene you do not get this error as seen in
https://github.com/leekgroup/derfinderPlot/actions/runs/87730429

TxDb.Hsapiens.UCSC.hg19.knownGene depends on GenomicFeatures, which
then depends on GenomeInfoDb. Maybe GenomicFeatures is the one missing
both the imports/depends on GenomeInfoDbData and tibble.


These issues with missing dependencies in the DESCRIPTION files likely
don't show up on the Bioconductor build machines since these packages
are installed already.

Best,
Leo

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[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

[Leonardo Collado Torres]

Hi Bioc-devel,

I think that there's a potential issue with either GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package.


On a fresh R 4.0 Windows installation with BioC 3.11, I get the
following error message when installing
TxDb.Hsapiens.UCSC.hg19.knownGene as shown at
https://github.com/leekgroup/derfinderPlot/runs/618370463?check_suite_focus=true#step:13:1225.


2020-04-25T18:32:26.0765748Z * installing *source* package
'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
2020-04-25T18:32:26.0769789Z ** using staged installation
2020-04-25T18:32:26.1001400Z ** R
2020-04-25T18:32:26.1044734Z ** inst
2020-04-25T18:32:26.2061605Z ** byte-compile and prepare package for
lazy loading
2020-04-25T18:32:30.7296724Z ##[error]Error: package or namespace load
failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc,
.libPaths()), versionCheck = vI[[i]]):
2020-04-25T18:32:30.7305615Z ERROR: lazy loading failed for package
'TxDb.Hsapiens.UCSC.hg19.knownGene'
2020-04-25T18:32:30.7306686Z * removing
'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
2020-04-25T18:32:30.7307196Z  there is no package called 'tibble'
2020-04-25T18:32:30.7310561Z ##[error]Error: package 'GenomicFeatures'
could not be loaded
2020-04-25T18:32:30.7311805Z Execution halted

>From looking at the bioc-devel landing pages for both GenomicFeatures
and TxDb.Hsapiens.UCSC.hg19.knownGene, I see that tibble is not listed
as a dependency for either package.

Best,
Leo

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Re: [Bioc-devel] Help with setting up a build environment to match

[Kieran O'Neill]

Thanks for the reply.


I don't believe --no-vignettes is set anywhere, unless there's some obscure 
config file for builds specifically that I don't know about, and that gets set 
in a clean Ubuntu 18.04 install?


Build definitely produces output suggesting it was building the vignette:


==> R CMD build ContiBAIT

* checking for file 'ContiBAIT/DESCRIPTION' ... OK
* preparing 'contiBAIT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'contiBAIT_1.15.0.tar.gz'

Source package written to ~/Work/github?



Also, once I've built the package, it successfully runs all the examples in the 
vignette without error.



From: Fan, Jean 
Sent: April 24, 2020 12:51 PM
To: Kieran O'Neill
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Help with setting up a build environment to match

Hi Kieran,

It looks like your Travis build is failing because of your vignettes:

Error: processing vignette 'contiBAIT.Rnw' failed with diagnostics:
6542 chunk 13 (label = orderAllLinkageGroupsExampleb)
6543Error in if (spearmanCor < 0) { : missing value where TRUE/FALSE needed
6544
6545





The BioC Test servers point to the same vignette issue.

Your R CMD build runs may have --no-build-vignettes or --no-vignettes by 
default.

Best,
Jean

On Apr 24, 2020, at 3:11 PM, Kieran O'Neill 
mailto:kone...@bcgsc.ca>> wrote:

A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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Re: [Bioc-devel] Help with setting up a build environment to match

[Kieran O'Neill]

?Thanks Stephanie, that's also a very helpful suggestion! I hadn't thought of 
using Docker containers.


From: Stephanie Gogarten 
Sent: April 24, 2020 4:34 PM
To: Kieran O'Neill
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Help with setting up a build environment to match

I have found the BIocnductor docker images very helpful in reproducing the 
build environment:
https://www.bioconductor.org/help/docker/

I used a combination of the examples under "modifying the images" to get a 
version of the docker images that would build my vignettes, and also install 
all dependencies needed to test my package. Then I mount the directory that 
contains my package repository when starting up a docker container:

docker run -it -v /Users/stephanie/Bioconductor:/home --user rstudio 
bioconductor_docker_genesis:devel bash

That gives me a shell prompt in which I can run "R CMD build" and "R CMD 
check". Since the docker container is viewing my local repository, I can make 
changes and then re-run the checks.

best wishes,
Stephanie

On Fri, Apr 24, 2020 at 2:03 PM Andris Jankevics 
mailto:a.jankev...@bham.ac.uk>> wrote:
Hi,


Are you using R 4.00 on Ubuntu?

Travis error indicates that you are using class(), output of this command has 
changed.

https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq

BW,
Andris

On 24 Apr 2020 20:40, kone...@bcgsc.ca wrote:
A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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--
Stephanie M. Gogarten, PhD
Team Lead, Sample QC and Analysis Software / TOPMed Data Coordinating 
Center
Senior Research Scientist / Genetic Analysis 
Center
Department of Biostatistics
UNIVERSITY OF WASHINGTON

UW Tower Box 359461
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Re: [Bioc-devel] Help with setting up a build environment to match

[Kieran O'Neill]

Hi,


Thanks! Yes, that'd be it. Looks like I have R 3.6 running locally.


And I suspect you've also identified the cause of the bug. I've tried subbing 
is() for class(), and am just waiting for the build to complete.


Kind regards,

Kieran



From: Andris Jankevics 
Sent: April 24, 2020 2:01 PM
To: Kieran O'Neill
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Help with setting up a build environment to match

Hi,


Are you using R 4.00 on Ubuntu?

Travis error indicates that you are using class(), output of this command has 
changed.

https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq

BW,
Andris

On 24 Apr 2020 20:40, kone...@bcgsc.ca wrote:
A package I maintain, contiBAIT, is failing to build on the BioC test servers.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


It's also failing on my Travis build set up on GitHub


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


But I can't reproduce this in my local environment. R CMD build runs just fine 
against the source, with no errors. I'm even running Ubuntu 18.04.



Can anyone suggest a relatively easy way to exactly reproduce the build 
environment on Travis or the BioC build servers so  I can reproduce this error 
and debug it?


Thanks!




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