Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Paul Shannon]

Hi Lori,

Excellent solution.  I will update my profile.  Thank you!

(I should have guessed bioc would have a mechanism for this)

> On Jun 5, 2020, at 10:16 AM, Shepherd, Lori  
> wrote:
> 
> Paul 
> 
>   -  On the support site,  you can edit your profile and put package names as 
> watchedtags.  When a person posts to the support site and tags with the 
> package name you would then be emailed.   This assumes they tag the post 
> correctly but also an option 
> 
> 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 Paul Shannon 
> 
> Sent: Friday, June 5, 2020 1:12 PM
> To: Nystrom, Spencer 
> Cc: bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey 
> database
>  
> Thanks, Spencer.  Sorry I missed the support posting - there’s no automatic 
> forwarding from there to maintainers.
> 
> I’ll take a look at this later today, then post back to the support list, and 
> we will get a fix in.
> 
> Thank you for pointing out the problem!
> 
>  - Paul
> 
> > On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer  wrote:
> > 
> > Hi,
> > 
> > I've identified a few missing PWMs from the MotifDb package and would like 
> > to help get them added. I posted on the support page but have not received 
> > a response after 10 days, so messaging here instead (link to forum post: 
> > https://secure-web.cisco.com/1TFAehHIfvF8C-fsHqKF9EZUlEaLQqYsIygNO_BAsoXZwv_Wu3u5B4wJVetP6b2oLhIIOFSZhhOumdKzED0ovgHBPNyPVtPXiHxRm8b66_DTxd3gOar2MNQ5l9qQH4_wqJMMJaxbnBCWUwAGnSDJO91ueABvVc6mU2FAghpGjUfBlWvlYMMhZzzmbgjYqsldl1Ta23cGowoJ3ncf7CeSKr6bKFMch5qHT0BqRq0t6Gi_b7w1KzlscAc0wC3Pxjq5gXX9vMchpSqTrtO3_MRw3Ojfo2wOimSuSsQL0RWe2mKIGnuSE0r8q7XSF0fsyFaH-DmeMbMdAxJok14mifZioaA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131312%2F).
> >  Full details can be found in the support post, but in summary, there are a 
> > small number of Drosophila transcription factors which do not have any 
> > entries in MotifDb, meaning anyone using that database for their motif 
> > analysis will not identify these factors as potential candidates. A .meme 
> > format file ("flyFactor_Missing_Motifdb.meme") of these missing motifs 
> > along with a reproducible script to identify these factors can be found at 
> > this gist: 
> > https://secure-web.cisco.com/1Hw4j-u2eWVf5hZXzqLZ4apPGgjUddOX5ixtNdTGwQZ4NPy_KaMZids5AaShi-S2meTRVKS9jM3cf2iEulIctx81-ZyEXDGgnDv79mSzGZG0QjWEwCoKwaCa8Eg2m1zL4AW14psIhbcmvxc36OZX77cPdvVBZBl0WIzqa0g6N2n6c75iPRS0Mi4k86awArVwZ6SMWbd9onXyqHQqqfNpEcQnilZw0UkOntlEVSBQWpNszEdDH6zw1gLuglq1F4JIJwa6onOYuveddTXIVT0r3veLCqhDXiDZIxFN9PmMrUUh9Xqiq2S2uRkK53JqfA-krBLQfCwo4agchyGpfqwWZOA/https%3A%2F%2Fgist.github.com%2Fsnystrom%2Fb7701858bec6bc4ce7758a7582422359.
> >  I am happy to help curate any additional metadata required to get these 
> > factors added to the database.
> > 
> > Best,
> >  -Spencer
> > 
> >[[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://secure-web.cisco.com/1phkYo14BRVEEfRyDeaWIrA_pTixsBkMhDEtZJJ_lcV4Ev3nOgpobNwVMNGC0rZ2PP6k0_GxcU4pZuXfj6Z7QQPVun1pslCmmsy8p06Qu26qc8oyiqhJjbddn3W2_2Ob0TkyCNLtOmsOod2iPUdW5HOZnOD8E-hbZEtkd686fRcOfBp0Jol1LdMws-yzTnx2tiY_wuC1fknOPQLjJGju7wMdRHS7Gs1hBT2TcDXo-S2HFRYoKlUZ3TdrVjREc1Lkb0Ik_wRG32UHcv2ZJFMDBlzvcGyI7wY1ihTeNfIGgVPAumaUWOyPKVVFnWC990wgBf1-PbTrIFFfwRUZhaHpnQw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
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Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Shepherd, Lori]

Paul

  -  On the support site,  you can edit your profile and put package names as 
watchedtags.  When a person posts to the support site and tags with the package 
name you would then be emailed.   This assumes they tag the post correctly but 
also an option


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 Paul Shannon 

Sent: Friday, June 5, 2020 1:12 PM
To: Nystrom, Spencer 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey 
database

Thanks, Spencer.  Sorry I missed the support posting - there�s no automatic 
forwarding from there to maintainers.

I�ll take a look at this later today, then post back to the support list, and 
we will get a fix in.

Thank you for pointing out the problem!

 - Paul

> On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer  wrote:
>
> Hi,
>
> I've identified a few missing PWMs from the MotifDb package and would like to 
> help get them added. I posted on the support page but have not received a 
> response after 10 days, so messaging here instead (link to forum post: 
> https://secure-web.cisco.com/1TFAehHIfvF8C-fsHqKF9EZUlEaLQqYsIygNO_BAsoXZwv_Wu3u5B4wJVetP6b2oLhIIOFSZhhOumdKzED0ovgHBPNyPVtPXiHxRm8b66_DTxd3gOar2MNQ5l9qQH4_wqJMMJaxbnBCWUwAGnSDJO91ueABvVc6mU2FAghpGjUfBlWvlYMMhZzzmbgjYqsldl1Ta23cGowoJ3ncf7CeSKr6bKFMch5qHT0BqRq0t6Gi_b7w1KzlscAc0wC3Pxjq5gXX9vMchpSqTrtO3_MRw3Ojfo2wOimSuSsQL0RWe2mKIGnuSE0r8q7XSF0fsyFaH-DmeMbMdAxJok14mifZioaA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131312%2F).
>  Full details can be found in the support post, but in summary, there are a 
> small number of Drosophila transcription factors which do not have any 
> entries in MotifDb, meaning anyone using that database for their motif 
> analysis will not identify these factors as potential candidates. A .meme 
> format file ("flyFactor_Missing_Motifdb.meme") of these missing motifs along 
> with a reproducible script to identify these factors can be found at this 
> gist: 
> https://secure-web.cisco.com/1Hw4j-u2eWVf5hZXzqLZ4apPGgjUddOX5ixtNdTGwQZ4NPy_KaMZids5AaShi-S2meTRVKS9jM3cf2iEulIctx81-ZyEXDGgnDv79mSzGZG0QjWEwCoKwaCa8Eg2m1zL4AW14psIhbcmvxc36OZX77cPdvVBZBl0WIzqa0g6N2n6c75iPRS0Mi4k86awArVwZ6SMWbd9onXyqHQqqfNpEcQnilZw0UkOntlEVSBQWpNszEdDH6zw1gLuglq1F4JIJwa6onOYuveddTXIVT0r3veLCqhDXiDZIxFN9PmMrUUh9Xqiq2S2uRkK53JqfA-krBLQfCwo4agchyGpfqwWZOA/https%3A%2F%2Fgist.github.com%2Fsnystrom%2Fb7701858bec6bc4ce7758a7582422359.
>  I am happy to help curate any additional metadata required to get these 
> factors added to the database.
>
> Best,
>  -Spencer
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1phkYo14BRVEEfRyDeaWIrA_pTixsBkMhDEtZJJ_lcV4Ev3nOgpobNwVMNGC0rZ2PP6k0_GxcU4pZuXfj6Z7QQPVun1pslCmmsy8p06Qu26qc8oyiqhJjbddn3W2_2Ob0TkyCNLtOmsOod2iPUdW5HOZnOD8E-hbZEtkd686fRcOfBp0Jol1LdMws-yzTnx2tiY_wuC1fknOPQLjJGju7wMdRHS7Gs1hBT2TcDXo-S2HFRYoKlUZ3TdrVjREc1Lkb0Ik_wRG32UHcv2ZJFMDBlzvcGyI7wY1ihTeNfIGgVPAumaUWOyPKVVFnWC990wgBf1-PbTrIFFfwRUZhaHpnQw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel

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This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Robert Castelo]

Vince, thanks for the suggestions, i've taken the serializing route and 
submitted the fix.

cheers,

robert.

On 05/06/2020 17:28, Vincent Carey wrote:
>
>
> On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo  > wrote:
>
> hi Vince,
>
> no worries, i've been finally able to reproduce the error in my
> computer and i'm afraid i'm probably using a deprecated dataset
> from 'gwascat', concretely the one that was stored as
>
> gwascat/data/ebicat37.rda
>
> what would be the replacement for the following kind of operation?
>
>
> The best thing to do from a scientific point of view would likely be
>
> curcat = gwascat::makeCurrentGwascat()
>
> then work with that, which will have GRCh38 coordinates.
>
> It is slow to run makeCurrentGwascat.  You might want to serialize 
> what you need.
> I can't place a snapshot in gwascat as I had in the past because the 
> image compressed
> with xz exceeds 5MB.  Any snapshot has to be in AnnotationHub.  I 
> don't have a
> plan for this at the moment.
>
> There is an object called ebicat_2020_04_30 in the data
> folder of gwascat on devel branch.  It is a sample of 5 records 
> from the full
> catalog of that date.  You might be able to use that for what you are 
> doing; I will
> be renaming it to clarify that it is a sample.
>
>
> data(ebicat37)
> eyersids <- unique(subsetByTraits(ebicat37, tr="Eye color")$SNPS)
> eyersids
>  [1] "rs12913832" "rs7173419"  "rs3002288" "rs12896399" "rs1408799"
>  [6] "rs12520016" "rs288139"   "rs1667394" "rs4596632"  "rs12203592"
> [11] "rs16891982" "rs1393350"  "rs1847134"
>
> thanks!
>
> robert.
>
> On 05/06/2020 14:06, Vincent Carey wrote:
>> I am really sorry about the situation with gwascat and will try
>> to straighten it out today.
>>
>> On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo
>> mailto:robert.cast...@upf.edu>> wrote:
>>
>> hi,
>>
>> my package GenomicScores is not building, see:
>>
>> 
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>>
>> apparently, it is breaking in the following lines of its
>> vignette:
>>
>> library(gwascat)
>> data(ebicat37)
>>
>> which in the report from the bioc build machine says:
>>
>> gwascat loaded.  Use makeCurrentGwascat() to extract current image.
>>   from EBI.  The data folder of this package has some legacy 
>> extracts.
>> Quitting from lines 404-408 (GenomicScores.Rmd)
>> Error: processing vignette 'GenomicScores.Rmd' failed with 
>> diagnostics:
>> object 'ebicat37' not found
>> --- failed re-building ‘GenomicScores.Rmd’
>>
>> however, in my installation of current bioc-devel on R-4.0
>> with all packages up to date, GenomicScores builds fine and i
>> cannot reproduce this error. below you can find my session
>> information after the previous two instructions. the logs of
>> 'gwascat' show changes in May 2nd that could be potentially
>> responsible for this but the fact is that 'gwascat' is not
>> building either and it does not seem that the changes
>> propagate through the build system, its version is still
>> 2.21.0, on which GenomicScores built without problems for the
>> current release.
>>
>> i'm cc'ing this email to Vince, as maintainer of 'gwascat',
>> in case he has some more specific suggestion about this but
>> any hint will be greatly appreciated.
>>
>> thanks!!
>>
>> sessionInfo()
>> R version 4.0.0 (2020-04-24)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
>>  [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
>>  [7] LC_PAPER=en_US.UTF8 LC_NAME=C
>>  [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets 
>> methods   base
>>
>> other attached packages:
>> [1] gwascat_2.21.0 colorout_1.2-2
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_1.0.4.6 lattice_0.20-41
>>  [3] prettyunits_1.1.1 Rsamtools_2.5.1
>>  [5] Biostrings_2.57.1 assertthat_0.2.1
>>  [7] digest_0.6.25 BiocFileCache_1.13.0
>>  [9] R6_2.4.1 GenomeInfoDb_1.25.1
>> [11] stats4_4.0.0 RSQLite_2.2.0
>> [13] httr_1.4.1 ggplot2_3.3.1
>> [15] pillar_1.4.4 zlibbioc_1.35.0
>> [17] rlang_0.4.6 GenomicFeatures_1.41.0
>> [19] 

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Paul Shannon]

Thanks, Spencer.  Sorry I missed the support posting - there’s no automatic 
forwarding from there to maintainers.

I’ll take a look at this later today, then post back to the support list, and 
we will get a fix in.

Thank you for pointing out the problem!

 - Paul

> On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer  wrote:
> 
> Hi,
> 
> I've identified a few missing PWMs from the MotifDb package and would like to 
> help get them added. I posted on the support page but have not received a 
> response after 10 days, so messaging here instead (link to forum post: 
> https://support.bioconductor.org/p/131312/). Full details can be found in the 
> support post, but in summary, there are a small number of Drosophila 
> transcription factors which do not have any entries in MotifDb, meaning 
> anyone using that database for their motif analysis will not identify these 
> factors as potential candidates. A .meme format file 
> ("flyFactor_Missing_Motifdb.meme") of these missing motifs along with a 
> reproducible script to identify these factors can be found at this gist: 
> https://gist.github.com/snystrom/b7701858bec6bc4ce7758a7582422359. I am happy 
> to help curate any additional metadata required to get these factors added to 
> the database.
> 
> Best,
>  -Spencer
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Bioconductor package tidybulk

[stefano]

Thanks Lori,

your email finally made me understand the relationship between my repo and
Bioc repo. I have to admit that I was not familiar of remote vs. upstream.

Now, I have pushed everything to RELEASE_3_11. But the tests did not
trigger.

I will push to develop as well early next week.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno gio 4 giu 2020 alle ore 23:11 Shepherd, Lori <
lori.sheph...@roswellpark.org> ha scritto:

>
> The master branch is the development branch (Bioc 3.12) .  The version
> of  x.y.z   The y is always odd in devel  and even in release.  This is the
> very first section on the page you referenced.
> http://bioconductor.org/developers/how-to/version-numbering/
>
> We do not jump full y versions in the middle of a release.
>
> The current RELEASE_3_11  version is  1.0.0  =  the appropriate version
> bump on this branch is  1.0.1
>
> The current master version is 1.1.0  = the appropriate version bump on
> this branch is  1.1.1
>
>
> If you are unfamiliar with git and github branches I encourage you to read
> more documentation about it.  There are many helpful tutorials.
> You can have as many branches on your local github repository as you like.
> We recommend creating unique branches for bioconductor releases to mimic
> our branch structure.   In general, and to make it less confusing we would
> highly recommend using the master branch as the development branch and link
> that to the master (development version) of Bioconductor.   This would be
> consistent and then you can following the guides and tutorials listed on
> the Bioconductor help pages
>
> http://bioconductor.org/developers/how-to/git/
>
>
> The release branch is designed to always be a stable branch and should
> only be updated for bug corrections.
> The master branch should be for development and new features.
>
>
>
> We will assume you ran the following to set up your remotes as
> recommended:
> git remote add upstream g...@git.bioconductor.org:packages/tidybulk.git
>
>
> if you do
> git remote -v
>
> you should see something similar:
> origin   (fetch)
> origin   (push)
> upstream g...@git.bioconductor.org:packages/tidybulk.git (fetch)
> upstream g...@git.bioconductor.org:packages/tidybulk.git (push)
>
>
> To create and work on a release branch:
>
> git fetch --all
> # this gets all branches from all remotes
>
>
> # The following would only need to be run once EVER!
> git checkout -b RELEASE_3_11  upstream/RELEASE_3_11
>
> # this says checkout  a branch (-b)  call it RELEASE_3_11  and have it
> copied/link to the code at  upstream/RELEASE_3_11 (the #bioconductor
> upstream remote branch of RELEASE_3_11)
>
> After it is created, to switch to this branch on a daily basis you can
> simply:
> git checkout RELEASE_3_11
>
>
>
> git pull upstream RELEASE_3_11
> # pulls changes from the upstream RELEASE_3_11 remote
>
>
> # The following would only need to be run once EVER!   It creates a branch
> on your local github called RELEASE_3_11
> git push -u origin RELEASE_3_11
>
>
>
> Make your code changes to fix bugs! Make sure to do a valid version bump
> by bumping the  z  of version  x.y.z
>
> git add 
> git commit# give an informative commit message
>
>
> git push upstream RELEASE_3_11
> # This should push to the Bioconductor git repository
>
> git push origin RELEASE_3_11
> # This should push to your github local git repository
>
>
> git checkout master
> # Switch back to your master branch for development and code changes
>
>
> If you are ever confused on what branch you are on you can do
> git branch
>
>
> To work on the devel master branch the commands would be similar to above
> but using master
>
> git pull upstream master  # pulls from git bioconductor
> git pull origin master# pull from your individual github
>
> # make changes, commit changes
>
> git push upstream master  # pushes to git Bioconductor
> git push origin master   # push to your github
>
>
> Hopefully that helped clarified and will get you started.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* stefano 
> *Sent:* Thursday, June 4, 2020 12:56 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: Bioconductor package tidybulk
>
> Thanks Lori,
>
> I have to questions
>
> 1)
> I got versioning error
>
>
> ```
>
> rstudio-1 267 % git push upstream master
> Counting objects: 372, done.
> Delta compression using up to 32 threads.
> Compressing objects: 100% (276/276), done.
> Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done.
> Total 290 (delta 208), reused 21 (delta 13)
> remote: Resolving deltas: 100% (208/208), completed with 41 local objects.
> *remote: Error: Illegal version bump from '1.1.0' to 

[Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Nystrom, Spencer]

Hi,

I've identified a few missing PWMs from the MotifDb package and would like to 
help get them added. I posted on the support page but have not received a 
response after 10 days, so messaging here instead (link to forum post: 
https://support.bioconductor.org/p/131312/). Full details can be found in the 
support post, but in summary, there are a small number of Drosophila 
transcription factors which do not have any entries in MotifDb, meaning anyone 
using that database for their motif analysis will not identify these factors as 
potential candidates. A .meme format file ("flyFactor_Missing_Motifdb.meme") of 
these missing motifs along with a reproducible script to identify these factors 
can be found at this gist: 
https://gist.github.com/snystrom/b7701858bec6bc4ce7758a7582422359. I am happy 
to help curate any additional metadata required to get these factors added to 
the database.

Best,
  -Spencer

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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Martin Morgan]

no, the build system should only propagate packages that have passed build and 
check -- the goal is to make the life of the user easier and more reliable, us 
developers have to sweat the details!

Usually there is a single package that has changed and causes problems, and 
like in the present case a little detective work (once one knows what to look 
for) leads quickly to the suspect.

Martin

On 6/5/20, 10:18 AM, "Robert Castelo"  wrote:

Thanks Martin, i wasn't aware about that fact. i've cloned the gwascat 
repo and been able to directly install from the directory and reproduce 
the error. in this case, this was easy because it involved just one 
package but with multiple broken package dependencies, i'd have to 
manually clone each of them and install them to reproduce the error.

would it be a good idea in the devel build system to propagate the tar 
ball resulting of

R CMD build --no-build-vignettes

so that we get automatically updates for at least those whose problem is 
in the vignettes only?

robert.

On 05/06/2020 15:37, Martin Morgan wrote:
> R CMD INSTALL  or install.packages("foo", repos = NULL) on a clone 
of the repository. A build might fail because the examples or vignette fail to 
build, whereas for installation the only requirement is that the package is 
syntactically correct.
>
> Martin
>
> On 6/5/20, 7:58 AM, "Robert Castelo"  wrote:
>
>  never thought about it this way, but how can the system install
>  something that does not build?
>
>  how should *i* install something that does not build to reproduce 
the error?
>
>  sorry if these are very naive questions!!
>
>  robert.
>
>  On 05/06/2020 13:34, Martin Morgan wrote:
>  > The build system installs the version of gwascat that is available 
from git checkout (anticipating that this will propagate). gwascat installs, 
but fails to pass check -- it is likely broken
>  >
>  >https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/
>  >
>  > in a way that causes your package to fail
>  >
>  > Martin
>  >
>  > On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" 
 wrote:
>  >
>  >  hi,
>  >
>  >  my package GenomicScores is not building, see:
>  >
>  >  
http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>  >
>  >  apparently, it is breaking in the following lines of its 
vignette:
>  >
>  >  library(gwascat)
>  >  data(ebicat37)
>  >
>  >  which in the report from the bioc build machine says:
>  >
>  >  gwascat loaded.  Use makeCurrentGwascat() to extract current 
image.
>  >from EBI.  The data folder of this package has some legacy 
extracts.
>  >  Quitting from lines 404-408 (GenomicScores.Rmd)
>  >  Error: processing vignette 'GenomicScores.Rmd' failed with 
diagnostics:
>  >  object 'ebicat37' not found
>  >  --- failed re-building ‘GenomicScores.Rmd’
>  >
>  >  however, in my installation of current bioc-devel on R-4.0 
with all
>  >  packages up to date, GenomicScores builds fine and i cannot 
reproduce
>  >  this error. below you can find my session information after 
the previous
>  >  two instructions. the logs of 'gwascat' show changes in May 
2nd that
>  >  could be potentially responsible for this but the fact is 
that 'gwascat'
>  >  is not building either and it does not seem that the changes 
propagate
>  >  through the build system, its version is still 2.21.0, on 
which
>  >  GenomicScores built without problems for the current release.
>  >
>  >  i'm cc'ing this email to Vince, as maintainer of 'gwascat', 
in case he
>  >  has some more specific suggestion about this but any hint 
will be
>  >  greatly appreciated.
>  >
>  >  thanks!!
>  >
>  >  sessionInfo()
>  >  R version 4.0.0 (2020-04-24)
>  >  Platform: x86_64-pc-linux-gnu (64-bit)
>  >  Running under: CentOS Linux 7 (Core)
>  >
>  >  Matrix products: default
>  >  BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
>  >  LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>  >
>  >  locale:
>  >[1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
>  >[3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
>  >[5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
>  >[7] LC_PAPER=en_US.UTF8   LC_NAME=C
>  >[9] LC_ADDRESS=C  

[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Robert Castelo]

hi,

my package GenomicScores is not building, see:

http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html

apparently, it is breaking in the following lines of its vignette:

library(gwascat)
data(ebicat37)

which in the report from the bioc build machine says:

gwascat loaded.  Use makeCurrentGwascat() to extract current image.
  from EBI.  The data folder of this package has some legacy extracts.
Quitting from lines 404-408 (GenomicScores.Rmd)
Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
object 'ebicat37' not found
--- failed re-building ‘GenomicScores.Rmd’

however, in my installation of current bioc-devel on R-4.0 with all 
packages up to date, GenomicScores builds fine and i cannot reproduce 
this error. below you can find my session information after the previous 
two instructions. the logs of 'gwascat' show changes in May 2nd that 
could be potentially responsible for this but the fact is that 'gwascat' 
is not building either and it does not seem that the changes propagate 
through the build system, its version is still 2.21.0, on which 
GenomicScores built without problems for the current release.

i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he 
has some more specific suggestion about this but any hint will be 
greatly appreciated.

thanks!!

sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8    LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8   LC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets methods   base

other attached packages:
[1] gwascat_2.21.0 colorout_1.2-2

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.4.6 lattice_0.20-41
  [3] prettyunits_1.1.1 Rsamtools_2.5.1
  [5] Biostrings_2.57.1 assertthat_0.2.1
  [7] digest_0.6.25 BiocFileCache_1.13.0
  [9] R6_2.4.1 GenomeInfoDb_1.25.1
[11] stats4_4.0.0 RSQLite_2.2.0
[13] httr_1.4.1 ggplot2_3.3.1
[15] pillar_1.4.4 zlibbioc_1.35.0
[17] rlang_0.4.6 GenomicFeatures_1.41.0
[19] progress_1.2.2 curl_4.3
[21] blob_1.2.1 S4Vectors_0.27.11
[23] Matrix_1.2-18 BiocParallel_1.23.0
[25] stringr_1.4.0 RCurl_1.98-1.2
[27] bit_1.1-15.2 biomaRt_2.45.0
[29] munsell_0.5.0 DelayedArray_0.15.1
[31] compiler_4.0.0 rtracklayer_1.49.3
[33] pkgconfig_2.0.3 askpass_1.1
[35] BiocGenerics_0.35.3 openssl_1.4.1
[37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
[39] tibble_3.0.1 GenomeInfoDbData_1.2.3
[41] IRanges_2.23.7 matrixStats_0.56.0
[43] XML_3.99-0.3 crayon_1.3.4
[45] dplyr_1.0.0 dbplyr_1.4.4
[47] GenomicAlignments_1.25.1 bitops_1.0-6
[49] rappdirs_0.3.1 grid_4.0.0
[51] gtable_0.3.0 lifecycle_0.2.0
[53] DBI_1.1.0 magrittr_1.5
[55] scales_1.1.1 stringi_1.4.6
[57] XVector_0.29.1 ellipsis_0.3.1
[59] generics_0.0.2 vctrs_0.3.0
[61] tools_4.0.0 bit64_0.9-7
[63] Biobase_2.49.0 glue_1.4.1
[65] purrr_0.3.4 hms_0.5.3
[67] parallel_4.0.0 colorspace_1.4-1
[69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
[71] memoise_1.1.0



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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Vincent Carey]

I am really sorry about the situation with gwascat and will try to
straighten it out today.

On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo 
wrote:

> hi,
>
> my package GenomicScores is not building, see:
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>
> apparently, it is breaking in the following lines of its vignette:
>
> library(gwascat)
> data(ebicat37)
>
> which in the report from the bioc build machine says:
>
> gwascat loaded.  Use makeCurrentGwascat() to extract current image.
>  from EBI.  The data folder of this package has some legacy extracts.
> Quitting from lines 404-408 (GenomicScores.Rmd)
> Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
> object 'ebicat37' not found
> --- failed re-building ‘GenomicScores.Rmd’
>
> however, in my installation of current bioc-devel on R-4.0 with all
> packages up to date, GenomicScores builds fine and i cannot reproduce this
> error. below you can find my session information after the previous two
> instructions. the logs of 'gwascat' show changes in May 2nd that could be
> potentially responsible for this but the fact is that 'gwascat' is not
> building either and it does not seem that the changes propagate through the
> build system, its version is still 2.21.0, on which GenomicScores built
> without problems for the current release.
>
> i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he has
> some more specific suggestion about this but any hint will be greatly
> appreciated.
>
> thanks!!
>
> sessionInfo()
> R version 4.0.0 (2020-04-24)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> Matrix products: default
> BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
> LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
>  [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
>  [7] LC_PAPER=en_US.UTF8   LC_NAME=C
>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] gwascat_2.21.0 colorout_1.2-2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_1.0.4.6lattice_0.20-41
>  [3] prettyunits_1.1.1   Rsamtools_2.5.1
>  [5] Biostrings_2.57.1   assertthat_0.2.1
>  [7] digest_0.6.25   BiocFileCache_1.13.0
>  [9] R6_2.4.1GenomeInfoDb_1.25.1
> [11] stats4_4.0.0RSQLite_2.2.0
> [13] httr_1.4.1  ggplot2_3.3.1
> [15] pillar_1.4.4zlibbioc_1.35.0
> [17] rlang_0.4.6 GenomicFeatures_1.41.0
> [19] progress_1.2.2  curl_4.3
> [21] blob_1.2.1  S4Vectors_0.27.11
> [23] Matrix_1.2-18   BiocParallel_1.23.0
> [25] stringr_1.4.0   RCurl_1.98-1.2
> [27] bit_1.1-15.2biomaRt_2.45.0
> [29] munsell_0.5.0   DelayedArray_0.15.1
> [31] compiler_4.0.0  rtracklayer_1.49.3
> [33] pkgconfig_2.0.3 askpass_1.1
> [35] BiocGenerics_0.35.3 openssl_1.4.1
> [37] tidyselect_1.1.0SummarizedExperiment_1.19.4
> [39] tibble_3.0.1GenomeInfoDbData_1.2.3
> [41] IRanges_2.23.7  matrixStats_0.56.0
> [43] XML_3.99-0.3crayon_1.3.4
> [45] dplyr_1.0.0 dbplyr_1.4.4
> [47] GenomicAlignments_1.25.1bitops_1.0-6
> [49] rappdirs_0.3.1  grid_4.0.0
> [51] gtable_0.3.0lifecycle_0.2.0
> [53] DBI_1.1.0   magrittr_1.5
> [55] scales_1.1.1stringi_1.4.6
> [57] XVector_0.29.1  ellipsis_0.3.1
> [59] generics_0.0.2  vctrs_0.3.0
> [61] tools_4.0.0 bit64_0.9-7
> [63] Biobase_2.49.0  glue_1.4.1
> [65] purrr_0.3.4 hms_0.5.3
> [67] parallel_4.0.0  colorspace_1.4-1
> [69] AnnotationDbi_1.51.0GenomicRanges_1.41.3
> [71] memoise_1.1.0
>
>
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Robert Castelo]

never thought about it this way, but how can the system install 
something that does not build?


how should *i* install something that does not build to reproduce the error?

sorry if these are very naive questions!!

robert.

On 05/06/2020 13:34, Martin Morgan wrote:

The build system installs the version of gwascat that is available from git 
checkout (anticipating that this will propagate). gwascat installs, but fails 
to pass check -- it is likely broken

   https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/

in a way that causes your package to fail

Martin

On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" 
 wrote:

 hi,

 my package GenomicScores is not building, see:

 
http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html

 apparently, it is breaking in the following lines of its vignette:

 library(gwascat)
 data(ebicat37)

 which in the report from the bioc build machine says:

 gwascat loaded.  Use makeCurrentGwascat() to extract current image.
   from EBI.  The data folder of this package has some legacy extracts.
 Quitting from lines 404-408 (GenomicScores.Rmd)
 Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
 object 'ebicat37' not found
 --- failed re-building ‘GenomicScores.Rmd’

 however, in my installation of current bioc-devel on R-4.0 with all
 packages up to date, GenomicScores builds fine and i cannot reproduce
 this error. below you can find my session information after the previous
 two instructions. the logs of 'gwascat' show changes in May 2nd that
 could be potentially responsible for this but the fact is that 'gwascat'
 is not building either and it does not seem that the changes propagate
 through the build system, its version is still 2.21.0, on which
 GenomicScores built without problems for the current release.

 i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he
 has some more specific suggestion about this but any hint will be
 greatly appreciated.

 thanks!!

 sessionInfo()
 R version 4.0.0 (2020-04-24)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: CentOS Linux 7 (Core)

 Matrix products: default
 BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
 LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so

 locale:
   [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
   [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
   [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
   [7] LC_PAPER=en_US.UTF8   LC_NAME=C
   [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats graphics  grDevices utils datasets methods   base

 other attached packages:
 [1] gwascat_2.21.0 colorout_1.2-2

 loaded via a namespace (and not attached):
   [1] Rcpp_1.0.4.6 lattice_0.20-41
   [3] prettyunits_1.1.1 Rsamtools_2.5.1
   [5] Biostrings_2.57.1 assertthat_0.2.1
   [7] digest_0.6.25 BiocFileCache_1.13.0
   [9] R6_2.4.1 GenomeInfoDb_1.25.1
 [11] stats4_4.0.0 RSQLite_2.2.0
 [13] httr_1.4.1 ggplot2_3.3.1
 [15] pillar_1.4.4 zlibbioc_1.35.0
 [17] rlang_0.4.6 GenomicFeatures_1.41.0
 [19] progress_1.2.2 curl_4.3
 [21] blob_1.2.1 S4Vectors_0.27.11
 [23] Matrix_1.2-18 BiocParallel_1.23.0
 [25] stringr_1.4.0 RCurl_1.98-1.2
 [27] bit_1.1-15.2 biomaRt_2.45.0
 [29] munsell_0.5.0 DelayedArray_0.15.1
 [31] compiler_4.0.0 rtracklayer_1.49.3
 [33] pkgconfig_2.0.3 askpass_1.1
 [35] BiocGenerics_0.35.3 openssl_1.4.1
 [37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
 [39] tibble_3.0.1 GenomeInfoDbData_1.2.3
 [41] IRanges_2.23.7 matrixStats_0.56.0
 [43] XML_3.99-0.3 crayon_1.3.4
 [45] dplyr_1.0.0 dbplyr_1.4.4
 [47] GenomicAlignments_1.25.1 bitops_1.0-6
 [49] rappdirs_0.3.1 grid_4.0.0
 [51] gtable_0.3.0 lifecycle_0.2.0
 [53] DBI_1.1.0 magrittr_1.5
 [55] scales_1.1.1 stringi_1.4.6
 [57] XVector_0.29.1 ellipsis_0.3.1
 [59] generics_0.0.2 vctrs_0.3.0
 [61] tools_4.0.0 bit64_0.9-7
 [63] Biobase_2.49.0 glue_1.4.1
 [65] purrr_0.3.4 hms_0.5.3
 [67] parallel_4.0.0 colorspace_1.4-1
 [69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
 [71] memoise_1.1.0



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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Martin Morgan]

The build system installs the version of gwascat that is available from git 
checkout (anticipating that this will propagate). gwascat installs, but fails 
to pass check -- it is likely broken

  https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/

in a way that causes your package to fail

Martin

On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" 
 wrote:

hi,

my package GenomicScores is not building, see:


http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html

apparently, it is breaking in the following lines of its vignette:

library(gwascat)
data(ebicat37)

which in the report from the bioc build machine says:

gwascat loaded.  Use makeCurrentGwascat() to extract current image.
  from EBI.  The data folder of this package has some legacy extracts.
Quitting from lines 404-408 (GenomicScores.Rmd)
Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
object 'ebicat37' not found
--- failed re-building ‘GenomicScores.Rmd’

however, in my installation of current bioc-devel on R-4.0 with all 
packages up to date, GenomicScores builds fine and i cannot reproduce 
this error. below you can find my session information after the previous 
two instructions. the logs of 'gwascat' show changes in May 2nd that 
could be potentially responsible for this but the fact is that 'gwascat' 
is not building either and it does not seem that the changes propagate 
through the build system, its version is still 2.21.0, on which 
GenomicScores built without problems for the current release.

i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he 
has some more specific suggestion about this but any hint will be 
greatly appreciated.

thanks!!

sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8   LC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets methods   base

other attached packages:
[1] gwascat_2.21.0 colorout_1.2-2

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.4.6 lattice_0.20-41
  [3] prettyunits_1.1.1 Rsamtools_2.5.1
  [5] Biostrings_2.57.1 assertthat_0.2.1
  [7] digest_0.6.25 BiocFileCache_1.13.0
  [9] R6_2.4.1 GenomeInfoDb_1.25.1
[11] stats4_4.0.0 RSQLite_2.2.0
[13] httr_1.4.1 ggplot2_3.3.1
[15] pillar_1.4.4 zlibbioc_1.35.0
[17] rlang_0.4.6 GenomicFeatures_1.41.0
[19] progress_1.2.2 curl_4.3
[21] blob_1.2.1 S4Vectors_0.27.11
[23] Matrix_1.2-18 BiocParallel_1.23.0
[25] stringr_1.4.0 RCurl_1.98-1.2
[27] bit_1.1-15.2 biomaRt_2.45.0
[29] munsell_0.5.0 DelayedArray_0.15.1
[31] compiler_4.0.0 rtracklayer_1.49.3
[33] pkgconfig_2.0.3 askpass_1.1
[35] BiocGenerics_0.35.3 openssl_1.4.1
[37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
[39] tibble_3.0.1 GenomeInfoDbData_1.2.3
[41] IRanges_2.23.7 matrixStats_0.56.0
[43] XML_3.99-0.3 crayon_1.3.4
[45] dplyr_1.0.0 dbplyr_1.4.4
[47] GenomicAlignments_1.25.1 bitops_1.0-6
[49] rappdirs_0.3.1 grid_4.0.0
[51] gtable_0.3.0 lifecycle_0.2.0
[53] DBI_1.1.0 magrittr_1.5
[55] scales_1.1.1 stringi_1.4.6
[57] XVector_0.29.1 ellipsis_0.3.1
[59] generics_0.0.2 vctrs_0.3.0
[61] tools_4.0.0 bit64_0.9-7
[63] Biobase_2.49.0 glue_1.4.1
[65] purrr_0.3.4 hms_0.5.3
[67] parallel_4.0.0 colorspace_1.4-1
[69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
[71] memoise_1.1.0



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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Martin Morgan]

R CMD INSTALL  or install.packages("foo", repos = NULL) on a clone of the 
repository. A build might fail because the examples or vignette fail to build, 
whereas for installation the only requirement is that the package is 
syntactically correct.

Martin

On 6/5/20, 7:58 AM, "Robert Castelo"  wrote:

never thought about it this way, but how can the system install 
something that does not build?

how should *i* install something that does not build to reproduce the error?

sorry if these are very naive questions!!

robert.

On 05/06/2020 13:34, Martin Morgan wrote:
> The build system installs the version of gwascat that is available from 
git checkout (anticipating that this will propagate). gwascat installs, but 
fails to pass check -- it is likely broken
>
>https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/
>
> in a way that causes your package to fail
>
> Martin
>
> On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" 
 wrote:
>
>  hi,
>
>  my package GenomicScores is not building, see:
>
>  
http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>
>  apparently, it is breaking in the following lines of its vignette:
>
>  library(gwascat)
>  data(ebicat37)
>
>  which in the report from the bioc build machine says:
>
>  gwascat loaded.  Use makeCurrentGwascat() to extract current image.
>from EBI.  The data folder of this package has some legacy 
extracts.
>  Quitting from lines 404-408 (GenomicScores.Rmd)
>  Error: processing vignette 'GenomicScores.Rmd' failed with 
diagnostics:
>  object 'ebicat37' not found
>  --- failed re-building ‘GenomicScores.Rmd’
>
>  however, in my installation of current bioc-devel on R-4.0 with all
>  packages up to date, GenomicScores builds fine and i cannot reproduce
>  this error. below you can find my session information after the 
previous
>  two instructions. the logs of 'gwascat' show changes in May 2nd that
>  could be potentially responsible for this but the fact is that 
'gwascat'
>  is not building either and it does not seem that the changes 
propagate
>  through the build system, its version is still 2.21.0, on which
>  GenomicScores built without problems for the current release.
>
>  i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case 
he
>  has some more specific suggestion about this but any hint will be
>  greatly appreciated.
>
>  thanks!!
>
>  sessionInfo()
>  R version 4.0.0 (2020-04-24)
>  Platform: x86_64-pc-linux-gnu (64-bit)
>  Running under: CentOS Linux 7 (Core)
>
>  Matrix products: default
>  BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
>  LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>
>  locale:
>[1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
>[3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
>[5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
>[7] LC_PAPER=en_US.UTF8   LC_NAME=C
>[9] LC_ADDRESS=C  LC_TELEPHONE=C
>  [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
>  attached base packages:
>  [1] stats graphics  grDevices utils datasets methods   base
>
>  other attached packages:
>  [1] gwascat_2.21.0 colorout_1.2-2
>
>  loaded via a namespace (and not attached):
>[1] Rcpp_1.0.4.6 lattice_0.20-41
>[3] prettyunits_1.1.1 Rsamtools_2.5.1
>[5] Biostrings_2.57.1 assertthat_0.2.1
>[7] digest_0.6.25 BiocFileCache_1.13.0
>[9] R6_2.4.1 GenomeInfoDb_1.25.1
>  [11] stats4_4.0.0 RSQLite_2.2.0
>  [13] httr_1.4.1 ggplot2_3.3.1
>  [15] pillar_1.4.4 zlibbioc_1.35.0
>  [17] rlang_0.4.6 GenomicFeatures_1.41.0
>  [19] progress_1.2.2 curl_4.3
>  [21] blob_1.2.1 S4Vectors_0.27.11
>  [23] Matrix_1.2-18 BiocParallel_1.23.0
>  [25] stringr_1.4.0 RCurl_1.98-1.2
>  [27] bit_1.1-15.2 biomaRt_2.45.0
>  [29] munsell_0.5.0 DelayedArray_0.15.1
>  [31] compiler_4.0.0 rtracklayer_1.49.3
>  [33] pkgconfig_2.0.3 askpass_1.1
>  [35] BiocGenerics_0.35.3 openssl_1.4.1
>  [37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
>  [39] tibble_3.0.1 GenomeInfoDbData_1.2.3
>  [41] IRanges_2.23.7 matrixStats_0.56.0
>  [43] XML_3.99-0.3 crayon_1.3.4
>  [45] dplyr_1.0.0 dbplyr_1.4.4
>  [47] GenomicAlignments_1.25.1 bitops_1.0-6
>  [49] rappdirs_0.3.1 grid_4.0.0
>  [51] gtable_0.3.0 lifecycle_0.2.0
>  [53] DBI_1.1.0 magrittr_1.5
>  [55] scales_1.1.1 

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Robert Castelo]

Thanks Martin, i wasn't aware about that fact. i've cloned the gwascat 
repo and been able to directly install from the directory and reproduce 
the error. in this case, this was easy because it involved just one 
package but with multiple broken package dependencies, i'd have to 
manually clone each of them and install them to reproduce the error.


would it be a good idea in the devel build system to propagate the tar 
ball resulting of


R CMD build --no-build-vignettes

so that we get automatically updates for at least those whose problem is 
in the vignettes only?


robert.

On 05/06/2020 15:37, Martin Morgan wrote:

R CMD INSTALL  or install.packages("foo", repos = NULL) on a clone of the 
repository. A build might fail because the examples or vignette fail to build, whereas for 
installation the only requirement is that the package is syntactically correct.

Martin

On 6/5/20, 7:58 AM, "Robert Castelo"  wrote:

 never thought about it this way, but how can the system install
 something that does not build?

 how should *i* install something that does not build to reproduce the 
error?

 sorry if these are very naive questions!!

 robert.

 On 05/06/2020 13:34, Martin Morgan wrote:
 > The build system installs the version of gwascat that is available from 
git checkout (anticipating that this will propagate). gwascat installs, but fails 
to pass check -- it is likely broken
 >
 >https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/
 >
 > in a way that causes your package to fail
 >
 > Martin
 >
 > On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" 
 wrote:
 >
 >  hi,
 >
 >  my package GenomicScores is not building, see:
 >
 >  
http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
 >
 >  apparently, it is breaking in the following lines of its vignette:
 >
 >  library(gwascat)
 >  data(ebicat37)
 >
 >  which in the report from the bioc build machine says:
 >
 >  gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 >from EBI.  The data folder of this package has some legacy 
extracts.
 >  Quitting from lines 404-408 (GenomicScores.Rmd)
 >  Error: processing vignette 'GenomicScores.Rmd' failed with 
diagnostics:
 >  object 'ebicat37' not found
 >  --- failed re-building ‘GenomicScores.Rmd’
 >
 >  however, in my installation of current bioc-devel on R-4.0 with all
 >  packages up to date, GenomicScores builds fine and i cannot 
reproduce
 >  this error. below you can find my session information after the 
previous
 >  two instructions. the logs of 'gwascat' show changes in May 2nd that
 >  could be potentially responsible for this but the fact is that 
'gwascat'
 >  is not building either and it does not seem that the changes 
propagate
 >  through the build system, its version is still 2.21.0, on which
 >  GenomicScores built without problems for the current release.
 >
 >  i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case 
he
 >  has some more specific suggestion about this but any hint will be
 >  greatly appreciated.
 >
 >  thanks!!
 >
 >  sessionInfo()
 >  R version 4.0.0 (2020-04-24)
 >  Platform: x86_64-pc-linux-gnu (64-bit)
 >  Running under: CentOS Linux 7 (Core)
 >
 >  Matrix products: default
 >  BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
 >  LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
 >
 >  locale:
 >[1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
 >[3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
 >[5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
 >[7] LC_PAPER=en_US.UTF8   LC_NAME=C
 >[9] LC_ADDRESS=C  LC_TELEPHONE=C
 >  [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
 >
 >  attached base packages:
 >  [1] stats graphics  grDevices utils datasets methods   base
 >
 >  other attached packages:
 >  [1] gwascat_2.21.0 colorout_1.2-2
 >
 >  loaded via a namespace (and not attached):
 >[1] Rcpp_1.0.4.6 lattice_0.20-41
 >[3] prettyunits_1.1.1 Rsamtools_2.5.1
 >[5] Biostrings_2.57.1 assertthat_0.2.1
 >[7] digest_0.6.25 BiocFileCache_1.13.0
 >[9] R6_2.4.1 GenomeInfoDb_1.25.1
 >  [11] stats4_4.0.0 RSQLite_2.2.0
 >  [13] httr_1.4.1 ggplot2_3.3.1
 >  [15] pillar_1.4.4 zlibbioc_1.35.0
 >  [17] rlang_0.4.6 GenomicFeatures_1.41.0
 >  [19] progress_1.2.2 curl_4.3
 >  [21] blob_1.2.1 S4Vectors_0.27.11
 >  [23] Matrix_1.2-18 BiocParallel_1.23.0
 >  [25] 

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Robert Castelo]

hi Vince,

no worries, i've been finally able to reproduce the error in my computer 
and i'm afraid i'm probably using a deprecated dataset from 'gwascat', 
concretely the one that was stored as

gwascat/data/ebicat37.rda

what would be the replacement for the following kind of operation?

data(ebicat37)
eyersids <- unique(subsetByTraits(ebicat37, tr="Eye color")$SNPS)
eyersids
  [1] "rs12913832" "rs7173419"  "rs3002288"  "rs12896399" "rs1408799"
  [6] "rs12520016" "rs288139"   "rs1667394"  "rs4596632" "rs12203592"
[11] "rs16891982" "rs1393350"  "rs1847134"

thanks!

robert.

On 05/06/2020 14:06, Vincent Carey wrote:
> I am really sorry about the situation with gwascat and will try to 
> straighten it out today.
>
> On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo  > wrote:
>
> hi,
>
> my package GenomicScores is not building, see:
>
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>
> apparently, it is breaking in the following lines of its vignette:
>
> library(gwascat)
> data(ebicat37)
>
> which in the report from the bioc build machine says:
>
> gwascat loaded.  Use makeCurrentGwascat() to extract current image.
>   from EBI.  The data folder of this package has some legacy extracts.
> Quitting from lines 404-408 (GenomicScores.Rmd)
> Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
> object 'ebicat37' not found
> --- failed re-building ‘GenomicScores.Rmd’
>
> however, in my installation of current bioc-devel on R-4.0 with
> all packages up to date, GenomicScores builds fine and i cannot
> reproduce this error. below you can find my session information
> after the previous two instructions. the logs of 'gwascat' show
> changes in May 2nd that could be potentially responsible for this
> but the fact is that 'gwascat' is not building either and it does
> not seem that the changes propagate through the build system, its
> version is still 2.21.0, on which GenomicScores built without
> problems for the current release.
>
> i'm cc'ing this email to Vince, as maintainer of 'gwascat', in
> case he has some more specific suggestion about this but any hint
> will be greatly appreciated.
>
> thanks!!
>
> sessionInfo()
> R version 4.0.0 (2020-04-24)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> Matrix products: default
> BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
> LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
>  [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
>  [7] LC_PAPER=en_US.UTF8 LC_NAME=C
>  [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] gwascat_2.21.0 colorout_1.2-2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_1.0.4.6 lattice_0.20-41
>  [3] prettyunits_1.1.1 Rsamtools_2.5.1
>  [5] Biostrings_2.57.1 assertthat_0.2.1
>  [7] digest_0.6.25 BiocFileCache_1.13.0
>  [9] R6_2.4.1 GenomeInfoDb_1.25.1
> [11] stats4_4.0.0 RSQLite_2.2.0
> [13] httr_1.4.1 ggplot2_3.3.1
> [15] pillar_1.4.4 zlibbioc_1.35.0
> [17] rlang_0.4.6 GenomicFeatures_1.41.0
> [19] progress_1.2.2 curl_4.3
> [21] blob_1.2.1 S4Vectors_0.27.11
> [23] Matrix_1.2-18 BiocParallel_1.23.0
> [25] stringr_1.4.0 RCurl_1.98-1.2
> [27] bit_1.1-15.2 biomaRt_2.45.0
> [29] munsell_0.5.0 DelayedArray_0.15.1
> [31] compiler_4.0.0 rtracklayer_1.49.3
> [33] pkgconfig_2.0.3 askpass_1.1
> [35] BiocGenerics_0.35.3 openssl_1.4.1
> [37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
> [39] tibble_3.0.1 GenomeInfoDbData_1.2.3
> [41] IRanges_2.23.7 matrixStats_0.56.0
> [43] XML_3.99-0.3 crayon_1.3.4
> [45] dplyr_1.0.0 dbplyr_1.4.4
> [47] GenomicAlignments_1.25.1 bitops_1.0-6
> [49] rappdirs_0.3.1 grid_4.0.0
> [51] gtable_0.3.0 lifecycle_0.2.0
> [53] DBI_1.1.0 magrittr_1.5
> [55] scales_1.1.1 stringi_1.4.6
> [57] XVector_0.29.1 ellipsis_0.3.1
> [59] generics_0.0.2 vctrs_0.3.0
> [61] tools_4.0.0 bit64_0.9-7
> [63] Biobase_2.49.0 glue_1.4.1
> [65] purrr_0.3.4 hms_0.5.3
> [67] parallel_4.0.0 colorspace_1.4-1
> [69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
> [71] memoise_1.1.0
>
>
>
> The information in this e-mail is intended only for th...{{dropped:18}}

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Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

[Vincent Carey]

On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo 
wrote:

> hi Vince,
>
> no worries, i've been finally able to reproduce the error in my computer
> and i'm afraid i'm probably using a deprecated dataset from 'gwascat',
> concretely the one that was stored as
>
> gwascat/data/ebicat37.rda
>
> what would be the replacement for the following kind of operation?
>

The best thing to do from a scientific point of view would likely be

curcat = gwascat::makeCurrentGwascat()

then work with that, which will have GRCh38 coordinates.

It is slow to run makeCurrentGwascat.  You might want to serialize what you
need.
I can't place a snapshot in gwascat as I had in the past because the image
compressed
with xz exceeds 5MB.  Any snapshot has to be in AnnotationHub.  I don't
have a
plan for this at the moment.

There is an object called ebicat_2020_04_30 in the data
folder of gwascat on devel branch.  It is a sample of 5 records from
the full
catalog of that date.  You might be able to use that for what you are
doing; I will
be renaming it to clarify that it is a sample.


>
> data(ebicat37)
> eyersids <- unique(subsetByTraits(ebicat37, tr="Eye color")$SNPS)
> eyersids
>  [1] "rs12913832" "rs7173419"  "rs3002288"  "rs12896399" "rs1408799"
>  [6] "rs12520016" "rs288139"   "rs1667394"  "rs4596632"  "rs12203592"
> [11] "rs16891982" "rs1393350"  "rs1847134"
>
> thanks!
>
> robert.
>
> On 05/06/2020 14:06, Vincent Carey wrote:
>
> I am really sorry about the situation with gwascat and will try to
> straighten it out today.
>
> On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo 
> wrote:
>
>> hi,
>>
>> my package GenomicScores is not building, see:
>>
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html
>>
>> apparently, it is breaking in the following lines of its vignette:
>>
>> library(gwascat)
>> data(ebicat37)
>>
>> which in the report from the bioc build machine says:
>>
>> gwascat loaded.  Use makeCurrentGwascat() to extract current image.
>>  from EBI.  The data folder of this package has some legacy extracts.
>> Quitting from lines 404-408 (GenomicScores.Rmd)
>> Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
>> object 'ebicat37' not found
>> --- failed re-building ‘GenomicScores.Rmd’
>>
>> however, in my installation of current bioc-devel on R-4.0 with all
>> packages up to date, GenomicScores builds fine and i cannot reproduce this
>> error. below you can find my session information after the previous two
>> instructions. the logs of 'gwascat' show changes in May 2nd that could be
>> potentially responsible for this but the fact is that 'gwascat' is not
>> building either and it does not seem that the changes propagate through the
>> build system, its version is still 2.21.0, on which GenomicScores built
>> without problems for the current release.
>>
>> i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he
>> has some more specific suggestion about this but any hint will be greatly
>> appreciated.
>>
>> thanks!!
>>
>> sessionInfo()
>> R version 4.0.0 (2020-04-24)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF8   LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8
>>  [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8
>>  [7] LC_PAPER=en_US.UTF8   LC_NAME=C
>>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> other attached packages:
>> [1] gwascat_2.21.0 colorout_1.2-2
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_1.0.4.6lattice_0.20-41
>>  [3] prettyunits_1.1.1   Rsamtools_2.5.1
>>  [5] Biostrings_2.57.1   assertthat_0.2.1
>>  [7] digest_0.6.25   BiocFileCache_1.13.0
>>  [9] R6_2.4.1GenomeInfoDb_1.25.1
>> [11] stats4_4.0.0RSQLite_2.2.0
>> [13] httr_1.4.1  ggplot2_3.3.1
>> [15] pillar_1.4.4zlibbioc_1.35.0
>> [17] rlang_0.4.6 GenomicFeatures_1.41.0
>> [19] progress_1.2.2  curl_4.3
>> [21] blob_1.2.1  S4Vectors_0.27.11
>> [23] Matrix_1.2-18   BiocParallel_1.23.0
>> [25] stringr_1.4.0   RCurl_1.98-1.2
>> [27] bit_1.1-15.2biomaRt_2.45.0
>> [29] munsell_0.5.0   DelayedArray_0.15.1
>> [31] compiler_4.0.0  rtracklayer_1.49.3
>> [33] pkgconfig_2.0.3 askpass_1.1
>> [35] BiocGenerics_0.35.3 openssl_1.4.1
>> [37] tidyselect_1.1.0SummarizedExperiment_1.19.4
>> [39] tibble_3.0.1GenomeInfoDbData_1.2.3
>> [41] IRanges_2.23.7  matrixStats_0.56.0
>> [43] XML_3.99-0.3