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corral #1492

Closed laurenhsu1 closed 4 years ago

laurenhsu1 commented 4 years ago

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bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

7b4291b updating namespace vignette bug https://bioconduct...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

a5d8c99 resize sticker 18bb408 fixing bug in https://bioconductor.org/spb_reports...

bioc-issue-bot commented 4 years ago

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Congratulations! The package built without errors or warnings on all platforms.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

3b2c071 update to input checks 117df66 Merge branch 'master' of https://github.com/lauren... 63a60c8 add more detail on the input/output structure into...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

c24a34f add comment clarifying devel branch of MAE can be ... eec5f09 version bump cb8813a update MAE implementation of data setup

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

551e86b import; fixing bug in: http://bioconductor.org/spb...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

6b4e951 reverting back to older version in vignette until ...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

019b485 fixing quotes https://bioconductor.org/spb_reports...

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

4cb4e06 version bump

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

laurenhsu1 commented 4 years ago

Hi Marcel @LiNk-NY,

I’ve pushed a version of the package that appears to pass the build (the warning is because it took > 20min to build, but I didn't substantially change from before so I am guessing this is some sort of system error? the one before that didn't get posted by bioc-issue-bot and appears to have some issues with loading the DuoClustering dataset which self-resolved when I just bumped version http://staging.bioconductor.org:8000/job/12422/).

It includes the rest of the updates to the package, including adding a visual explainer of the input/output formats for the methods in the respective vignettes. In the alignment vignette I also added the MAE lines that you added as commented out with a brief note about the devel branch, and will plan to uncomment them after the new version of MAE is released (for the time being, I get a build error when I leave them there.)

Per the conversation in slack on SCE list, I have not made a new class. I did add checks in the functions to ensure all elements of list are consistent. There is also a way to toggle into having the full output using the fullout argument in either method.

Let me know what the next steps are.

Thanks, Lauren

LiNk-NY commented 4 years ago

Hi Lauren, @laurenhsu1

Thank you for making those changes.

Once the package is accepted, it will go into the devel branch. You don't have to mention that you are using Bioconductor devel because your initial users will all be using Bioconductor devel. You can uncomment the code since it should now work in the devel branch (the change in MultiAssayExperiment has propagated).

Regarding the DuoClustering dataset, it may have been an intermittent connection issue.

Please make the change and bump the version of the package. Thank you.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

929ba17 uncomment out MAE implementation in alignment vign... 7cf011d version bump

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

cf90b68 . 000746e version bump

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

laurenhsu1 commented 4 years ago

Hi Marcel @LiNk-NY , I'm still getting the same error: Quitting from lines 81-85 (corralm_alignment.Rmd) Error: processing vignette 'corralm_alignment.Rmd' failed with diagnostics: no method or default for coercing "list" to "MultiAssayExperiment" --- failed re-building corralm_alignment.Rmd (as in this build report: https://bioconductor.org/spb_reports/corral_buildreport_20200520145233.html)

LiNk-NY commented 4 years ago

Hi Lauren, @laurenhsu1

This is strange. It looks like the SPB is using Bioconductor 3.11.

Lori @lshep, Kayla @Kayla-Morrell : Shouldn't it be using Bioconductor 3.12?

I've tried to replicate this locally with Bioc-devel and I get an error on different lines.

Rdev CMD build corral
--- re-building ‘corralm_alignment.Rmd’ using rmarkdown
Loading required package: magrittr
Loading required package: tibble
Quitting from lines 115-116 (corralm_alignment.Rmd) 
Error: processing vignette 'corralm_alignment.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘corralm_alignment.Rmd’

When I Stangle, I get: 

Rdev CMD Stangle corral/vignettes/corralm_alignment.Rmd
Output file:  corralm_alignment.R
mr148@mr148-Z68MA-D2H-B3 ~/bioconductor $ Rdev -e "source('corralm_alignment.R')"
Error: subscript contains invalid names
In addition: Warning message:
In load(data_path1) : invalid or incomplete compressed data
Execution halted

I think I have the latest packages:

> BiocManager::valid()

* sessionInfo()

R version 4.0.0 Patched (2020-05-16 r78478)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.0      tools_4.0.0        

Bioconductor version '3.12'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("RcisTarget", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new
laurenhsu1 commented 4 years ago

Hi Marcel @LiNk-NY, the error you're getting locally is because I didn't update the rest of the code based on what MAE does with colData names, I'll fix that.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

4aa20c2 fixing coldata field name based on MAE

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

34a38a6 address corralm on single SCE issue when 'splitby'...

laurenhsu1 commented 4 years ago

Hi Marcel @LiNk-NY ,

What is the name of the colData attribute that using as on a list of SCEs will put the names of the experiments? From looking at the MAE github (https://github.com/waldronlab/MultiAssayExperiment/blob/d5b55e205beb55c8c43cb1da31e8796bcafd4b55/R/MultiAssayExperiment-class.R#L648 is this the right place?), it looks like it is going into an attribute called 'experiment_name', but the latest build is giving me an error on that (http://staging.bioconductor.org:8000/job/12475/ --> line 115 is where the name of the experiment is first referenced)

Thanks, Lauren

LiNk-NY commented 4 years ago

Hi Lauren, @laurenhsu1 Apologies for the delay in getting back to you. I've had a look at the code. I only add 'experiment_name' to the colData of the MultiAssayExperiment and not the individual elements. If you'd like to extract a single experiment with the colData we have a helper called getWithColData but it only works on the original MultiAssayExperiment object. 

scmix_mae <- as(scmix_dat,'MultiAssayExperiment')
scmix_mae <- intersectRows(scmix_mae)
scmix_sce <- SingleCellExperiment::cbind(
    getWithColData(scmix_mae, 1L),
    getWithColData(scmix_mae, 2L),
    getWithColData(scmix_mae, 3L)
)
bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

3b0c986 add colData for Method in vignette addressing http...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

3be9d2e missing comma; fixing https://bioconductor.org/spb...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

96a3e30 notes in https://bioconductor.org/spb_reports/corr...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

c4a3682 version bump

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

laurenhsu1 commented 4 years ago

Hi Marcel @LiNk-NY , Thanks for clarifying. I have updated the package, and it has now built without errors.

It was odd though, because on the most recent, version 31 (http://staging.bioconductor.org:8000/job/12490/), there were no errors. On version 30 (http://staging.bioconductor.org:8000/job/12489/), there was a build error on macOS related to importing MultiAssayExperiment. On version 29 (http://staging.bioconductor.org:8000/job/12488/) it passed on macOS but failed linux and windows

However, the only change between v 30 and 31 was a version bump, and between v 29 and 30 was a single change from ::: to :: (unrelated to MultiAssayExperiment)

Is this normal for the check to vary this much between runs?

Thanks, Lauren

LiNk-NY commented 4 years ago

Hi Lauren, @laurenhsu1

It is not normal. Lori @lshep has been working hard on updating the SPB to use Bioc devel and this likely has caused some instability in the test results. Thanks for making those changes. Your package has been accepted :tada:

Best regards, Marcel

bioc-issue-bot commented 4 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

lshep commented 4 years ago

Yes sorry for any confusion. We were running updates on the SPB and it may take a few days to settle. Glad your package is accepted. Welcome to Bioconductor.

laurenhsu1 commented 4 years ago

Thanks @LiNk-NY and @lshep!

mtmorgan commented 4 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/laurenhsu1.keys is not empty), then no further steps are required. Otherwise, do the following:

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See further instructions at

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to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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