HDCytoData (ExperimentHub)

lmweber commented 6 years ago

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Repository: https://github.com/lmweber/HDCytoData

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bioc-issue-bot commented 6 years ago

Hi @lmweber

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: HDCytoData
Title: High-dimensional cytometry data sets in SummarizedExperiment and flowSet formats
Description: A set of example high-dimensional cytometry data sets, formatted into SummarizedExperiment and flowSet objects, and containing meta-data including sample IDs, group IDs, cluster labels, and protein marker names.
Version: 0.99.0
Author: Lukas M. Weber <lukmweber@gmail.com>, Charlotte Soneson <charlottesoneson@gmail.com>
Maintainer: Lukas M. Weber <lukmweber@gmail.com>
License: MIT + file LICENSE
Depends: ExperimentHub
Imports: 
    flowCore, 
    SummarizedExperiment, 
    utils, 
    methods
Suggests: 
    knitr
VignetteBuilder: knitr
biocViews: 
    FlowCytometry, 
    Proteomics, 
    SingleCell, 
    Clustering, 
    ExpressionData
NeedsCompilation: no

lmweber commented 6 years ago

We have sent an email to request temporary access to an AWS S3 bucket to upload the data files. Thank you.

lmweber commented 6 years ago

Tagging @csoneson for submission process

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

3959c8b version

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

50455dd fix RDataPath for directory structure

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

f0b6ada fix RDataPath entries

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

99647e3 fix checks

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

895c1e0 fix vignette

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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bioc-issue-bot commented 6 years ago

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

b50dcc1 version

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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bioc-issue-bot commented 6 years ago

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

d07d418 fix vignette

bioc-issue-bot commented 6 years ago

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lmweber commented 6 years ago

It passes the checks now. I will add a more detailed vignette (with a short example analysis workflow) over the next few days. Thank you.

bioc-issue-bot commented 6 years ago

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

aed1141 version

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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

On one or more platforms, the build results were: "WARNINGS, 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 6 years ago

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

c9a1283 try to fix links

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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

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bioc-issue-bot commented 6 years ago

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

fe3b2e4 fix DESCRIPTION

bioc-issue-bot commented 6 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.

bioc-issue-bot commented 6 years ago

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

106292a vignette

bioc-issue-bot commented 6 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.

lmweber commented 6 years ago

There is still a WARNING on Windows due to problems with links to external packages in the .Rd files. I'm not sure why this is happening on Windows only. It seems to be a problem for other packages too, e.g. the current build report for the SummarizedExperiment package is showing some similar warnings (also my other submitted package, issue #703). I could just remove all the cross-links from the documentation, but I'll leave them for now in case I find another way to fix it.

lshep commented 6 years ago

It was suggestion on another issue to look at cross references. And perhaps you are trying to \link[]{} to a documentation object that doesn't actually have an \alias{}. For example \alias{SummarizedExperiment}, but there are no documentation objects with that alias (specifically, there are no aliases with that identifier at link

lshep commented 6 years ago

I had a quick glance and besides fixing the above links and expanding on the vignette:

Please only use biocViews terms under the ExperimentData header - http://bioconductor.org/packages/release/BiocViews.html#___ExperimentData

Please place your .travis.yml file in a .buildignore

Otherwise it looks good and close to being accepted.

bioc-issue-bot commented 6 years ago

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

34763c1 version

bioc-issue-bot commented 6 years ago

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lmweber commented 6 years ago

Great, thank you for looking at the package! I have made the following changes:

updated biocViews
added .Rbuildignore with .travis.yml
expanded vignette with a short analysis workflow
removed all the cross-links to fix the WARNING on Windows. I couldn't find any other way to fix it (and the same WARNING is still shown in the build reports for several other packages that are already in devel), so I just removed the cross-links to get rid of the WARNING for now.

lshep commented 6 years ago

When I try to build your package locally I'm getting a segfault ERROR:

lori@lori-HP-ZBook-15-G2:~/pkgReview$ R CMD build HDCytoData/
Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite for help
* checking for file 'HDCytoData/DESCRIPTION' ... OK
* preparing 'HDCytoData':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR

 *** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
lori@lori-HP-ZBook-15-G2:~/pkgReview$

lmweber commented 6 years ago

That is strange. I tried it again here just now, and it worked fine. It is also passing everything on the build reports.

I will investigate some more to see if I can figure it out. Do you have any suggestions for how to approach this? I will start by trying to reproduce the error, but so far I am not getting the same error either locally or in the Bioconductor or Travis builds. I will ask someone else here if they can try installing the package locally on their machine.

lshep commented 6 years ago

Thank you. I will also ask someone else from my group to try too. Maybe its something with my local system.

lshep commented 6 years ago

I had two other colleagues here try and both also encountered segfaults.

Here is output I collected from valgrind

==15165== Invalid read of size 4
==15165==    at 0x8CC0443: std::locale::~locale() (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19)
==15165==    by 0x1707F572: ~basic_streambuf (streambuf:198)
==15165==    by 0x1707F572: ~Rstreambuf (Rstreambuf.h:31)
==15165==    by 0x1707F572: Rcpp::Rostream<false>::~Rostream() (Rstreambuf.h:44)
==15165==    by 0x6E2E1A8: __run_exit_handlers (exit.c:82)
==15165==    by 0x6E2E1F4: exit (exit.c:104)
==15165==    by 0x5EA90F: Rstd_CleanUp (sys-std.c:1213)
==15165==    by 0x511062: end_Rmainloop (main.c:1072)
==15165==    by 0x511062: run_Rmainloop (main.c:1083)
==15165==    by 0x41B5F7: main (Rmain.c:29)
==15165==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
==15165== 

 *** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
==15165== 
==15165== HEAP SUMMARY:
==15165==     in use at exit: 813,376,421 bytes in 122,347 blocks
==15165==   total heap usage: 28,196,126 allocs, 28,073,779 frees, 15,171,402,514 bytes allocated
==15165== 
==15165== LEAK SUMMARY:
==15165==    definitely lost: 160 bytes in 1 blocks
==15165==    indirectly lost: 0 bytes in 0 blocks
==15165==      possibly lost: 106 bytes in 1 blocks
==15165==    still reachable: 813,376,155 bytes in 122,345 blocks
==15165==         suppressed: 0 bytes in 0 blocks
==15165== Rerun with --leak-check=full to see details of leaked memory
==15165== 
==15165== For counts of detected and suppressed errors, rerun with: -v
==15165== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)

bioc-issue-bot commented 6 years ago

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

1a72a1e version

bioc-issue-bot commented 6 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.

lmweber commented 6 years ago

Ok, thank you. I will try it on some more machines here, to see if I can find the problem. In the meantime, I have put eval = FALSE for the newer parts of the vignette; maybe that will help.

lshep commented 6 years ago

It seems to be something inside that new code - with the eval=FALSE I don't get a segfault

lmweber commented 6 years ago

Ok great, thanks. That helps me narrow it down. I think it's probably the t-SNE plot.

bioc-issue-bot commented 6 years ago

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

6bca194 put back all vignette sections except t-SNE

lshep commented 6 years ago

negative - now I pull and it segfaults again.

bioc-issue-bot commented 6 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.

bioc-issue-bot commented 6 years ago

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

ecf9221 'eval = FALSE' for vignette sections again

lmweber commented 6 years ago

Ok, thanks for checking it again. In that case I'll try a few things on different machines. At least I know more or less where the problem is now.

lshep commented 6 years ago

Just let me know when you would like me to try it again. Cheers

bioc-issue-bot commented 6 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.

Bioconductor / Contributions

HDCytoData (ExperimentHub) #702