optimalFlow

[HristoInouzhe]

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[bioc-issue-bot]

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]

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

c7f85e6 bump

[bioc-issue-bot]

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]

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

6efd934 bump, bump, bump again

[bioc-issue-bot]

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]

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

2348295 bmp, bmp, bmp again

[bioc-issue-bot]

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.

[HristoInouzhe]

Hi @lshep ,

I've managed to solve the warning that I was getting in Linux. Its a bit dirty, but I've used \dontrun in two of the examples associated to labelTransfer and voteLableTransfer. It seems to be related to rnorm, although I export stats and explictely rnorm or maybe with the names of the variables, data.example or test.labels, are creating some conflict.

On the other hand the error I'm getting in windows is due to the fact that optimalFlowData is only built in Linux, therefore it is not able to locate that package.

I hope that now the rest of the revision process can continue.

Best regards and thanks for the attention.

[lshep]

@hpages is your reviewer and will review the packages.

Please use donttest instead of dontrun as donttest requires valid R code. @hpages will review the appropriate use of this.

It has been awhile since we looked at this issue. optimalFlowData should be available on all platforms unless you specified it not to build on windows. If it did not build on windows may I suggest doing a version bump on the data package so it is available for your software package to run.

[hpages]

@HristoInouzhe Are you going to follow @lshep's suggestion to bump optimalFlowData's version? Thanks!

[bioc-issue-bot]

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

8eb9da1 bump

[bioc-issue-bot]

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]

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

7ef5986 bump in v

[bioc-issue-bot]

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.

[HristoInouzhe]

@hpages, I have done the bump in the version of optimalFlowData and changed dontrun for donttest. Thanks for the attention!

[hpages]

Thanks. Unfortunately I get a crash when running R CMD build on the package. I've just spent the last 5 hours trying to isolate the problem and was finally able to produce a minimal reproducible example that seems to be suggesting that the culprit is the cytolib package (which you indirectly depend on via the flowMeans package). I just opened an issue here.

The issue is unrelated with optimalFlow but unfortunately the code in optimalFlow's vignette triggers the crash, which is a blocking issue at the moment. FWIW here is what I get:

hpages@spectre:~$ R CMD build optimalFlow
* checking for file ‘optimalFlow/DESCRIPTION’ ... OK
* preparing ‘optimalFlow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...*** Error in `/home/hpages/R/R-4.0.r78037/bin/exec/R': double free or corruption (out): 0x00007f1c160d0270 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f1c154c87e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f1c154d137a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f1c154d553c]
/home/hpages/R/R-4.0.r78037/library/Rfast/libs/Rfast.so(_Z15row_max_indicesN4Rcpp6MatrixILi14ENS_15PreserveStorageEEE+0x154)[0x7f1bf0327b44]
/home/hpages/R/R-4.0.r78037/library/Rfast/libs/Rfast.so(Rfast_row_max_indices+0x6f)[0x7f1bf032d27f]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0xfcaa0)[0x7f1c15b34aa0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13a55e)[0x7f1c15b7255e]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f1c15b7eb34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f1c15b764f7]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f1c15b7eb34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x2ce)[0x7f1c15b7c0fe]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1490e9)[0x7f1c15b810e9]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x53d)[0x7f1c15b7c36d]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x14a51f)[0x7f1c15b8251f]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x134601)[0x7f1c15b6c601]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f1c15b7eb34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f1c15b764f7]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1449c9)[0x7f1c15b7c9c9]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x818)[0x7f1c15b7c648]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x14abec)[0x7f1c15b82bec]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x18682f)[0x7f1c15bbe82f]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x136175)[0x7f1c15b6e175]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
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/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
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/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x144e17)[0x7f1c15b7ce17]
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/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
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/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1449c9)[0x7f1c15b7c9c9]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x144e17)[0x7f1c15b7ce17]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13a242)[0x7f1c15b72242]
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/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f1c15b764f7]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1449c9)[0x7f1c15b7c9c9]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x144e17)[0x7f1c15b7ce17]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13a242)[0x7f1c15b72242]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f1c15b7eb34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f1c15b764f7]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f1c15b7eb34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f1c15b764f7]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f1c15b7bfd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f1c15b7dd91]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:32 23419198                           /home/hpages/R/R-4.0.r78037/bin/exec/R
00600000-00601000 r--p 00000000 00:32 23419198                           /home/hpages/R/R-4.0.r78037/bin/exec/R
00601000-00602000 rw-p 00001000 00:32 23419198                           /home/hpages/R/R-4.0.r78037/bin/exec/R
00f1f000-1f6cd000 rw-p 00000000 00:00 0                                  [heap]
7f1be0000000-7f1be0021000 rw-p 00000000 00:00 0 
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7f1bf8ecf000-7f1bf8f01000 r-xp 00000000 103:02 9969994                   /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7f1bf8f01000-7f1bf9100000 ---p 00032000 103:02 9969994                   /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
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7f1bf9102000-7f1bf9225000 r-xp 00000000 103:02 9962162                   /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7f1bf9225000-7f1bf9424000 ---p 00123000 103:02 9962162                   /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7f1bf9424000-7f1bf942f000 r--p 00122000 103:02 9962162                   /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7f1bf942f000-7f1bf9431000 rw-p 0012d000 103:02 9962162                   /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7f1bf9431000-7f1bf9432000 rw-p 00000000 00:00 0  ERROR
--- re-building ‘optimalFlow_vignette.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: rlang

Attaching package: 'ellipse'

The following object is masked from 'package:graphics':

    pairs

Rfast_row_max_indices: ok1
row_max_indices: ok1
row_max_indices: ok2
row_max_indices: ok3
Aborted (core dumped)

A workaround is to make sure that Rfast's namespace gets loaded before cytolib's namespace. I think you can achieve this by making sure to have import(Rfast) before import(flowMeans) in your NAMESPACE file. Although I'm not sure this is doable with an roxygen2- generated NAMESPACE.

Best, H.

[bioc-issue-bot]

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

887a28f bump

[HristoInouzhe]

@hpages I have implemented your suggestion. Now imort(Rfast) comes before import(FlowMeans). I hope that this will solve the crash. Best regards and sorry for the troubles caused, I know how tediuos it can be to solve that kind of problems.

[bioc-issue-bot]

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.

[hpages]

Yes this avoids the crash. Thanks for implementing the workaround. Note that the R CMD check warnings reported by the latest automated build require your attention.

When loading the package, I now get the following warning:

Warning messages:
1: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘optimalFlow’ 
2: replacing previous import ‘Rfast::is_integer’ by ‘rlang::is_integer’ when loading ‘optimalFlow’ 
3: replacing previous import ‘Rfast::as_integer’ by ‘rlang::as_integer’ when loading ‘optimalFlow’ 

Since the only things you use from Rfast are dista and rowMaxs, you don't need to import the full Rfast's namespace. Instead you could import selectively the things you need. You will also need to do the same for flowMeans (you seem to only use the flowMeans function from this package). So in the end you will end up with something like this in your NAMESPACE file:

...
importFrom(Rfast,dista)
importFrom(Rfast,rowMaxs)
...
importFrom(flowMeans,flowMeans)
...

This should avoid the name collisions between Rfast and dplyr/rlang. It's important that the import from flowMeans come after the imports from Rfast to avoid the cytolib/Rfast crash.

Thanks, H.

[bioc-issue-bot]

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

537012d bump

[bioc-issue-bot]

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.

[HristoInouzhe]

@hpages I have eliminated all warnings except the one concerning multiple plot versions. I hope taht this is what you were asking for.

[hpages]

THANK YOU! We're done... finally... and just in time for the 3.11 release. Thanks for your quick response to the latest issues I reported.

Cheers, H.

[bioc-issue-bot]

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!

[HristoInouzhe]

@hpages and @lshep thanks a lot for your attention and hard work! It is very statisfying to have my package on Bioconductor and I hope it will be an useful contribution for the interested user. Best regards, Hristo.

[HristoInouzhe]

@hpages I have an urgent question, I need to make a change on the optimalFlowData package since I've been informed of a problem with the data. Can I still do it now or do I need to wait untill the package is released. The change only concernes the data, I will just change the .RData files and everything else will stay the same.

[HristoInouzhe]

@hpages I can bump the version and do the new build as soon as you give me the green light.

[mtmorgan]

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/HristoInouzhe.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("optimalFlowData"). The package 'landing page' will be created at

https://bioconductor.org/packages/optimalFlowData

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

[mtmorgan]

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/HristoInouzhe.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("optimalFlow"). The package 'landing page' will be created at

https://bioconductor.org/packages/optimalFlow

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

[hpages]

I need to make a change on the optimalFlowData package since I've been informed of a problem with the data. Can I still do it now or do I need to wait untill the package is released.

We run the data experiment builds only twice a week (on Mondays and Thursdays):

https://bioconductor.org/checkResults/3.11/data-experiment-LATEST/

Until then, optimalFlow will look broken on the build report for software packages because optimalFlowData won't be on the build machines yet:

https://bioconductor.org/checkResults/3.11/bioc-LATEST/

If you didn't push your change to optimalFlowData in time before @mtmorgan added the package to our git server at git.bioconductor.org, then push them now. It makes no difference. Except that from now on you'll need to remember to also push any change you make to your packages to git.bioconductor.org in addition to GitHub. Make sure to look at the documentation for how to keep your GitHub and Bioconductor repositories in sync (see the links that Martin sent you above). Note that your changes to optimalFlowData won't be picked up by our build system before the next data experiment builds (will be next Monday).

This issue is closed so I will no longer be monitoring it. Please use the bioc-devel mailing list for any further questions about the development of your packages (git, build system, etc...)

Thanks, H.