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gwasurvivr #749

Closed aarizvi closed 6 years ago

aarizvi commented 6 years ago

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bioc-issue-bot commented 6 years ago

Hi @aarizvi

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: gwasurvivr
Type: Package
Title: GWAS survival analysis
Version: 0.99.0
Author: Abbas Rizvi, Ezgi Karaesmen, Martin Morgan, Lara Sucheston-Campbell
Maintainer: Abbas Rizvi <aarizv@gmail.com>
Description: gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.
VignetteBuilder:
    rmarkdown
Imports:
    GWASTools,
    survival,
    VariantAnnotation,
    parallel,
    matrixStats,
    SummarizedExperiment,
    stats,
    utils
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    tidyverse,
    magrittr
License: Artistic-2.0
URL: https://github.com/suchestoncampbelllab/gwasurvivr
biocViews: 
    GenomeWideAssociation,
    Survival,
    Regression,
    Genetics,
    SNP,
    GeneticVariability,
    Pharmacogenomics,
    BiomedicalInformatics
RoxygenNote: 6.0.1

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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:

ca2a731 patch version bump removed html from vignettes

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:

da7cb96 version bump

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: "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:

71efc21 building vignette

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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Error response

Error response

Error code 414.

Message: Request-URI Too Long.

Error code explanation: 414 = URI is too long.. ". 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][1] for more details. [1]: http://bioconductor.org/spb_reports/gwasurvivr_buildreport_20180502172720.html

bioc-issue-bot commented 6 years ago

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

2ef81ef removed core options in vignette and version bump

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.

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bioc-issue-bot commented 6 years ago

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

bb8a0c1 version bump

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:

526ef98 version bump and smaller data examples

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:

3a7fbba version bump description fix

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:

0586a20 version bump, changed namespace rm tidyverse for d...

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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

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

9428ada removed tidyverse completely, version bump

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: "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 6 years ago

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

1834a52 typo in example of michigan

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: "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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aarizvi commented 6 years ago

I'm not sure what's going on with Windows installation. It seemed to have been working in my earlier commits. It seems like it has to do something with the stringi package that is being called from one of the packages in my NAMESPACE. I'm not sure how to narrow that down. And should I be more explicit with my importFrom calls from some of the packages I depend on? Thanks.

bioc-issue-bot commented 6 years ago

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

c8264d7 version bump

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.

aarizvi commented 6 years ago

Any suggestions on whats going on with the Windows build and why the time elapses are so long for the build and the examples. It seems like the user functions are finishing in a second or so. Is something getting caught up on the Windows machine? The Linux/Mac ones seem to building and executing the examples much faster.

I could make the example files smaller - just want to hear if you have any suggestions before I do that.

Thank you for your time!

Abbas

bioc-issue-bot commented 6 years ago

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

82c9f11 version bump

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:

4f688ec version bump

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:

6d63448 smaller pheno data 968bed7 smaller pheno, version bump

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:

13296e9 smaller data, version bump 832f78d smaller pheno

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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On one or more platforms, the build results were: "TIMEOUT". 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:

2d1f6ed impute data reduced

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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vobencha commented 6 years ago

Referring to question asked in https://github.com/Bioconductor/Contributions/issues/749#issuecomment-386436253.

The Windows builders only have 32GB of RAM and the 32-bit arch can only allocate 2-3GB for an R process. So, yes, please do reduce the size of data used/processed in the man page examples and vignette to play nice with the Windows restrictions. We are planning to get more RAM for the Windows builders in the next couple of months.

bioc-issue-bot commented 6 years ago

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

93fd8b7 only 3 snps in data, fixed typo in sangerCoxSurv, ...

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, 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.

aarizvi commented 6 years ago

Referring to https://github.com/Bioconductor/Contributions/issues/749#issuecomment-387586127

I'm having some trouble understanding whats going on here. Originally when I started the submission process, the data I was using was "small" but considerably larger than my current data. In those earlier commits, it seemed like everything was building and installing properly (< 5 min, with the exception of Windows which was about 6 minutes). So I understood the warnings with Windows because the R CMD CHECK time was > 5 minutes. And then yesterday I kept getting TIMEOUT, which didn't make much sense to me, because all I did was reduce the size of my data.

Now I've greatly reduced the data (all < 5 KB). The package after R CMD BUILD is ~ 70KB. On my personal laptop it seems to be getting through R CMD CHECK under 5 min with no errors. As well as no errors with R CMD BioCheck.

With this last commit, I'm not seeing the ERROR in the OS X build, besides "/Library/Frameworks/R.framework/Resources/bin/Rcmd: line 62: exec: BiocCheck: not found"

I suspect that this one is not on my end.

I'm wondering how I can get the Windows to be <5 minutes, I certainly can evaluate less in the vignette (right now at 41% not being evaluated, and it seems like there is a 50% allowance), because reducing the size of the data doesn't seem to doing anything.

I also have a suspicion that because this package does parallel computing by default that maybe creating workers is slowing things down? I would prefer to keep this option, but I suppose that we can make an option that does not parallelize if you think this will be speed it up enough to make it past these checks. On my side I have always seen more efficient (faster) computation when running in parallel, but with these small datasets I'm not sure if it is somehow making things slower.

These computations should not be very RAM intensive, particularly with the size of the data, so I don't think that we are exceeding our memory allowances in these vignette and man examples.

Thank you very any advice/suggestions and of course for reviewing the package!

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: "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.

vobencha commented 6 years ago

Hi, If you have reasonable examples that don't use much RAM then we should be ok. I can give you more input when I've had a chance to do a full review and look at the examples in detail.

As for parallel computations, man page examples and the vignette should use minimal cores (not max). Remember your package will be built and checked with 1500+ other packages nightly and it should not monopolize resources. Some parallel evaluation is not available on Windows - depending on how you're using 'parallel' this may or may not be the case. Again, I can comment more when I've had a chance to do a full review.

This package was submitted 8 days ago. We try to get comments back within 2 weeks of submission. If I can't get to this tomorrow I'll do it next week.

Valerie

bioc-issue-bot commented 6 years ago

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

b9bd4b4 removed error in code that was setting clusterobj ... 1f00922 version bump

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.

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bioc-issue-bot commented 6 years ago

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

074f5ab minimize core number, version bump

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: "

Error response

Error response

Error code 414.

Message: Request-URI Too Long.

Error code explanation: 414 = URI is too long.. ". 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][1] for more details. [1]: http://bioconductor.org/spb_reports/gwasurvivr_buildreport_20180514162705.html

bioc-issue-bot commented 6 years ago

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

e5d4bc3 try again

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:

4526715 removed artifact index in impute2CoxSurv 8b199ed -merged branches Merge branch 'master' of https://... 2747074 version bump, removed artifact index