Closed aarizvi closed 6 years ago
Hi @aarizvi
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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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1834a52 typo in example of michigan
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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.
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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
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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.
Received a valid push; starting a build. Commits are:
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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!
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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
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Received a valid push; starting a build. Commits are:
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Dear Package contributor,
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Error code 414.
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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
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