library(cytolib) crashes Rfast::rowMaxs() #38
Comments
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I can't seem to reproduce it > library(cytolib)
> library(Rfast)
Loading required package: Rcpp
Loading required package: RcppZiggurat
> x <- matrix(runif(40), nrow=8)
> Rfast::rowMaxs(x)
[1] 3 3 2 5 3 5 3 4
> sessionInfo()
R Under development (unstable) (2020-04-13 r78216)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /media/wjiang2/real_home/wjiang2/mylib/R-devel-build/lib/libRblas.so
LAPACK: /media/wjiang2/real_home/wjiang2/mylib/R-devel-build/lib/libRlapack.so
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
other attached packages:
[1] Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.4.6 cytolib_1.99.28
loaded via a namespace (and not attached):
[1] compiler_4.1.0 RProtoBufLib_1.99.8 parallel_4.1.0
[4] RcppParallel_5.0.0 |
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Yes, as I mentioned, I don't always get the crash either. For example I always get it on my laptop but not on malbec2 where I only get it about 6-8 times out of 10 there. I see that you're using R 4.1 though. I get the crash with R 4.0. Didn't try with R 4.1. (Note that the next devel version of Bioconductor, BioC 3.12, will still be based on R 4.0 so I will stay away from R 4.1 for the next 6 months.) |
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I've installed R 4.0, but still can't reproduce it > library(cytolib)
> library(Rfast)
Loading required package: Rcpp
Loading required package: RcppZiggurat
> x <- matrix(runif(40), nrow=8)
> Rfast::rowMaxs(x)
[1] 3 3 3 1 2 2 4 3
> sessionInfo()
R version 4.0.0 RC (2020-04-21 r78276)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /media/wjiang2/real_home/wjiang2/mylib/R-devel-build/lib/libRblas.so
LAPACK: /media/wjiang2/real_home/wjiang2/mylib/R-devel-build/lib/libRlapack.so
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
other attached packages:
[1] Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.4.6 cytolib_1.99.28
loaded via a namespace (and not attached):
[1] compiler_4.0.0 RProtoBufLib_1.99.8 parallel_4.0.0
[4] RcppParallel_5.0.0 Note that my R revision is two-day later than bioc, not sure if that makes difference. |
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addressed by #45 |
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Hi,
The following code crashes my session if I load cytolib before running it:
For example in a fresh R session on my laptop:
sessionInfo():
FWIW I also get a crash on other Linux machines e.g. on Bioconductor build machine malbec2 where I get:
Note that on this machine I get the crash most of the time but not every time (e.g. 6-8 times out of 10).
sessionInfo():
Finally it's worth noting that I don't get a crash with R 3.6.0 and the RELEASE_3_10 branch of cytolib:
sessionInfo():
Thanks,
H.
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