Question

BiocParallel/scater warning after move to R 3.4.0

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nhejazi • 0

@nhejazi-10825

Last seen 5.2 years ago

UC Berkeley

After the recent update to R 3.4.0, updates and installation of several Bioconductor packages return a warning during installation -- specifically, there seems to be an issue in how BiocParallel sets up its core classes:

Warning in is.na(x[[i]]) :
  is.na() applied to non-(list or vector) of type 'environment'
'BiocParallel' did not register default BiocParallelParams:
  invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1

This is returned after running `biocLite(c("scater", "scran", "SC3"))`. The installations seems to complete correctly, but perhaps there is some error that I am missing?

Session Info:

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin16.5.0 (64-bit)
Running under: macOS Sierra 10.12.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0

biocparallel scater • 6.5k views

ADD COMMENT • link updated 7.4 years ago by andrew.blake ▴ 40 • written 7.6 years ago by nhejazi • 0

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I had the exact same issue today, I cannot run fgsea package anymore.

> library("fgsea", lib.loc="/usr/local/lib/R/site-library")
Loading required package: Rcpp
'BiocParallel' did not register default BiocParallelParams:
  invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1
Warning messages:
1: R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 
2: In is.na(x[[i]]) :
  is.na() applied to non-(list or vector) of type 'environment'

Here is my session info :

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils    
[5] datasets  methods   base     

other attached packages:
[1] fgsea_1.0.2  Rcpp_0.12.10

loaded via a namespace (and not attached):
 [1] grid_3.4.0         plyr_1.8.4        
 [3] gtable_0.2.0       scales_0.4.1      
 [5] ggplot2_2.2.1      lazyeval_0.2.0    
 [7] data.table_1.10.4  fastmatch_1.1-0   
 [9] BiocParallel_1.9.2 tools_3.4.0       
[11] munsell_0.4.3      parallel_3.4.0    
[13] compiler_3.4.0     colorspace_1.3-2  
[15] gridExtra_2.2.1    tibble_1.3.0

ADD REPLY • link 7.6 years ago adesrichard ▴ 30

0

Entering edit mode

fgsea is loaded, so what says you can't run it? Is it possible to work around the BiocParallel issue by saying

library(BiocParallel)
register(MulticoreParam())

? (there is an outstanding report that that too fails...)

ADD REPLY • link 7.6 years ago Martin Morgan 25k

0

Entering edit mode

Hi Martin!

You are correct. fgsea loads but I can't use it unless I use serial parameters, not multicore.

Here is what I am getting when trying to register :

> library(BiocParallel)
> register(MulticoreParam())
Error in validObject(.Object) : 
  invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1
In addition: Warning message:
In is.na(x[[i]]) :
  is.na() applied to non-(list or vector) of type 'environment'

My only way around this is so far

register(SerialParam())

Which makes fgsea work for me.

Thanks!

ADD REPLY • link 7.6 years ago adesrichard ▴ 30

0

Entering edit mode

Just thought I'd note here that, at least in my case, updating from Bioconductor 3.4 to 3.5 (with BiocInstaller 1.26.0), and then updating all packages via `biocLite()`, fixed this issue. I had to uninstall and then re-install "BiocInstaller", as noted on the Bioconductor webpage for using the "Devel" version of Bioconductor here:

```

remove.packages("BiocInstaller")  # repeat until R says there is no
                                  # package 'BiocInstaller' to remove
source("https://bioconductor.org/biocLite.R")  # install correct version
BiocInstaller::biocValid()

```

ADD REPLY • link 7.6 years ago nhejazi • 0

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Entering edit mode

I'll update BiocParallel to use a different initialization strategy in the next few days.

ADD REPLY • link 7.6 years ago Martin Morgan 25k

score 4 · Answer 1 · 2017-06-29

4

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andrew.blake ▴ 40

@andrewblake-11043

Last seen 7.4 years ago

biocLite("devtools")
BiocInstaller::biocLite("Bioconductor/BiocParallel", ref="release-3.5")

fixed it for me - I think that this fix will make it out eventually

ADD COMMENT • link 7.4 years ago andrew.blake ▴ 40

score 0 · Answer 2 · 2017-05-05

0

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

BiocParallel in release (version 1.10.1) and devel (version 1.11.1) now take a different approach to initializing the registered back-ends.

ADD COMMENT • link 7.6 years ago Martin Morgan 25k