BiocParallel did not register default BiocParallelParams about biocparallel

[mtmorgan]

It is a warning not an error.
What is the output of sessionInfo()?
How are you running R, e.g., under RStudio?

[RNA-Ninja]

@mtmorgan You are right, it is a warning not an error.
I got the same message in both under RStudio and R-terminal.
Here is the sessionInfo()

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] BiocParallel_1.8.2

loaded via a namespace (and not attached):
[1] compiler_3.4.0 parallel_3.4.0

[mtmorgan]

In a new R session does BiocParallel::MulticoreParam() generate the same error?

[RNA-Ninja]

Yes it gives same error

> BiocParallel::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'

[mtmorgan]

I 'know' what the problem is but don't know how to fix it. BiocParallel is trying to register(MulticoreParam()) when the package starts, but for some reason this is failing. It only happens under some configurations; I don't know what the configuration is, other than that this 'works for me'.

A workaround while I try to understand this is

library(BiocParallel)  ## ignore warning
register(MulticoreParam())

[warrenmcg]

Hello,

I have the same issue, and your suggested workaround register(MulticoreParam()) also fails for me with the same error as when running BiocParallel::MulticoreParam() [mentioned by RNA-Ninja].

I modified the code in the setValidity function to print out the object fields to see what the issue is, and here was the output:

> print(sapply(fields, function(i) object[[i]])
$cluster
list()
attr(,"class")
[1] "NULLcluster" "cluster"    

$.clusterargs
$.clusterargs$spec
[1] 62

$.clusterargs$type
[1] "FORK"


$.controlled
[1] TRUE

$.uid
character(0)

$RNGseed
NULL

$logdir
[1] NA

$resultdir
[1] NA

$finalizer_env
<environment: 0x4c943b8>

Let me know if you need more specific information about my configuration.

[FMKerckhof]

I am experiencing the same issue with the following configuration:

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/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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

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

other attached packages:
[1] BiocParallel_1.8.2   BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 parallel_3.4.0 tools_3.4.0

The fixes proposed above are not helping for me either.

[FMKerckhof]

I could replicate the issue on another machine running ubuntu server 16.04.2 LTS:

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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] BiocInstaller_1.24.0

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

[mtmorgan]

Please try BiocInstaller::biocLite("Bioconductor/BiocParallel", ref="release-3.5") or wait (approximately 36 hours) until version 1.10.1 is available via biocLite("BiocParallel").

[FMKerckhof]

Thank you, that indeed did solve the issue (using BiocInstaller::biocLite("Bioconductor/BiocParallel", ref="release-3.5")). Afterwards, I had issues with other Bioconductor packages which led me to update my BiocInstaller (required some troubleshooting from http://bioconductor.org/install/) allowing me to run biocLite("BiocParallel").