Question: install ChAMP under Ubuntu 18.04 in R 3.4.4 with error "maximal number of DLLs reached..."
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gravatar for chxp
13 months ago by
chxp0
chxp0 wrote:

I cannot install ChAMP under Ubuntu 18.04 in R 3.4.4, it shows the error:

it shows:

> biocLite('ChAMP')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘ChAMP’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/ChAMP_2.9.10.tar.gz'
Content type 'application/x-gzip' length 15513863 bytes (14.8 MB)
==================================================
downloaded 14.8 MB

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/chxp/R/x86_64-pc-linux-gnu-library/3.4/jsonlite/libs/jsonlite.so':
  `maximal number of DLLs reached...
ERROR: lazy loading failed for package 'ChAMP'
* removing '/home/chxp/R/x86_64-pc-linux-gnu-library/3.4/ChAMP'

The downloaded source packages are in
    ‘/tmp/Rtmp9IHIgK/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ChAMP’ had non-zero exit status

it shows the same error when I tried ChAMP 2.10.1/2.10.0 by using 'R CMD INSTALL PACKAGE'

Further I set 'R_MAX_NUM_DLLs=2000' in .Renviron the same error repears.

I check the DLLs by using:

> Sys.getenv('R_MAX_NUM_DLLs', unset=NA)
[1] "2000"
> length(getLoadedDLLs())
[1] 15

So my setting in .Renviron works, however the setting cannot resolve the error.

How will I do? Thanks.

This is the sessionInfo() of R:

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=zh_CN.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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] ChAMPdata_2.10.0     GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 
[4] IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0 
[7] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0        compiler_3.4.4         XVector_0.18.0        
[4] tools_3.4.4            GenomeInfoDbData_1.0.0 RCurl_1.95-4.10       
[7] bitops_1.0-6
ADD COMMENTlink modified 13 months ago • written 13 months ago by chxp0

Hello:

This error used to appear on R version 3.4.X... The newest R version, say 3.5, should no longer have this problem. But I think what you are doing here is very much correct, setting R_MAX_NUM_DLLs is my way for these errors.

But I always fix this by setting /etc file with sudo right. So I suggest you may also try this way, or try a newer version R.

Best

Yuan Tian

ADD REPLYlink written 13 months ago by Yuan Tian110
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