Conda Env & biocLite("affyio") : < undefined symbol: gzclose >
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@benjaminsaintpierre-17683
Last seen 3.0 years ago

Hi everyone,

I am currently trying to configure conda environments for Affymetrix data normalization using Brain Array Custom CDF. For this I need to install R, wich is simple and done, and R packages : BiocGenerics, Biobase, affyio, BiocInstaller and preprocessCore.

These packages have to be installed to configure the "affy" package from Brain Array, then I will be able to install the custom cdf libraries for any versions of Brain Array (current: v22).

But when I try to install the "affyio" package in the new environment, i get the following error:

path/to/envs/lib/R/library/affyio/libs/affyio.so: undefined symbol: gzclose

I don't get why, because if I deactivate the environment, i can install R and this package with no problem...

In the conda environment:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /home/genomic/anaconda3/envs/Normalisation.v22/lib/R/lib/libRblas.so
LAPACK: /home/genomic/anaconda3/envs/Normalisation.v22/lib/R/lib/libRlapack.so
locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] BiocInstaller_1.30.0 RevoUtils_11.0.1     RevoUtilsMath_11.0.0
loaded via a namespace (and not attached):
[1] compiler_3.5.1

and in the "base" environment:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 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=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1 

If anyone got an idea, it would be great!

Thanks

Conda affyio error • 576 views
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gzclose is from libz, does your conda environment have that system library?

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