Error in dyn.load(file, DLLpath = DLLpath, ...) :
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@hakusen03-10599
Last seen 5 weeks ago
United States

Hi,

I'm using the script analyze_diff_expr.pl (trinity script), and I'm getting the following error: 

> library(qvalue)

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '~/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so':
  libicui18n.so.55: cannot open shared object file: No such file or directory
Error: package or namespace load failed for 'qvalue'
Execution halted

Error, cmd: R --vanilla -q < my_TPM_diffexpression.matrix.R died with ret 256 at ~/liaguiro/Trinityrnaseq2.2/trinityrnaseq-2.2.0/Analysis/DifferentialExpression/PtR line 1599.

Error, Error, cmd: ~/Trinityrnaseq2.2/trinityrnaseq-2.2.0/Analysis/DifferentialExpression/PtR -m ~/my_trinity_run/my_TPM_diffexpression.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  -s ~/my_trinity_run/my_deseq2/my_trt_info.txt died with ret 6400 at ~/Trinityrnaseq2.2/trinityrnaseq-2.2.0/Analysis/DifferentialExpression/analyze_diff_expr.pl line 267.

I'm getting this error after I qsub this job because running this job from my command prompt exceeded the limit memory on the headnodes. When I run this job from my command prompt I didn't get the error above.

When I tried to specify the path to stringe.so , it didn't worked either. export PATH=/homes/liaguiro/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringe.so:$PATH

What should I do? Do you know how to fix this problem?

Thanks,

R qvalue • 4.1k views
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@storey-john-d-6576
Last seen 20 months ago
United States

Your error indicates there is a problem with the stringi package, which is not used by the qvalue package.

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@martin-morgan-1513
Last seen 10 weeks ago
United States

Likely the stringi package was installed on the 'head' node, linking to a library libicui18n available on the head node. You're trying to run on a cluster node where the library is not available. Probably you need to speak with your cluster administrator to arrange for the library to be available (via ldconfig) on the cluster node. It might also be possible to arrange for the library to be found using LD_LIBRARY_PATH set to include a directory, accessible from the cluster node, where the library is available.

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