Number of genes provided in input: 14
Number of genes in input after p-value filtering: 13
Found interactions for all genes in the PIN
Final number of genes in input: 13
Performing Active Subnetwork Search and Enrichment
Processing the enrichment results over all iterations
Annotating involved genes and visualizing enriched terms
Downloading pathway diagrams of 1 KEGG pathways
| | 0%Cannot retrieve PNG url: hsa05418
Here's the original error message:
'color.pathway.by.objects()' failed to extract KEGG image path from response.
Cannot download PNG file: NA
Here's the original error message:
invalid 'url' argument
|============================================================================================================================| 100%
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/geode2/soft/hps/rhel7/r/4.0.4/lib64/R/library/magick/libs/magick.so':
libMagick++-7.Q16HDRI.so.5: cannot open shared object file: No such file or directory
This is the sessionInfo:
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
egeulgen
commented
2 years ago
I am using the pathfindR package. I get an error when I run this command:
output_df <- run_pathfindR(DEG,gene_sets = 'KEGG', iterations = 5, n_processes = 2)
This is the error:
Testing input
The input looks OK
Processing input. Converting gene symbols,
Number of genes provided in input: 14 Number of genes in input after p-value filtering: 13 Found interactions for all genes in the PIN Final number of genes in input: 13
Performing Active Subnetwork Search and Enrichment
Processing the enrichment results over all iterations
Annotating involved genes and visualizing enriched terms
Downloading pathway diagrams of 1 KEGG pathways
| | 0%Cannot retrieve PNG url: hsa05418 Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument |============================================================================================================================| 100% Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/geode2/soft/hps/rhel7/r/4.0.4/lib64/R/library/magick/libs/magick.so': libMagick++-7.Q16HDRI.so.5: cannot open shared object file: No such file or directory
This is the sessionInfo:
R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux
Matrix products: default BLAS/LAPACK: /geode2/soft/hps/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_rt.so
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] pathfindR_1.6.3 pathfindR.data_1.1.2 KEGGREST_1.30.1
[4] KEGGgraph_1.50.0 packagestats_0.0.5.0000