openPrimeR does not recognize external MELTING installation
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@9195e11b
Last seen 8 days ago
Germany

I am trying to analyze some Primers with R but it seems openPrimeR can't find MELTING even though it is installed. Am I missing something obvious?

library(openPrimeR)

There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are

                installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
The number of cores for was set to '2' by 'parallel_setup()'.

sessionInfo( )

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
[1] openPrimeR_1.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7              plyr_1.8.6              RColorBrewer_1.1-2     
 [4] pillar_1.6.1            compiler_4.1.0          GenomeInfoDb_1.28.1    
 [7] XVector_0.32.0          iterators_1.0.13        zlibbioc_1.38.0        
[10] tools_4.1.0             bitops_1.0-7            lifecycle_1.0.0        
[13] tibble_3.1.2            gtable_0.3.0            pkgconfig_2.0.3        
[16] rlang_0.4.11            foreach_1.5.1           rstudioapi_0.13        
[19] DBI_1.1.1               parallel_4.1.0          GenomeInfoDbData_1.2.6 
[22] stringr_1.4.0           dplyr_1.0.7             generics_0.1.0         
[25] Biostrings_2.60.1       vctrs_0.3.8             S4Vectors_0.30.0       
[28] IRanges_2.26.0          stats4_4.1.0            grid_4.1.0             
[31] tidyselect_1.1.1        glue_1.4.2              R6_2.5.0               
[34] fansi_0.5.0             reshape2_1.4.4          ggplot2_3.3.5          
[37] purrr_0.3.4             magrittr_2.0.1          codetools_0.2-18       
[40] GenomicRanges_1.44.0    scales_1.1.1            ellipsis_0.3.2         
[43] BiocGenerics_0.38.0     assertthat_0.2.1        colorspace_2.0-2       
[46] utf8_1.2.1              stringi_1.7.3           lpSolveAPI_5.5.2.0-17.7
[49] doParallel_1.0.16       RCurl_1.98-1.3          munsell_0.5.0          
[52] crayon_1.4.1

Newest version of MELTING is installed and executables are in PATH

(base) ngs-benedikt@ngsbenedikt-desktop:~$ melting -V

 This MELTING program is the version 5.2.0.

Thanks!

openPrimeR • 55 views
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openPrimeR requires and checks for melting-batch rather than melting. Could you verify whether that's in your PATH as well?

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