openPrimeR does not recognize external MELTING installation
0
0
Entering edit mode
@9195e11b
Last seen 3.3 years 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 • 765 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 504 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6