MSGFplus: fail to load on Mac OSX 10.13.6 due to javaVersion error
Entering edit mode
dgemoets • 0
Last seen 5.6 years ago


I'm getting the following error message when I try to load MSGFplus on Mac OSX

​> library("MSGFplus")
Error: package or namespace load failed for ‘MSGFplus’:
 .onLoad failed in loadNamespace() for 'MSGFplus', details:
  call: if (as.numeric(sub(".*\"\\d\\.(\\d).*", "\\1", javaVersion[1])) < 
  error: missing value where TRUE/FALSE needed
In addition: Warning message:
In fun(libname, pkgname) : NAs introduced by coercion

I found the offending line of code in a file (zzz.R).  Tried commenting out the line and compiling package from source but still does not work.

All of the RforProtemics package works swimmingly on Ubuntu 16.04 (including MSFGplus).

Thanks for your help.



Here is the sessionInfo() output:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] mzID_1.18.0           rpx_1.16.0            RforProteomics_1.18.1 MSnbase_2.6.1         ProtGenerics_1.12.0  
 [6] BiocParallel_1.14.2   mzR_2.14.0            Rcpp_0.12.17          Biobase_2.40.0        BiocGenerics_0.26.0  

loaded via a namespace (and not attached):
 [1] vsn_3.48.1                    splines_3.5.0                 bit64_0.9-7                   jsonlite_1.5                 
 [5] interactiveDisplay_1.18.0     foreach_1.4.4                 R.utils_2.6.0                 shiny_1.1.0                  
 [9] assertthat_0.2.0              interactiveDisplayBase_1.18.0 BiocManager_1.30.1            affy_1.58.0                  
[13] stats4_3.5.0                  RBGL_1.56.0                   blob_1.1.1                    Category_2.46.0              
[17] yaml_2.1.19                   impute_1.54.0                 pillar_1.2.3                  RSQLite_2.1.1                
[21] lattice_0.20-35               glue_1.2.0                    limma_3.36.2                  RUnit_0.4.32                 
[25] digest_0.6.15                 RColorBrewer_1.1-2            promises_1.0.1                colorspace_1.3-2             
[29] Matrix_1.2-14                 htmltools_0.3.6               httpuv_1.4.4.2                preprocessCore_1.42.0        
[33] R.oo_1.22.0                   plyr_1.8.4                    GSEABase_1.42.0               MALDIquant_1.18              
[37] XML_3.98-1.11                 pkgconfig_2.0.1               genefilter_1.62.0             zlibbioc_1.26.0              
[41] purrr_0.2.5                   xtable_1.8-2                  scales_0.5.0                  affyio_1.50.0                
[45] later_0.7.3                   annotate_1.58.0               tibble_1.4.2                  biocViews_1.48.2             
[49] IRanges_2.14.10               ggplot2_3.0.0                 DT_0.4                        lazyeval_0.2.1               
[53] survival_2.42-6               magrittr_1.5                  mime_0.5                      memoise_1.1.0                
[57] R.methodsS3_1.7.1             doParallel_1.0.11             MASS_7.3-50                   xml2_1.2.0                   
[61] graph_1.58.0                  BiocInstaller_1.30.0          tools_3.5.0                   stringr_1.3.1                
[65] S4Vectors_0.18.3              munsell_0.5.0                 AnnotationDbi_1.42.1          bindrcpp_0.2.2               
[69] pcaMethods_1.72.0             compiler_3.5.0                rlang_0.2.1                   grid_3.5.0                   
[73] RCurl_1.95-4.10               iterators_1.0.10              htmlwidgets_1.2               bitops_1.0-6                 
[77] gtable_0.2.0                  codetools_0.2-15              curl_3.2                      DBI_1.0.0                    
[81] reshape2_1.4.3                R6_2.2.2                      dplyr_0.7.6                   bit_1.1-14                   
[85] bindr_0.1.1                   gridSVG_1.6-0                 stringi_1.2.3                 tidyselect_0.2.4  


msgfplus mac java • 1.3k views
Entering edit mode
Mike Smith ★ 6.5k
Last seen 3 hours ago
EMBL Heidelberg

This was patched on Github in the last week

I don't know if it's made its way it the version on Bioconductor yet, but you can install the Github version with:


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