MSGFplus: fail to load on Mac OSX 10.13.6 due to javaVersion error
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dgemoets • 0
@dgemoets-16467
Last seen 3.0 years ago

Hi,

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.

Darren

-----------------------------------

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

locale:
[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 • 765 views
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Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 1 hour ago
EMBL Heidelberg / de.NBI

This was patched on Github in the last week https://github.com/thomasp85/MSGFplus/pull/13

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

BiocInstaller::biocLite('thomasp85/MSGFplus')
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