package ‘MSGFplus’ is not available (for R
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0
Entering edit mode
yueli7 ▴ 20
@yueli7-8401
Last seen 3.0 years ago
China

Hello

I tried to install MSGFplus in R version 3.6.1.

It said: package ‘MSGFplus’ is not available (for R version 3.6.1).

What can I do in this step?

Thank you in advance for great help!

Best,

Yue

>install.packages("MSGFplus")
Installing package into ‘/home/li/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘MSGFplus’ is not available (for R version 3.6.1)

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )


R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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] rTANDEM_1.26.0    data.table_1.13.2 Rcpp_1.0.5        XML_3.99-0.3      rpx_1.22.0       

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1            ellipsis_0.3.1              htmlTable_2.1.0             XVector_0.26.0              GenomicRanges_1.38.0       
  [6] base64enc_0.1-3             rstudioapi_0.11             mzR_2.20.0                  affyio_1.56.0               bit64_4.0.5                
 [11] AnnotationDbi_1.48.0        fansi_0.4.1                 xml2_1.3.2                  codetools_0.2-18            splines_3.6.1              
 [16] ncdf4_1.17                  doParallel_1.0.16           impute_1.60.0               geneplotter_1.64.0          knitr_1.30                 
 [21] Formula_1.2-4               isobar_1.32.0               annotate_1.64.0             cluster_2.1.0               vsn_3.54.0                 
 [26] dbplyr_2.0.0                png_0.1-7                   startupmsg_0.9.6            sfsmisc_1.1-7               BiocManager_1.30.10        
 [31] compiler_3.6.1              httr_1.4.2                  backports_1.2.0             assertthat_0.2.1            Matrix_1.2-17              
 [36] limma_3.42.2                cli_2.1.0                   htmltools_0.5.0             prettyunits_1.1.1           tools_3.6.1                
 [41] gtable_0.3.0                glue_1.4.2                  GenomeInfoDbData_1.2.2      affy_1.64.0                 dplyr_1.0.2                
 [46] rappdirs_0.3.1              MALDIquant_1.19.3           Biobase_2.46.0              vctrs_0.3.4                 preprocessCore_1.48.0      
 [51] iterators_1.0.13            xfun_0.19                   stringr_1.4.0               lifecycle_0.2.0             zlibbioc_1.32.0            
 [56] MASS_7.3-53                 scales_1.1.1                MSnbase_2.12.0              pcaMethods_1.78.0           hms_0.5.3                  
 [61] ProtGenerics_1.18.0         parallel_3.6.1              SummarizedExperiment_1.16.1 RColorBrewer_1.1-2          curl_4.3                   
 [66] memoise_1.1.0               gridExtra_2.3               ggplot2_3.3.2               biomaRt_2.42.1              rpart_4.1-15               
 [71] latticeExtra_0.6-29         stringi_1.5.3               RSQLite_2.2.1               genefilter_1.68.0           S4Vectors_0.24.4           
 [76] foreach_1.5.1               checkmate_2.0.0             BiocGenerics_0.32.0         BiocParallel_1.20.1         GenomeInfoDb_1.22.1        
 [81] rlang_0.4.8                 pkgconfig_2.0.3             bitops_1.0-6                matrixStats_0.57.0          mzID_1.24.0                
 [86] lattice_0.20-41             purrr_0.3.4                 htmlwidgets_1.5.2           bit_4.0.4                   tidyselect_1.1.0           
 [91] plyr_1.8.6                  magrittr_1.5                DESeq2_1.26.0               R6_2.5.0                    IRanges_2.20.2             
 [96] generics_0.1.0              Hmisc_4.4-1                 DelayedArray_0.12.3         DBI_1.1.0                   pillar_1.4.6               
[101] foreign_0.8-76              survival_3.2-7              RCurl_1.98-1.2              nnet_7.3-14                 tibble_3.0.4               
[106] crayon_1.3.4                BiocFileCache_1.10.2        jpeg_0.1-8.1                progress_1.2.2              locfit_1.5-9.4             
[111] grid_3.6.1                  blob_1.2.1                  distr_2.8.0                 digest_0.6.27               xtable_1.8-4               
[116] openssl_1.4.3               stats4_3.6.1                munsell_0.5.0               askpass_1.1
MSGFplus • 781 views
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Entering edit mode
@laurent-gatto-5645
Last seen 15 days ago
Belgium

MSGFplus is a Bioconductor package and this needs to be installed with the BiocManager::install() function:

 BiocManager::install("MSGFplus")

You might also want to consider updating your R to version 4.0.

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Entering edit mode

Hello Laurent Gatto,

Thank you so much for your great help!

Best,

Yue

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