Errors installing RforProteomics
Entering edit mode
Last seen 5.5 years ago

I'm having trouble installing RforProteomics after the other dependencies have been installed. I think the problem is related to unzipping and then loading the library. I wanted to report this because of the error message I received. However, if anyone has ideas on how to solve the problem I'd be very receptive to that as well.

mzR has been built against a different Rcpp version (0.12.1)
than is installed on your system (0.12.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum...
Warning messages:
1: running command '"C:/Users/path" CMD INSTALL -l "C:/Users/path/library" C:/Users/path/synapterdata_1.8.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘synapterdata’ had non-zero exit status
3: running command '"C:/Users/path/R" CMD INSTALL -l "C:/Users/path/library" C:/Users/path/RforProteomics_1.8.0.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RforProteomics’ had non-zero exit status
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] msdata_0.8.0         BiocInstaller_1.20.1 hpar_1.12.0          rols_1.12.1          pRolocdata_1.8.0     cluster_2.0.3        annotate_1.48.0     
 [8] XML_3.98-1.4         AnnotationDbi_1.32.3 IRanges_2.4.8        S4Vectors_0.8.11     rpx_1.6.0            MSnbase_1.18.1       ProtGenerics_1.2.1  
[15] BiocParallel_1.4.3   Biobase_2.30.0       BiocGenerics_0.16.1  MSnID_1.4.0          mzID_1.8.0           mzR_2.4.0            Rcpp_0.12.3         

loaded via a namespace (and not attached):
 [1] SSOAP_0.8-0           rda_1.0.2-2           magrittr_1.5          fpc_2.1-10            MASS_7.3-45           sfsmisc_1.1-0         zlibbioc_1.16.0      
 [8] mclust_5.1            R.cache_0.12.0        xtable_1.8-2          colorspace_1.2-6      impute_1.44.0         lattice_0.20-33       R6_2.1.2             
[15] foreach_1.4.3         R.oo_1.20.0           futile.logger_1.4.1   lambda.r_1.1.7        class_7.3-14          ggvis_0.4.2           iterators_1.0.8      
[22] htmltools_0.3         modeltools_0.2-21     assertthat_0.1        digest_0.6.9          preprocessCore_1.32.0 shiny_0.13.1          RCurl_1.95-4.8       
[29] limma_3.26.8          DEoptimR_1.0-4        threejs_0.2.1         scales_0.4.0          pls_2.5-0             pcaMethods_1.60.0     R.methodsS3_1.7.1    
[36] diptest_0.75-7        httpuv_1.3.3          flexmix_2.3-13        munsell_0.4.3         doParallel_1.0.10     XMLSchema_0.7-2       plyr_1.8.3           
[43] dplyr_0.4.3           stringr_1.0.0         prabclus_2.2-6        tools_3.2.3           grid_3.2.3            nnet_7.3-12           data.table_1.9.6     
[50] gtable_0.2.0          affy_1.48.0           DBI_0.3.1             affyio_1.40.0         kernlab_0.9-23        trimcluster_0.1-2     ggplot2_2.1.0        
[57] reshape2_1.4.1        htmlwidgets_0.6       base64enc_0.1-3       bitops_1.0-6          R.utils_2.2.0         codetools_0.2-14      futile.options_1.0.0 
[64] rpart_4.1-10          MALDIquant_1.14       robustbase_0.92-5     RSQLite_1.0.0         mime_0.4              mlbench_2.1-1         stringi_1.0-1        
[71] mvtnorm_1.0-5         vsn_3.38.0            chron_2.3-47         


Bioc package installation rforproteomics • 992 views
Entering edit mode
Last seen 2 days ago

The message about mzR and Rcpp can be ignored - it only warns that the former was build with a different version that what you have. This happens every now and then and is generally not a problem.

The problem you experience is with the experiment package synapterdata, which leads to RforProteomics not to install. I can't see why it fails. Could you report the output of biocLite("synapterdata") and hopefully, we'll see something useful.


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