Failed to install 'MetaboAnalystR' from GitHub
Entering edit mode
Last seen 12 months ago

Trying to install MetaboAnalystR using following command:

devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_vignettes = FALSE)

but it fails probably because "mzR has been built against a different Rcpp version"?

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

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

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

loaded via a namespace (and not attached):
 [1] pillar_1.4.6        compiler_4.0.2     
 [3] RColorBrewer_1.1-2  BiocManager_1.30.10
 [5] remotes_2.2.0       prettyunits_1.1.1  
 [7] tools_4.0.2         testthat_2.3.2     
 [9] pkgload_1.1.0       digest_0.6.25      
[11] pkgbuild_1.1.0      memoise_1.1.0      
[13] lifecycle_0.2.0     tibble_3.0.3       
[15] gtable_0.3.0        pkgconfig_2.0.3    
[17] rlang_0.4.7         cli_2.0.2          
[19] rstudioapi_0.11     curl_4.3           
[21] withr_2.3.0         dplyr_1.0.2        
[23] httr_1.4.2          desc_1.2.0         
[25] generics_0.0.2      fs_1.5.0           
[27] vctrs_0.3.4         devtools_2.3.2     
[29] rprojroot_1.3-2     grid_4.0.2         
[31] tidyselect_1.1.0    glue_1.4.2         
[33] R6_2.4.1            processx_3.4.4     
[35] fansi_0.4.1         pacman_0.5.1       
[37] sessioninfo_1.1.1   pheatmap_1.0.12    
[39] ggplot2_3.3.2       purrr_0.3.4        
[41] callr_3.4.4         magrittr_1.5       
[43] backports_1.1.10    scales_1.1.1       
[45] ps_1.3.4            matrixStats_0.56.0 
[47] ellipsis_0.3.1      usethis_1.6.3      
[49] assertthat_0.2.1    colorspace_1.4-1   
[51] munsell_0.5.0       crayon_1.3.4      
software error MetaboAnalystR mzR • 532 views
Entering edit mode

As Laurent mentioned below you can usually ignore that warning message - only that install_github does not install packages when there is a warning thrown during installation. To force installing a package even if there are warnings you can set Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true") before calling install_github.

Generally you should not use this option, but in this case it should be safe.

cheers, jo

Entering edit mode
Last seen 5 hours ago

it fails probably because "mzR has been built against a different Rcpp version"?

No, that would be unlikely. This had an impact many years ago but isn't an issue anymore. Without the incriminating error messages, it won't be possible to help out.

Note that MetaboAnalystR isn't a Bioconductor package, and this is a forum that is dedicated to Bioconductor packages. You might want to consider seeking help on the GitHub repository.


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