New computer won't install DESeq2
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jyoung • 0
@jyoung-13447
Last seen 2.9 years ago

 

I recently got a new computer and I'm trying to do some analyses on it with Rstudio and I'm having trouble installing packages.  I was able to install the tidyverse but I keep getting errors when installing DESeq2.

Here are the errors I'm getting:

ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/johnyoung/Library/R/3.3/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)

The downloaded source packages are in
    ‘/private/var/folders/10/l49wwtqn4gsbl8xc3h3ry5jm0000gn/T/RtmpI2NgY1/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘cluster’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘Matrix’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘mgcv’ had non-zero exit status
> library(DESeq2)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘htmlTable’
Error: package or namespace load failed for ‘DESeq2’

Any help would be amazing!  Thank you

Session info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.13.6 (unknown)

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  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.3       SummarizedExperiment_1.2.3 Biobase_2.32.0            
[4] GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1             
[7] S4Vectors_0.10.3           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19        RColorBrewer_1.1-2  pillar_1.3.0        plyr_1.8.4         
 [5] XVector_0.12.1      bindr_0.1.1         base64enc_0.1-3     tools_3.3.1        
 [9] zlibbioc_1.18.0     rpart_4.1-13        tibble_1.4.2        gtable_0.2.0       
[13] lattice_0.20-35     pkgconfig_2.0.2     rlang_0.2.2         Matrix_1.2-12      
[17] rstudioapi_0.8      bindrcpp_0.2.2      gridExtra_2.3       cluster_2.0.6      
[21] dplyr_0.7.6         nnet_7.3-12         grid_3.3.1          tidyselect_0.2.5   
[25] glue_1.3.0          R6_2.3.0            survival_2.42-6     BiocParallel_1.6.6 
[29] foreign_0.8-71      latticeExtra_0.6-28 Formula_1.2-3       purrr_0.2.5        
[33] ggplot2_3.0.0       magrittr_1.5        scales_1.0.0        splines_3.3.1      
[37] assertthat_0.2.0    colorspace_1.3-2    acepack_1.4.1       lazyeval_0.2.1     
[41] munsell_0.5.0       crayon_1.3.4     

deseq2 rstudio install error • 747 views
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Go after the first hint of trouble, and try to install / troubleshoot the installation of RcppArmadillo.

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I am getting the issue to install DESeq2 on my system. What should I do to resolve this issue? I install Avast antivirus and also try on avast customer service for the help purpose but did not get any response.

 

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@mikelove
Last seen 8 hours ago
United States

Can you try with R 3.5? Do you have a reason to use a version from 2 years ago?

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that was it, needed to update R.  Thank you

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