SARTools instalation error: DESeq2 1.10.1 was found but >= 1.12.0 is required

Question

[Farbod]

Dear Biostars, Hi

In order to installing SARTools package, in Ubuntu 14.04 command line R (R version 3.3.3 RC (2017-02-27 r72279) -- "Another Canoe" ), I tried the step by step guideline from this link.

But at the last step of running : install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)

I recieved the error about DESeq2 version as:

* installing *source* package ‘SARTools’ ...
** R
** inst
** preparing package for lazy loading 
Error : package ‘DESeq2’ 1.10.1 was found, but >= 1.12.0 is required by ‘SARTools’ 
ERROR: lazy loading failed for package ‘SARTools’

* removing ‘/tmp/RtmpDGyIGM/Rinstfa46b09f9ed/SARTools’
ERROR: package installation failed Installation failed: Command failed (1)

I have tried to upgrade the DESeq2, but it did not solve the problem (BiocInstaller version 3.2 is too old for R version 3.3.3).

Please help me to install SARtools.

Thanks

[h.mon]

What is the output of .libPaths()? After you upgraded DESeq2, what is the output of sessionInfo()?

[Farbod]

Hi,

for the .libPaths() :

[1] "/home/emami/R/x86_64-pc-linux-gnu-library/3.3"

[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"

and for the second :

>   
> 
> >   R version 3.3.3 RC (2017-02-27 r72279)
> >     Platform: x86_64-pc-linux-gnu (64-bit)
> >     Running under: Ubuntu 14.04.2 LTS
> >     
> >     locale:
> >      [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=fa_IR          
> >      [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=fa_IR       LC_MESSAGES=en_US.UTF-8
> >      [7] LC_PAPER=fa_IR          LC_NAME=C               LC_ADDRESS=C           
> >     [10] LC_TELEPHONE=C          LC_MEASUREMENT=fa_IR    LC_IDENTIFICATION=C    
> >     
> >     attached base packages:
> >     [1] stats     graphics  grDevices utils     datasets  methods   base     
> >     
> >     other attached packages:
> >     [1] devtools_1.13.5      BiocInstaller_1.20.3
> >     
> >     loaded via a namespace (and not attached):
> >      [1] Rcpp_0.12.16       digest_0.6.15      withr_2.1.2        R6_2.2.2          
> >      [5] grid_3.3.3         plyr_1.8.4         gtable_0.2.0       git2r_0.21.0      
> >      [9] scales_0.5.0.9000  httr_1.3.1         ggplot2_2.2.1.9000 pillar_1.2.2      
> >     [13] rlang_0.2.0        curl_3.2           lazyeval_0.2.1     tools_3.3.3       
> >     [17] munsell_0.4.3      colorspace_1.3-2   memoise_1.1.0      knitr_1.20        
> >     [21] tibble_1.4.2

BiocInstaller version 3.2 is too old for R version 3.3.3

Answer 1

[Farbod]

Hi,

The issue has been solved by removing BiocInstaller, and trying some other unknown scripts.

Thanks

[h.mon]

The issue has been solved by removing BiocInstaller, and trying some other unknown scripts.

Could you elaborate? The solution as it stands now is not of much help to anyone. What are those "unknown scripts"?