There is a convenient way to use not up-to-date packages in R?

Question

[yussab]

Hi everybody,

I'm trying to replicate an article from 2018, in which they used these two packages:

InSilicoDb: https://www.bioconductor.org/packages//2.13/bioc/html/inSilicoDb.html

InSilicoMerging : https://www.bioconductor.org/packages//2.13/bioc/html/inSilicoDb.html

I'm not able to install those packages in R, I would like to know which is the convenient way to use this packages? Even if they are not up to date.

Thank you in advance!

[Jean-Karim Heriche]

Each version of bioconductor is in principle tied to a version of R. So the procedure would be to find out which version of R goes with the version of bioconductor that includes these packages then install this R version and the corresponding bioconductor then you can install the packages using the standard bioconductor installation method.

[h.mon]

Old versions of Windows R here: https://cran.r-project.org/bin/windows/base/old/

If you want the 2.13 version of the BioConductor package, you will need R 3.0.2, see here.

[cpad0112]

Did the methods section in manuscript mention the version of R and library used in analysis? If not , try to contact manuscript author for R session information.

Answer 1

[yussab]

R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

I was able to install the packages by:

1)Downloading Package Source from Package Archive

2)Installing the tar.gz from R Studio; Tools --> Install Packages... --> Package Archive File (tar.gz)

It's necessary to install all the required depencies, after that the packages were installed correctly

Answer 2

[dariober]

I think you can install from source like this using your required versions:

install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz')
install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoMerging_1.6.0.tar.gz')

(You may need to install some dependencies - check error messages)

Note that inSilicoDb and inSilicoMerging have been removed from bioconductor 3.4 onwards

[yussab]

I get the following error, anyway I'm not able to install R tools:

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/ Installing package into ‘C:/Users/yabili/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘https://cran.rstudio.com/bin/windows/Rtools/’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

[yussab]

I get WARNING about Rtools also for other packages, but they get installed anyway.

[dariober]

Looking at this, it seems that Rtools for R 4.0 is actually Rtools40. Try following instructions there.

I don't mean to sound discouraging but you are a bit in a tricky situation because 1) You are using Windows (most bioinformatics tools are designed for Linux) 2) You are installing unmaintained packages designed for R 3 on R 4.

[yussab]

1) thank you very much , I followed your instruction and now i don't have any Rtools WARNING on my Windows machine 2) I also have a Linux Machine with Ubuntu 20.04 and R version 3.6.3.

install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz') Installing package into ‘/home/youssef/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz’ is not available (for R version 3.6.3)

I don't know how to proceed. Should I install a specific version of R?? Which one in case??

[dariober]

Odd... Can you post the output of sessionInfo()? This works for me on R3.6:

install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz')
inferring 'repos = NULL' from 'pkgs'
trying URL 'https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz'
Content type 'application/x-tar' length 181579 bytes (177 KB)
==================================================
downloaded 177 KB

* installing *source* package ‘inSilicoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (inSilicoDb)
> library(inSilicoDb)
Loading required package: rjson
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max,
    which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
    and for packages 'citation("pkgname")'.

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/dario/miniconda3/envs/tritume/lib/libopenblasp-r0.3.10.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] inSilicoDb_1.10.1   Biobase_2.46.0      BiocGenerics_0.32.0 rjson_0.2.20       

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3    RCurl_1.98-1.2 bitops_1.0-6

[yussab]

sessionInfo()

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.1 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached): [1] compiler_3.6.3 tools_3.6.3 tinytex_0.26 xfun_0.18

[dariober]

I can't tell for sure what's going on but you may need to install some additional packages like Biobase, rjson, RCurl (in my sessionInfo, check the list under other attached packages: and loaded via a namespace)

[yussab]

I tried to install the packages but nothing changed. Furthermore the packages are loaded when: library(InSilicoDb). I can't figure out what is the problem, the main difference that I noticed is that you're using miniconda3...

[dariober]

Try downloading the tar.gz file to your machine then do install.packages('inSilicoDb_1.10.1.tar.gz', repos= NULL)