Question: There is a convenient way to use not up-to-date packages in R?
0
gravatar for yussab
5 weeks ago by
yussab10
Italy
yussab10 wrote:

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!

packages R installation • 234 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by yussab10
2

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.

ADD REPLYlink written 5 weeks ago by Jean-Karim Heriche23k
1

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.

ADD REPLYlink written 5 weeks ago by h.mon31k

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.

ADD REPLYlink written 5 weeks ago by cpad011214k
1
gravatar for yussab
5 weeks ago by
yussab10
Italy
yussab10 wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by yussab10
1
gravatar for dariober
5 weeks ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

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

ADD COMMENTlink written 5 weeks ago by dariober11k

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

ADD REPLYlink written 5 weeks ago by yussab10

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

ADD REPLYlink written 5 weeks ago by yussab10
2

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.

ADD REPLYlink written 5 weeks ago by dariober11k

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??

ADD REPLYlink written 5 weeks ago by yussab10

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
ADD REPLYlink written 5 weeks ago by dariober11k

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by yussab10

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)

ADD REPLYlink written 5 weeks ago by dariober11k

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...

ADD REPLYlink written 5 weeks ago by yussab10
1

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

ADD REPLYlink written 5 weeks ago by dariober11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2048 users visited in the last hour