Question: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
0
gravatar for chokoiboko
9 months ago by
chokoiboko0
chokoiboko0 wrote:

Hello,

I'm looking for the source tar balls for these specific versions of IRanges, S4Vectors  and XVector. It looks like Bioconductor 3.4 has the updated versions of these. I looked in various places for the source - bioconductor.org, cran.r-project.orghttps://conda.anaconda.org/bioconda/linux-64, https://github.com/Bioconductor, but couldn't find these specific versions.

I need to install these packages from the source to build a validated environment.

If someone can point to the right place to find these, it would be highly appreciated.

 

Thanks,

 

Oleg

ADD COMMENTlink modified 9 months ago by becker.gabriel10 • written 9 months ago by chokoiboko0

For what it's worth, not helpful to you but perhaps to people with similar questions, starting from Bioconductor 3.6 all release versions are archived, e.g., https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 23k

This is good to know. Thank you.

ADD REPLYlink written 9 months ago by chokoiboko0
Answer: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
0
gravatar for James W. MacDonald
9 months ago by
United States
James W. MacDonald49k wrote:

Those versions were part of Bioconductor 3.4, but the available versions aren't exactly what you are looking for (e.g., IRanges is 2.8.2, S4Vectors is 0.12.2, etc), so you can't just install R-3.3.x and then use biocLite to get what you want. Unless a change of 1 for the minor version number is OK for your validated environment.

An alternative would be to use the switchr package, which was developed by some people associated with Bioconductor, but is on CRAN. I believe you can use that package to do what you want, but it's a CRAN package, not Bioconductor, so if you need help please ask any questions on R-help, not here.

ADD COMMENTlink written 9 months ago by James W. MacDonald49k

Thank you for your reply.

Unfortunately I can't replace these versions or packages with alternatives. I'm not using biocLite to install the packages, but I'm installing from the source tar balls.

 

ADD REPLYlink written 9 months ago by chokoiboko0

Then try switchr, or alternatively clone the git repos for those packages (see e.g., the Package Archive section for IRanges for an example), and troll through the log to find the commits for the version you want and then revert to that commit and install.

ADD REPLYlink written 9 months ago by James W. MacDonald49k

Archives are not available for Bioconductor 3.4.

ADD REPLYlink written 9 months ago by chokoiboko0

What do you mean by that, exactly?

ADD REPLYlink written 9 months ago by James W. MacDonald49k

There is no Package Archive section for Bioconductor 3.4.  Martin Morgan mentioned above that the archives are available, starting from Bioconductor 3.6

ADD REPLYlink written 9 months ago by chokoiboko0

If I clone the IRanges repo and look for the 3_4 release I get

linux$ git log -v | grep -B 4 3_4 
commit c1148c04d74c659663b0bc5f929dc1970fc40643
Author: Herve Pages <hpages@fhcrc.org>
Date:   Mon Oct 17 19:10:43 2016 +0000

    bump x.y.z versions to odd 'y' after creation of 3_4 branch
--
commit 516126f83b8f446e5b731012872ed2af614caf37
Author: Herve Pages <hpages@fhcrc.org>
Date:   Mon Oct 17 18:45:06 2016 +0000

    bump x.y.z versions to even 'y' prior to creation of 3_4 branch

grep log -v | grep -B 4 bump 

commit c1148c04d74c659663b0bc5f929dc1970fc40643
Author: Herve Pages <hpages@fhcrc.org>
Date:   Mon Oct 17 19:10:43 2016 +0000

    bump x.y.z versions to odd 'y' after creation of 3_4 branch
--
commit 516126f83b8f446e5b731012872ed2af614caf37
Author: Herve Pages <hpages@fhcrc.org>
Date:   Mon Oct 17 18:45:06 2016 +0000

    bump x.y.z versions to even 'y' prior to creation of 3_4 branch

Which gives you the commit number, which you can then use git reset to go back to.

ADD REPLYlink written 9 months ago by James W. MacDonald49k

James,

You can use switchr to more easily get back to exact package versions if you need to. It has the crawl git/SVN/CRAN webarchive functionality built in so you don't have to worry about it.

Best,

~G

ADD REPLYlink written 9 months ago by becker.gabriel10

I thought that was true, but left it for the OP to figure out the technical details of using switchr to get exact versions. Thanks!

ADD REPLYlink written 9 months ago by James W. MacDonald49k
Answer: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
0
gravatar for becker.gabriel
9 months ago by
becker.gabriel10 wrote:

Hi all,

My switchr package  (on CRAN) has functionality to do this. To create a new switchr library which uses Bioc 3.4, you can do:

> library(switchr)
> switchTo("bioc3.4test", seed = BiocVers("3.4"))
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocInstaller_1.24.0.tar.gz'
Content type 'application/x-gzip' length 17756 bytes (17 KB)
==================================================
downloaded 17 KB

* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning: Bioconductor version 3.4 is too old for R version 3.4.4; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
* DONE (BiocInstaller)

The downloaded source packages are in
    ‘/private/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/RtmpsFnfmI/downloaded_packages’

Switched to the 'bioc3.4test' computing environment.
30 packages are currently available.
Packages installed in your site library are suppressed.
To switch back to your previous environment type switchBack()

Warning message:
In annotateDESCs(installedpkgs, man) :
  Not annotating newly installed versions of switchr dependencies

> library(BiocInstaller)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.4; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller

> biocLite("S4Vectors")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.4 Patched (2018-03-19\
  r74581).

Installing package(s) ‘S4Vectors’
also installing the dependency ‘BiocGenerics’

Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4/PACKAGES'

<snip>

Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘S4Vectors’

Do you want to attempt to install these from sources?
y/n: y

installing the source packages ‘BiocGenerics’, ‘S4Vectors’

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz'
Content type 'application/x-gzip' length 40398 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/S4Vectors_0.12.2.tar.gz'
Content type 'application/x-gzip' length 414697 bytes (404 KB)
==================================================
downloaded 404 KB

<snip>

> library(S4Vectors)

<snip>

> sessionInfo()
R version 3.4.4 Patched (2018-03-19 r74581)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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
[8] methods   base     

other attached packages:
[1] S4Vectors_0.12.2     BiocGenerics_0.20.0  BiocInstaller_1.24.0
[4] switchr_0.12.7      

loaded via a namespace (and not attached):
[1] compiler_3.4.4  tools_3.4.4     RCurl_1.95-4.10 bitops_1.0-6   


 

Hope that helps.

~G

ADD COMMENTlink written 9 months ago by becker.gabriel10

switchr can also install exact, old sets of R packages if that's what you need to do (I don't recommend installing a single historical package version on top of an otherwise modern package library in most cases ). See our paper in JSS https://www.jstatsoft.org/article/view/v082i01 and the package vignette and documentation for more details.

ADD REPLYlink written 9 months ago by becker.gabriel10
Answer: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
0
gravatar for becker.gabriel
9 months ago by
becker.gabriel10 wrote:

Sorry, I misread your question when posting my previous answer, though I'll leave it up in the hopes perhaps it is useful to someone. switchr can also install exact historical versions of packages.

Make sure you have switchr version 0.12.9 (currently only available from http://github.com/gmbecker/switchr) or higher (I just commited this and it fixes a bug that would have bitten you) and BiocInstaller installed (a future version will support BiocManager). then do the following:

> library(switchr)
> man = PkgManifest(name = c("IRanges", "S4Vectors", "XVector"), type = "bioc", dep_repos = biocReposForVers("3.4"))
> vers = c(IRanges= "2.8.1", S4Vectors =  "0.12.1", XVector = "0.14.0")
> install_packages(names(vers), repos = man, versions = vers)
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.r-project.org/src/contrib/Archive/IRanges/IRanges_2.8.1.tar.gz'
Cloning into 'IRanges'...
remote: Counting objects: 21987, done.
remote: Compressing objects: 100% (6601/6601), done.
remote: Total 21987 (delta 17258), reused 19495 (delta 15337)
Receiving objects: 100% (21987/21987), 4.13 MiB | 200.00 KiB/s, done.
Resolving deltas: 100% (17258/17258), done.
Switched to a new branch 'RELEASE_3_4'
Note: checking out '3c3880cb42a1bff3c123d7343376df1eeeaf763b'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 3c3880c... port setdiff,CompressedIRangesList fix from devel
* checking for file ‘/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T//RtmpikpcwH/IRanges/DESCRIPTION’ ... OK
* preparing ‘IRanges’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘IRanges_2.8.1.tar.gz’

<snip, retrieves the other two requested packages>

Installing packages into ‘/Users/beckerg4/Rlib/3.4.4-current’
(as ‘lib’ is unspecified)
* installing *source* package ‘S4Vectors’ ...
** libs
<snip>
** R
** inst
** preparing package for lazy loading
<snip>
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RleTricks.Rnw’ using ‘UTF-8’ 
   ‘S4QuickOverview.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘S4Vectors’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘S4Vectors’
* DONE (S4Vectors)
<snip, installs other two>
The downloaded source packages are in

‘/private/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/RtmpikpcwH/downloaded_packages’
    IRanges   S4Vectors     XVector 
  "IRanges" "S4Vectors"   "XVector" 
Warning messages:
1: In download.file(url, destfile, method, ...) :
  cannot open URL 'http://cran.r-project.org/src/contrib/Archive/IRanges/IRanges_2.8.1.tar.gz': HTTP status was '404 Not Found'
2: In download.file(url, destfile, method, ...) :
  cannot open URL 'http://cran.r-project.org/src/contrib/Archive/S4Vectors/S4Vectors_0.12.1.tar.gz': HTTP status was '404 Not Found'
3: In download.file(url, destfile, method, ...) :
  cannot open URL 'http://cran.r-project.org/src/contrib/Archive/XVector/XVector_0.14.0.tar.gz': HTTP status was '404 Not Found'
> library(XVector)
<snip>

> sessionInfo()
R version 3.4.4 Patched (2018-03-19 r74581)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] XVector_0.14.0      IRanges_2.8.1       S4Vectors_0.12.1   
[4] BiocGenerics_0.24.0 switchr_0.12.8     

loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0      compiler_3.4.4       BiocInstaller_1.28.0
[4] tools_3.4.4          RCurl_1.95-4.10      bitops_1.0-6        
[7] tcltk_3.4.4         

 

There are ways to control where the checkouts are put so that they are not in a temporary location, but please see the docs for the details on that.

ADD COMMENTlink written 9 months ago by becker.gabriel10

I ended up not using these packages. Thank you all for your tips and advices! It's very helpful information. 

ADD REPLYlink written 7 months ago by chokoiboko0
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