I have a list of files that I am trying to cluster hypermethylated genes into cluster sites based on their distance from each other. I've read about a package called "AClust" for R that would allow me to annotate and cluster genes into specific regions. However, I can't seem to find a working link/method to download the package. Does anyone know if this package is still available for download on R or if it was removed? Or if there's another good way to cluster the genes without the package
I don't see any evidence that a package called AClust ever existed as part of Bioconductor. A Google search (likely your best bet for this sort of thing) brings up a GitHub repository containing an R package that somebody named Pete Haitch got from Tamar Sofer's website before that was (apparently) taken down. So if that sounds like what you are after, then it still exists.
I'll leave it to you to do your own Google searching, but will give you a hint - installing from github is really easy if you use the devtools package. As a secondary hint, I will note that biocLite() will install a package from almost anywhere (and in the devel version, apparently even from GitHub repos), whereas install.packages() is primarily for CRAN packages. So if you need to install a package, and don't know what repo hosts it, biocLite("packagename") is far more likely to Do The Right Thing(TM).
Hi, thanks for answering, and yes that is the Aclust file from Pete Haitch I was talking about. I didn't know R could download from github but after looking a few things up I found this code:
I tried to install the package, and I got an error message that there was no package called Rcpp. I've tried to redownload the rcpp package and checked the library paths but I'm still getting the same error in the Loadspacename. Any idea what could be causing this?
This is the code I used:
> install.packages("devtools")
> devtools::install_github("PeteHaitch/Aclust")
"Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Rcpp’"
> devtools::install_github("PeteHaitch/Aclust", dependencies=TRUE)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Rcpp’
When I run loadNamespace("Rcpp"), it still says it can't find the package. I'm thinking the problem might be with the library path or where it is loading from, but I'm not sure
Rcpp is another R package, so just install it via biocLite('Rcpp'), you may run into a problem, however, since Rcpp was just upgraded to v0.12.0, which may hose whichever package is depending on it.
> biocLite("Rcpp")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.19.9), R 3.2.0 (2015-04-16).
Installing package(s) ‘Rcpp’
trying URL 'http://www.go-parts.com/mirrors-usa/cran/bin/windows/contrib/3.2/Rcpp_0.12.0.zip'
Content type 'application/zip' length 3112709 bytes (3.0 MB)
downloaded 3.0 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
> grep("Rcpp", row.names(installed.packages()), value = TRUE)
[1] "RcppArmadillo" "RcppEigen"
But the Rcpp directory does exist there, so R thinks it's installed in some scenarios and not in others. Close R, go to where ever .libPaths()[1] points to, and delete the Rcpp dir. Then start R and start over again.
> biocLite("Rcpp")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.19.9), R 3.2.0 (2015-04-16).
Installing package(s) ‘Rcpp’
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/Rcpp_0.12.0.zip'
Content type 'application/zip' length 3112868 bytes (3.0 MB)
downloaded 3.0 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
> devtools::install_github("PeteHaitch/Aclust")
Downloading github repo PeteHaitch/Aclust@master
Installing Aclust
"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" --no-site-file --no-environ --no-save \
--no-restore CMD INSTALL \
"C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c" \
--library="C:/Users/BioinfAdmin/R/win-library/3.2" --install-tests
* installing *source* package 'Aclust' ...
** R
** data
** preparing package for lazy loading
Warning: package 'geepack' was built under R version 3.2.1
** help
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/Aclust-package.Rd:31: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/calc.dist.clusters.Rd:22: unknown macro '\cor'
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:30: unexpected UNKNOWN '\example'
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:40: unexpected '}'
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:32: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:33: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:35: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:36: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:37: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:38: All text must be in a section
Warning: C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/create.annot.triche.Rd:39: All text must be in a section
*** installing help indices
Error in Rd_info(db[[i]]) :
missing/empty \title field in 'C:/Users/BioinfAdmin/AppData/Local/Temp/RtmpWUA9lz/devtoolsea44bab5c7a/PeteHaitch-Aclust-fbb825c/man/expit.Rd'
Rd files must have a non-empty \title.
See chapter 'Writing R documentation' in manual 'Writing R Extensions'.
* removing 'C:/Users/BioinfAdmin/R/win-library/3.2/Aclust'
Error: Command failed (1)
So if you want to use this package, and since it isn't a Bioconductor package, nor CRAN, you are on your own. You can open your own GitHub repository, fork the package, and then fix the help page for expit.Rd to have an existing \title, at which time it may or may not install. There is lots of information in Writing R Extensions that you can read, if you really want to use this package and are willing to do the work to get it installed.
But I found that there is some issue with Github "username/packagename" with "PeteHaitch/Aclust". So I used Aclust's main Github "username/pckagename" i.e. "tamartsi/Aclust"
biocLite("tamartsi/Aclust") or adding repos=BiocInstaller::biocinstallRepos() to install_github() will ensure that the dependencies for your version of Bioconductor are installed, too.
Hi Lilly,
I just installed Aclust yesterday, initially I face same problem. Now I figure out this problem.
I think at this poin you are using command
library("devtools")
install_github("PeteHaitch/Aclust", dependencies=TRUE)But I found that there is some issue with Github"username/packagename" with"PeteHaitch/Aclust". So I used Aclust's main Github "username/pckagename" i.e. "tamartsi/Aclust"Final command was:
library("devtools")
install_github("tamartsi/Aclust", dependencies=TRUE)By using this command I installed Aclust in my latest R-3.2.1, I hope this command will work for you.ThanksNitish