Question: Old jmosaics working package
0
gravatar for james.dalgleish
20 months ago by
james.dalgleish30 wrote:

I've had a hard time finding it, but is there a jmosaics package that is version 1.1.0? I've been trying to find it and had old code that required it's use for chipseq.

http://www.bioconductor.org/packages//2.13/bioc/html/jmosaics.html The package binary (zip) listed here doesn't actually contain all the needed functions to run tutorial code, for example:

> bin1 <- readBins(type = c("chip","input"),
+                  fileName = c(system.file(file.path("extdata","h3k27me3_chip_chr10.txt"),
+                                           package="jmosaics"),
+                               system.file(file.path("extdata","h3k27me3_input_chr10.txt"),
+                                           package="jmosaics")))
Info: reading and preprocessing bin-level data...
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 1 did not have 3 elements

Upon inspecting the package, the namespace has the following contents:

import(mosaics)
export(jmosaicsPattern,
readBinsMultiple
    )

The R directory doesn't have the functions I'm looking for, as far as I can tell and I can't pull up documentation for the readBins function.

 

So the key question is... where is the old version (1.1.0) that actually had all the functions needed to run the tutorial code?  I can't get the old versions because the bioconductor github mirror doesn't have the file any longer.

jmosaics • 358 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by james.dalgleish30

Is there a replacement that does something similar? I've never seen anything quite like it previously.

ADD REPLYlink written 20 months ago by james.dalgleish30
Answer: Old jmosaics working package
0
gravatar for James W. MacDonald
20 months ago by
United States
James W. MacDonald51k wrote:

The jmosaics package was deprecated in 3.3 and removed for the 3.4 release. So technically it's no longer a Bioconductor package, and no longer tracked in the Bioc git server.  Nor is it supported in any way on this support site. In addition, the git mirror is defunct as well. We now use git for version control and if I am not mistaken, the only way for non-developers to access a git repository is if the developer also maintains a github version as well. 

You can install any of the versions of R that correspond to any of the Bioc versions that did include jmosaics and install via biocLite, but otherwise you are unlikely to get any between-release versions of that package.

ADD COMMENTlink written 20 months ago by James W. MacDonald51k
1

Actually, it's still alive, for the moment, in svn

svn checkout https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/jmosaics

The svn log leads to

jmosaics$ svn diff -c75270 DESCRIPTION
Index: DESCRIPTION
===================================================================
--- DESCRIPTION    (revision 75269)
+++ DESCRIPTION    (revision 75270)
@@ -1,7 +1,7 @@
 Package: jmosaics
 Type: Package
 Title: Joint analysis of multiple ChIP-Seq data sets
-Version: 1.0.0
+Version: 1.1.0
 Date: 2013-01-29
 Author: Xin Zeng
 Maintainer: Xin Zeng <xinzeng@stat.wisc.edu>

So it looks like the source code is available as

svn checkout -r75270 https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/jmosaics

(There were no commits on master between this version bump and the 1.2.0 release, so except for the version bump 1.1.0 and 1.2.0 are the same).

ADD REPLYlink modified 20 months ago • written 20 months ago by Martin Morgan ♦♦ 24k

I should also note that the error you see doesn't indicate that a function is missing. It says that the file it is trying to read in doesn't have three items in the first line. This is usually what you see if the function being used to read in a file has the wrong delimiter, and is e.g., confusing tabs and spaces so you get lines of different lengths. You could always download the source file from one of the old release versions and fix it, but like I said, with defunct packages you are completely on your own.

ADD REPLYlink written 20 months ago by James W. MacDonald51k
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