[BioC] Bioconductor installation problem on Mac

[Steven McKinney]

Hi Debashis,


I had the same issue, and raised it here back in July
See e.g.
https://stat.ethz.ch/pipermail/bioconductor/2006-July/013691.html

It appears that your download and installation
did work alright.  Two warnings were issued,
but no errors.

Warning 1:

Warning messages:
1: number of rows of result
   is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)


The first warning occurs when an empty package
repository is in place in BioC, usually because
a package had errors in testing and did not compile.
This is reportedly fixed in the upcoming release of R,
but not in the current release.

Simon Urbanek reported:
"For the record, the other warning mentioned appears when installing 
from empty repositories - it is not Mac specific. (The lindsey 
repository is empty on Bioc, because none of the packages compiles). 
I have now also committed the fix (thanks to Seth for the correct 
analysis and fix)."


Warning 2:

Warning messages:

2: cannot create HTML package index in: make.packages.html()

If you run

> help.start()

before you run

> source("http://www.bioconductor.org/biocLite.R")
> biocLite(c("affy"))

then I believe you should not see the second warning,
as help.start() will create the directories and files
that biocLite() is trying to modify.  biocLite() wants
to add help information to the help HTML package index,
but that index is not in place until help.start() sets it all up.

Simon Urbanek reported:
"Yes, it fails because it expects the help system to have created them 
already and you're not supposed to mess with that manually. (Again, 
this is not Mac-specific - until help.start is invoked, the 
directories are not there on any unix)."


Try loading and running some examples for the packages
you've installed, they should work alright.

Hopefully these warnings will no longer appear
in the next release of R, as they continue to confuse
new users who are earnestly striving to ensure 
that software was properly downloaded and installed.



Best regards


Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Debashis Bhattacharya
Sent: Tue 8/29/2006 11:20 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Bioconductor installation problem on Mac
 
I have posted this problem earlier, but there was no response. Hence, 
I'm posting this again.

I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo 
iMac).

When I try to install bioconductor -- following instructions, using 
biocLite() -- it downloads
the packages mentioned on the install page. However, the instatllation 
does not complete.

I get the following message after the downloads are complete:

------
The downloaded packages are in
   /tmp/RtmpJdBYlA/downloaded_packages
Warning messages:
1: number of rows of result
   is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)
2: cannot create HTML package index in: make.packages.html()
------

I have tried installation with only one package (affy), and still face 
the same problem. The entire log
for affy is as follows:

--------
 > source("http://www.bioconductor.org/biocLite.R")
 > biocLite(c("affy"))
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3/affy_1.10.0.tgz' 

Content type 'application/x-gzip' length 1733585 bytes
opened URL
==================================================
downloaded 1692Kb


The downloaded packages are in
   /tmp/RtmpJdBYlA/downloaded_packages
Warning messages:
1: number of rows of result
   is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)
2: cannot create HTML package index in: make.packages.html()
---------

Please help.



Debashis Bhattacharya.

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