Steve:

Thanks for the pointer to the July posting. I missed that while looking 
through
the archives.  Moreover, for some strange reason, Seth's response to my 
original
posting did not arrive in my mailbox -- leading to the 2nd posting.

This is most helpful. Testing the presence of library "affy", I see that the
installation did happen.


Regards.
Debashis.


Steven McKinney wrote:
> 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@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@stat.math.ethz.ch on behalf of Debashis Bhattacharya
> Sent: Tue 8/29/2006 11:20 AM
> To: bioconductor@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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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
>
>
>   


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