[BioC] annmap installation window

[Tim Yates]

Hi Chris,

This sounds like a problem with the RMySQL installation on your machine.
Can you verify it works before trying to install annmap?

Unfortunately, we don't have a Windows machine with enough horsepower to
build, run or test annmap on the Windows platform, and that (and that I
had some problems getting RMySQL up and running on Windows) is why I
marked the project to not build a Windows binary.

There is a post here[1] on StackOverflow which explains the steps that
should be necessary to get RMySQL installed correctly.

But as I said, I haven't tried them :-(

Tim

 1:
http://stackoverflow.com/questions/5223113/using-mysql-in-r-for-windows/523
0980#5230980


On 17/01/2013 16:38, "Chris Banerji [guest]" <guest at bioconductor.org>
wrote:

>
>Hi all,
>
>I've been trying to install annmap on a windows workstation and have run
>into a few difficulties (I believe to be specific to the windows
>installation, which is a bit tricky due to lack of windows binaries for
>this pre-required packages).
>
>I installed MySQL, obtained the annmap database annmap_homo_sapiens_68
>and imported it to MySQL as per the instructions provided with the annmap
>package. I then installed the pre-requisite package RMySQL after
>shuffling the files libmysql.lib and libmysql.dll appropriately to meet
>dependencies.
>
>I then attempted to install the annmap package from source (a tarball
>file downloaded from the bioconductor website), but I got some issues
>regarding the architecture of the install (32 bit vs 64 bit).
>
>On my first attempt the version of MySQL downloaded was x64 so I had to
>install the x64 version of RMySQL, I believe it is this that led to the
>error printed first below, where loading fails for the i386 arch because
>RMySQL is not installed in that architecture.
>
>So I tried uninstalling MySQL x64 and re-installing a 32 bit version and
>reinstalling RMySQL in 32 bit only using the command line:
>
>"c:\Program Files\R\R-2.15.1\bin\i386\R" CMD INSTALL RMySQL_0.9-3.tar.gz
>
>then I re-attempted to install annmap in the 32 bit arch which gave the
>second error listed.
>
>So I think this may be happening because the command:
>
>R CMD INSTALL "annmap_1.1.1.tar.gz" fails if it can't install on both 64
>and 32 bit rather than just one of the two, and my version of MySQL can
>only be one or the other.
>
>Is there a way to force R to only install the 32 bit is 64 bit version
>and not both, or is there an easy way to install this that I'm not seeing?
>
>Thanks very much!
>Best wishes,
>Chris
>
> -- output of sessionInfo():
>
>#Error if using x64 version of MySQL and RMySQL
>>
>>install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",repos=N
>>ULL,type="source")
>Installing package(s) into
>‘C:/Users/ucbpban/Documents/R/win-library/2.15’
>(as ‘lib’ is unspecified)
>* installing *source* package 'annmap' ...
>** R
>** inst
>** preparing package for lazy loading
>MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5
>** help
>*** installing help indices
>** building package indices
>** installing vignettes
>   'INSTALL.Rnw'
>   'annmap.Rnw'
>   'cookbook.Rnw'
>** testing if installed package can be loaded
>*** arch - i386
>MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5
>Error : .onLoad failed in loadNamespace() for 'RMySQL', details:
>  call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll)
>  error: DLL 'RMySQL' not found: maybe not installed for this
>architecture?
>Error: loading failed
>Execution halted
>*** arch - x64
>MYSQL_HOME defined as C:/Program Files/MySQL/MySQL Server 5.5
>ERROR: loading failed for 'i386'
>* removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap'
>Warning in install.packages :
>  running command 'C:/PROGRA~1/R/R-215~1.2/bin/x64/R CMD INSTALL -l
>"C:/Users/ucbpban/Documents/R/win-library/2.15"
>"C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz"' had status 1
>Warning in install.packages :
>  installation of package
>‘C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz’ had non-zero exit
>status
>
>#Error if using x32 version of MySQL and RMySQL
>>
>>install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",type="s
>>ource")
>Installing package(s) into 'C:/Users/ucbpban/Documents/R/win-library/2.15'
>(as 'lib' is unspecified)
>inferring 'repos = NULL' from the file name
>* installing *source* package 'annmap' ...
>** R
>** inst
>** preparing package for lazy loading
>MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5
>** help
>*** installing help indices
>** building package indices
>** installing vignettes
>   'INSTALL.Rnw'
>   'annmap.Rnw'
>   'cookbook.Rnw'
>** testing if installed package can be loaded
>*** arch - i386
>MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5
>*** arch - x64
>MYSQL_HOME defined as C:/Program Files (x86)/MySQL/MySQL Server 5.5
>Error : .onLoad failed in loadNamespace() for 'RMySQL', details:
>  call: library.dynam("RMySQL", pkgname, libname, DLLpath = dll)
>  error: DLL 'RMySQL' not found: maybe not installed for this
>architecture?
>Error: loading failed
>Execution halted
>ERROR: loading failed for 'x64'
>* removing 'C:/Users/ucbpban/Documents/R/win-library/2.15/annmap'
>Warning message:
>In install.packages("C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz",  :
>  installation of package
>'C:/Users/ucbpban/Downloads/annmap_1.1.1.tar.gz' had non-zero exit status
>>
>
>
>--
>Sent via the guest posting facility at bioconductor.org.
>
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