[BioC] annmap installation window

[Dan Tenenbaum]

On Thu, Jan 17, 2013 at 8:38 AM, 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?
>


R CMD INSTALL --no-multiarch RMySQL_0.9-3.tar.gz

Dan


> 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=NULL,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="source")
> 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
>>
>
>
> --
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>
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