[BioC] annmap installation window

[Chris Banerji [guest]]

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=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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