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Last seen 10.3 years ago
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",re
pos=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",ty
pe="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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