Which version of Opal are you using? New versions of Opal, 2.16 and after (if memory serves me right), you should use āDSIā and āDSOpalā R packages to interact with the Opal server.
If you are seeing āresourcerā package I suspect you are running a relatively new version of Opal, which I suspect āopalā and āopaladminā R packages will only partially work.
I think the best way to proceed is to initially confirm which version of Opal you are using.
The way I do this would be to log into the Opal Web Portal (usually on port 8080) with my
web browser and (after login in) check the version which is displayed in the bottom right corner
of the page.
Hank,
In that case you will need to use the āDSIā and āDSOpalā R packages. I would advice uninstalling the āopalā and āopaladminā packages if they are installed on your client.
Are you trying to login to the Opal server using āhttpsā or āhttpā? The error messages does look like a SSL certificate issue.
Sorry for confusing you. I have three opal servers, two of them have problems for using but different issues.
For this server, the issue is the missing dsBase package. I can login but cannot install dsBase from opalr. For DSI and DSOpal, I still can login but cannot find functions to install server-side packages. Could you please suggest one?
If you have access to the administrative account, I find the easiest way to install the ādsBaseā package is via the Opal Web Portal: āAdministrationā -> āDataSHIELDā then
use ā+ Add Packageā button.
dsBase fails at being installed in your R server. You should check the R server logs for error messages: in Opal, go to Administration > R and then click Download.
There are indeed errors when instaling the dependency. See below:
... ...
checking for ranlib... ERROR: no information for variable 'RANLIB'
... ...
libtool: link: ERROR: no information for variable 'AR' cru .libs/libutil.a .libs/mt19937ar.o .libs/sobolseq.o .libs/timer.o .libs/stop.o .libs/redblack.o .libs/qsort_r.o .libs/rescale.o
../libtool: line 1102: ERROR:: command not found
make[2]: *** [libutil.la] Error 127
make[2]: Leaving directory `/tmp/Rtmpz57bwJ/R.INSTALL743e428fe501/nloptr/src/nlopt_src/util'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/Rtmpz57bwJ/R.INSTALL743e428fe501/nloptr/src/nlopt_src'
make: *** [all] Error 2
ERROR: configuration failed for package ānloptrā
* removing ā/var/lib/rserver/R/library/nloptrā
ERROR: dependency ānloptrā is not available for package ālme4ā
* removing ā/var/lib/rserver/R/library/lme4ā
ERROR: dependency ālme4ā is not available for package ādsBaseā
* removing ā/var/lib/rserver/R/library/dsBaseā
ERROR: dependency ādsBaseā is not available for package ādatashieldā
* removing ā/var/lib/rserver/R/library/datashieldā
It says that libtool command is failing because of ranlib not configured. Seems a bit cryptic but sounds like a compiler error (gcc). How was installed R on this server ?
This error is due to the new version of nloptr not applicable to 3+ version of R.Thus, installation of an older version of nloptr would solve it. For example,
@swheater Thanks for this information.
My r-server is 3.6.0.
From CRAN page of nloptr(https://cran.r-project.org/web/packages/nloptr/index.html), the auther forgot to say the minumum available version of R. Therefore, my r-server tried to install the newest version. However it seams the nloptr 1.2.2.2 is not compitiable with R 3.6
Anyone know how I can install a old-version package into the r-server of opal?
Opal has no requirements regarding the R server (as soon as it is accessible), and is also not responsible for the R server failures by the wayā¦ Then update whatever you want in R, just make sure you have a clean install (i.e. not mixing R 3.x and R 4.x packages).