tranSMART 16.3 Installation error

[Helmut Spengler]

I am trying to install tranSMART 13.3 using the install script referenced at https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Runtheinstallscript.

When executing the command

     ./Scripts/install-ubuntu/InstallTransmart.sh 2>&1 | tee ~/install.log

I get following error message:

++++++++++++++++++++++++++++

+  Install R, Rserve and other packages

++++++++++++++++++++++++++++

+  installing R at /home/transmart/transmart/transmart-data/R/root/bin

make: Entering directory '/home/transmart/transmart/transmart-data/R'

curl -f http://cran-mirror.cs.uu.nl/src/base/R-3/R-3.2.1.tar.gz | tar xzf -

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (6) Could not resolve host: cran-mirror.cs.uu.nl

Seems like the host "cran-mirror.cs.uu.nl" dows not exist. Therefore, I tried to declare an alternative mirror in "transmart/transmart-data/R/Makefile" (e.g. https://cran.cnr.berkeley.edu). This however resulted in another error:

Some packages not installed

Execution halted

Makefile:39: recipe for target 'cran_packages' failed

make: *** [cran_packages] Error 1

Any ideas on how to solve this problem?

Kind regards

[Peter Rice]

Hi Helmut,

Oh no, not again! Now there are no CRAN servers in the Netherlands
(transmart-data originally came from the Hyve in Utrecht). Who to pick next?

Given their tranSMART history, let's opt in R/Makefile for:

R_MIRROR ?= http://cran.ma.imperial.ac.uk

But having changed that, there seems to be a problem with one or more of
the R-packages. For the version of R we have been using - 3.2.1 - some
of the dependencies are now broken.

We try to fix on a version of R so we can avoid changes to the analysis
results - but that can still happen with more recent versions of
packages (for example - survival analysis broke in 16.1 when the package
output format changed).

I was able to get everything to load with the latest R (3.5.1) defined
in R/Makefile ... but have not yet tested the various workflows for any
side effects.

I can raise this with the tranSMART PMC on Monday - in the hope they can
help with testing so we can be confident which R version to upgrade to.

Hope that helps

Peter Rice
Axiomedix Inc.

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[Helmut Spengler]

Hi Peter,

thanks for your reply. It helped a lot!

I used

    R_MIRROR ?= http://cran.ma.imperial.ac.uk 

    R_VERSION = 3.5.1

in R/Makefile and

    desiredRVersion="3.5.1"

in checkR.sh

and also managed to load everything in R/Makefile.

Thanks a lot!

[ssm...@txbiomed.org]

Hi, can you share exactly what your modified on the Makefile?   I changed the R_MIRROR = https://cran.r-project.org which worked fine for installing R, but didn't work to install Rserve.  

Thanks,

Sandy

[Peter Rice]

Hi Sandy,

I updated tranSMART 16.3 to use R_MIRROR = http://cran.ma.imperial.ac.uk

I also had to update the R version number to 3.5.1

When installing the packages there was a dependency on a package nlme
that now requires 3.4.0 or higher.

What was the problem you found with Rserve ?

Peter Rice
Axiomedix Inc.

On 24/09/2018 20:48, ssm...@txbiomed.org wrote:
> Hi, can you share exactly what your modified on the Makefile?   I
> changed the R_MIRROR = https://cran.r-project.org which worked fine for
> installing R, but didn't work to install Rserve.
>
> Thanks,
>
> Sandy
>
> On Friday, September 7, 2018 at 8:44:08 AM UTC-5, Helmut Spengler wrote:
>
> I am trying to install tranSMART 13.3 using the install script
> referenced at
> https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Runtheinstallscript

> <https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Runtheinstallscript>.

>
> When executing the command
>
>      ./Scripts/install-ubuntu/InstallTransmart.sh 2>&1 | tee
> ~/install.log
>
> I get following error message:
>
>
>
>
> ++++++++++++++++++++++++++++
> +  Install R, Rserve and other packages
> ++++++++++++++++++++++++++++
> +  installing R at /home/transmart/transmart/transmart-data/R/root/bin
> make: Entering directory '/home/transmart/transmart/transmart-data/R'
> curl -f http://cran-mirror.cs.uu.nl/src/base/R-3/R-3.2.1.tar.gz
> <http://cran-mirror.cs.uu.nl/src/base/R-3/R-3.2.1.tar.gz> | tar xzf -
>   % Total    % Received % Xferd  Average Speed   Time    Time
>  Time  Current
>                                  Dload  Upload   Total   Spent
> Left  Speed
>   0     0    0     0    0     0      0      0 --:--:-- --:--:--
> --:--:--     0curl: (6) Could not resolve host: cran-mirror.cs.uu.nl

> <http://cran-mirror.cs.uu.nl>

>
>
>
>
> Seems like the host "cran-mirror.cs.uu.nl

> <http://cran-mirror.cs.uu.nl>" dows not exist. Therefore, I tried to

> declare an alternative mirror in
> "transmart/transmart-data/R/Makefile" (e.g.

> https://cran.cnr.berkeley.edu <https://cran.cnr.berkeley.edu>). This

> however resulted in another error:
>
>
> Some packages not installed
> Execution halted
> Makefile:39: recipe for target 'cran_packages' failed
> make: *** [cran_packages] Error 1
>
>
>
> Any ideas on how to solve this problem?
>
> Kind regards
>

> --
> For more ways to get in contact with the tranSMART community visit
> https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support
> ---
> You received this message because you are subscribed to the Google
> Groups "transmart-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to transmart-disc...@googlegroups.com
> <mailto:transmart-disc...@googlegroups.com>.
> To post to this group, send email to transmar...@googlegroups.com
> <mailto:transmar...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/transmart-discuss/795d9811-034f-49e5-9cff-7f3672746e7c%40googlegroups.com
> <https://groups.google.com/d/msgid/transmart-discuss/795d9811-034f-49e5-9cff-7f3672746e7c%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Sandra Smith]

Hi Peter,

That worked! Thank you!

Sandy

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