Installing Rapache

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Venkatachalam Kannadasan

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Jun 29, 2016, 2:25:13 AM6/29/16
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Hi Phil


I was trying to install Rapache from Harvard website but found the following problems. Can you please let me know where can I find these files.


rpm -ivh http://mirror.hmdc.harvard.edu/HMDC-Public/RedHat-6/rapache-1.2.6-rpm0.x86_64.rpm

Retrieving http://mirror.hmdc.harvard.edu/HMDC-Public/RedHat-6/rapache-1.2.6-rpm0.x86_64.rpm

error: Failed dependencies:

        libicui18n.so.42()(64bit) is needed by rapache-1.2.6-rpm0.x86_64

        libicuuc.so.42()(64bit) is needed by rapache-1.2.6-rpm0.x86_64


We are using Linux OS "Red Hat Enterprise Linux Server release 7.2 (Maipo)" and I am not sure where to find these files.


Thank you for your kind help.


Regards

Venki




Philip Durbin

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Jun 29, 2016, 1:02:45 PM6/29/16
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Hi Venki,

Instead of `rpm` I would suggest using `yum` instead, which will pull in dependencies such as libicu, which is what the error you mentioned seems to be about.

You would run this instead:

I see you're on RHEL/CentOS 7 rather than RHEL/CentOS 6 (which is what the Dataverse dev team uses), but hopefully, you'll see something similar to the output below and can just hit "y" to install all the dependencies.

[root@dvnweb-vm2 ~]# yum install http://mirror.hmdc.harvard.edu/HMDC-Public/RedHat-6/rapache-1.2.6-rpm0.x86_64.rpm
Loaded plugins: fastestmirror, priorities, protectbase, security, transaction-json, versionlock
Setting up Install Process
rapache-1.2.6-rpm0.x86_64.rpm                                                                                                       |  59 kB     00:00    
Examining /var/tmp/yum-root-nl7ona/rapache-1.2.6-rpm0.x86_64.rpm: rapache-1.2.6-rpm0.x86_64
Marking /var/tmp/yum-root-nl7ona/rapache-1.2.6-rpm0.x86_64.rpm to be installed
Loading mirror speeds from cached hostfile
 * base: mirror.hmdc.harvard.edu
 * centosplus: mirror.hmdc.harvard.edu
 * contrib: mirror.hmdc.harvard.edu
 * epel: mirror-60ox.priv.hmdc.harvard.edu
 * extras: mirror.hmdc.harvard.edu
 * groonga: mirror-60ox.priv.hmdc.harvard.edu
 * hmdc: mirror-60ox.priv.hmdc.harvard.edu
 * htcondor: mirror-60ox.priv.hmdc.harvard.edu
 * puias_6_computational: mirror-60ox.priv.hmdc.harvard.edu
 * puias_6_core_base: mirror-60ox.priv.hmdc.harvard.edu
 * puias_6_unsupported: mirror-60ox.priv.hmdc.harvard.edu
 * rpmforge: mirror-60ox.priv.hmdc.harvard.edu
 * sl_swcollections: mirror-60ox.priv.hmdc.harvard.edu
 * updates: mirror.hmdc.harvard.edu
 * vmware_tools_55: mirror-60ox.priv.hmdc.harvard.edu
 * xpra: mirror-60ox.priv.hmdc.harvard.edu
1817 packages excluded due to repository priority protections
0 packages excluded due to repository protections
Resolving Dependencies
--> Running transaction check
---> Package rapache.x86_64 0:1.2.6-rpm0 will be installed
--> Processing Dependency: R-core for package: rapache-1.2.6-rpm0.x86_64
--> Processing Dependency: libapreq2 for package: rapache-1.2.6-rpm0.x86_64
--> Processing Dependency: libR.so()(64bit) for package: rapache-1.2.6-rpm0.x86_64
--> Processing Dependency: libapreq2.so.3()(64bit) for package: rapache-1.2.6-rpm0.x86_64
--> Processing Dependency: libicui18n.so.42()(64bit) for package: rapache-1.2.6-rpm0.x86_64
--> Processing Dependency: libicuuc.so.42()(64bit) for package: rapache-1.2.6-rpm0.x86_64
--> Running transaction check
---> Package R-core.x86_64 0:3.3.0-8.el6 will be installed
--> Processing Dependency: libgfortran.so.3(GFORTRAN_1.0)(64bit) for package: R-core-3.3.0-8.el6.x86_64
--> Processing Dependency: cups for package: R-core-3.3.0-8.el6.x86_64
--> Processing Dependency: libtk8.5.so()(64bit) for package: R-core-3.3.0-8.el6.x86_64
--> Processing Dependency: libtcl8.5.so()(64bit) for package: R-core-3.3.0-8.el6.x86_64
--> Processing Dependency: libgfortran.so.3()(64bit) for package: R-core-3.3.0-8.el6.x86_64
--> Processing Dependency: libXmu.so.6()(64bit) for package: R-core-3.3.0-8.el6.x86_64
---> Package libapreq2.x86_64 0:2.13-1.el6 will be installed
---> Package libicu.x86_64 0:4.2.1-14.el6 will be installed
--> Running transaction check
---> Package cups.x86_64 1:1.4.2-74.el6 will be installed
--> Processing Dependency: portreserve for package: 1:cups-1.4.2-74.el6.x86_64
--> Processing Dependency: poppler-utils for package: 1:cups-1.4.2-74.el6.x86_64
---> Package libXmu.x86_64 0:1.1.1-2.el6 will be installed
---> Package libgfortran.x86_64 0:4.4.7-17.el6 will be installed
---> Package tcl.x86_64 1:8.5.7-6.el6 will be installed
---> Package tk.x86_64 1:8.5.7-5.el6 will be installed
--> Running transaction check
---> Package poppler-utils.x86_64 0:0.12.4-10.el6 will be installed
--> Processing Dependency: poppler = 0.12.4-10.el6 for package: poppler-utils-0.12.4-10.el6.x86_64
--> Processing Dependency: libpoppler.so.5()(64bit) for package: poppler-utils-0.12.4-10.el6.x86_64
--> Processing Dependency: libopenjpeg.so.2()(64bit) for package: poppler-utils-0.12.4-10.el6.x86_64
--> Processing Dependency: liblcms.so.1()(64bit) for package: poppler-utils-0.12.4-10.el6.x86_64
---> Package portreserve.x86_64 0:0.0.4-11.el6 will be installed
--> Running transaction check
---> Package lcms-libs.x86_64 0:1.19-1.el6 will be installed
---> Package openjpeg-libs.x86_64 0:1.3-11.el6 will be installed
---> Package poppler.x86_64 0:0.12.4-10.el6 will be installed
--> Processing Dependency: poppler-data >= 0.4.0 for package: poppler-0.12.4-10.el6.x86_64
--> Running transaction check
---> Package poppler-data.noarch 0:0.4.0-1.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

==================================================================================================================================================================
 Package                              Arch                          Version                               Repository                                         Size
==================================================================================================================================================================
Installing:
 rapache                              x86_64                        1.2.6-rpm0                            /rapache-1.2.6-rpm0.x86_64                        141 k
Installing for dependencies:
 R-core                               x86_64                        3.3.0-8.el6                           epel                                               52 M
 cups                                 x86_64                        1:1.4.2-74.el6                        base                                              2.3 M
 lcms-libs                            x86_64                        1.19-1.el6                            base                                              100 k
 libXmu                               x86_64                        1.1.1-2.el6                           base                                               66 k
 libapreq2                            x86_64                        2.13-1.el6                            epel                                               56 k
 libgfortran                          x86_64                        4.4.7-17.el6                          base                                              268 k
 libicu                               x86_64                        4.2.1-14.el6                          base                                              4.9 M
 openjpeg-libs                        x86_64                        1.3-11.el6                            base                                               60 k
 poppler                              x86_64                        0.12.4-10.el6                         base                                              558 k
 poppler-data                         noarch                        0.4.0-1.el6                           base                                              2.2 M
 poppler-utils                        x86_64                        0.12.4-10.el6                         base                                               74 k
 portreserve                          x86_64                        0.0.4-11.el6                          base                                               23 k
 tcl                                  x86_64                        1:8.5.7-6.el6                         base                                              1.9 M
 tk                                   x86_64                        1:8.5.7-5.el6                         base                                              1.4 M

Transaction Summary
==================================================================================================================================================================
Install      15 Package(s)

Total size: 66 M
Total download size: 66 M
Installed size: 151 M
Is this ok [y/N]:

I hope this helps. Please let me know if it does and I'll add a note to improve what's written at http://guides.dataverse.org/en/4.3.1/installation/r-rapache-tworavens.html#c-rapache

Phil
 

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Venkatachalam Kannadasan

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Jul 1, 2016, 2:32:43 AM7/1/16
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Hi Phil

When I run that command I get the following error

Loaded plugins: product-id, search-disabled-repos, subscription-manager
rapache-1.2.6-rpm0.x86_64.rpm                            |  59 kB     00:01
Examining /var/tmp/yum-root-DdWfFC/rapache-1.2.6-rpm0.x86_64.rpm: rapache-1.2.6-rpm0.x86_64
Marking /var/tmp/yum-root-DdWfFC/rapache-1.2.6-rpm0.x86_64.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package rapache.x86_64 0:1.2.6-rpm0 will be installed
--> Processing Dependency: libicui18n.so.42()(64bit) for package: rapache-1.2.6-rpm0.x86_64
epel/x86_64/metalink                                     | 4.7 kB     00:00
epel                                                     | 4.3 kB     00:00
rhel-7-server-extras-rpms                                | 2.9 kB     00:00
rhel-7-server-optional-rpms                              | 3.5 kB     00:00
rhel-7-server-rpms                                       | 3.7 kB     00:00
rhel-server-rhscl-7-rpms                                 | 3.4 kB     00:00
vmware-tools                                             |  951 B     00:00
(1/4): epel/x86_64/group_gz                                | 170 kB   00:02
(2/4): epel/x86_64/updateinfo                              | 577 kB   00:02
(3/4): rhel-7-server-rpms/7Server/x86_64/primary_db        |  22 MB   00:02
(4/4): epel/x86_64/primary_db                              | 4.2 MB   00:06
rhel-7-server-rpms/7Server/x86_64/updateinfo               | 1.2 MB   00:00
--> Processing Dependency: libicuuc.so.42()(64bit) for package: rapache-1.2.6-rpm0.x86_64
--> Finished Dependency Resolution
Error: Package: rapache-1.2.6-rpm0.x86_64 (/rapache-1.2.6-rpm0.x86_64)
           Requires: libicuuc.so.42()(64bit)
Error: Package: rapache-1.2.6-rpm0.x86_64 (/rapache-1.2.6-rpm0.x86_64)
           Requires: libicui18n.so.42()(64bit)
**********************************************************************
yum can be configured to try to resolve such errors by temporarily enabling
disabled repos and searching for missing dependencies.
To enable this functionality please set 'notify_only=0' in /etc/yum/pluginconf.d/search-disabled-repos.conf
**********************************************************************

Error: Package: rapache-1.2.6-rpm0.x86_64 (/rapache-1.2.6-rpm0.x86_64)
           Requires: libicuuc.so.42()(64bit)
Error: Package: rapache-1.2.6-rpm0.x86_64 (/rapache-1.2.6-rpm0.x86_64)
           Requires: libicui18n.so.42()(64bit)
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

For your advice please.

Thanks and Regards
Venki
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Philip Durbin

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Jul 1, 2016, 6:43:26 AM7/1/16
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Uh oh, that's no good. :(

Can you please email sup...@dataverse.org about this? The developer who wrote http://guides.dataverse.org/en/4.4/installation/r-rapache-tworavens.html (Leonid) may have a suggestion.

Members of the community who have already upgraded to RHEL or CentOS 7 may be able to help. I think Odum, DANS, and Johns Hopkins have but I don't know if they are using rApache. Maybe there are others out there who have figured this out. The thing about RHEL is that it's supported for a very long time so technically, the Harvard Dataverse has until 2020 to upgrade from RHEL 6. Let's try to find you a solution before then. :)

http://stackoverflow.com/questions/34756938/issues-with-installing-r-on-centos-7 has me wondering if you were able to install R or not. The previous step was `yum install R R-devel`. Can you please provide the output of `rpm -qi R`? I'm wondering if your version of R comes from EPEL or not.

I hope this helps. Please do open a support ticket.

Thanks,

Phil


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Venkatachalam Kannadasan

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Jul 1, 2016, 10:47:11 PM7/1/16
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Hi Phil

Please see the output of the command 'rpm -qi R' below

[venki@dataversedev ~]$ rpm -qi R
Name        : R
Version     : 3.3.0
Release     : 3.el7
Architecture: x86_64
Install Date: Mon 06 Jun 2016 10:38:01 PM
Group       : Applications/Engineering
Size        : 0
License     : GPLv2+
Signature   : RSA/SHA256, Mon 16 May 2016 11:55:59 PM, Key ID 6a2faea2352c64e5
Source RPM  : R-3.3.0-3.el7.src.rpm
Build Date  : Sat 14 May 2016 03:58:45 AM
Relocations : (not relocatable)
Packager    : Fedora Project
Vendor      : Fedora Project
URL         : http://www.r-project.org
Summary     : A language for data analysis and graphics
Description :
This is a metapackage that provides both core R userspace and
all R development components.

R is a language and environment for statistical computing and graphics.
R is similar to the award-winning S system, which was developed at
Bell Laboratories by John Chambers et al. It provides a wide
variety of statistical and graphical techniques (linear and
nonlinear modelling, statistical tests, time series analysis,
classification, clustering, ...).

R is designed as a true computer language with control-flow
constructions for iteration and alternation, and it allows users to
add additional functionality by defining new functions. For
computationally intensive tasks, C, C++ and Fortran code can be linked
and called at run time.

I will send an email to the support to ask for help on the installation.

Regards
Venki
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Philip Durbin

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Jul 14, 2016, 4:14:01 PM7/14/16
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Hi Venki,

Nice meeting you at the community meeting! As I mentioned in person, I created an issue about running rApache on RHEL/CentOS 7 and just successfully built and installed an RPM. The instructions for how to download and install the RPM are in a comment on the issue: https://github.com/IQSS/dataverse/issues/3208

I actually don't know much about rApache so I'm hoping that you or someone else in the Dataverse community that has access to RHEL/CentOS 7 (again, the dev team uses CentOS 6) can try out the rApache RPM and let me know if it works.

Phil

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Donald Sizemore II

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Jul 15, 2016, 8:16:32 AM7/15/16
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Hello,

I did a test installation of TwoRavens on a CentOS 6-based test system, and ~almost~ got it working!

I'm trying today on our soon-to-be-production RHEL7 machine. To get the missing packages not included in standard RHEL/CentOS:

CentOS users may simply install the epel-release RPM.

RHEL users will want to go into their organization's respective RHN interface, find the particular machine in question and:

• click on "Subscribed Channels: Alter Channel Subscriptions"
• enable EPEL, Server Extras, Server Optional

Back on the server, run a yum check-update and be sure the new repositories show up. If you feel that your package database has gotten corrupted or in a bad caching state, simply run

$ yum clean all

to clear the cache and do another check-update.

I hope this helps,
Donald

Venkatachalam Kannadasan

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Aug 10, 2016, 11:23:23 PM8/10/16
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Hi Donald

Thanks for the details. I have installed it in my development server and it works fine. 

Thanks and Regards
Venki

Venkatachalam Kannadasan

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Aug 10, 2016, 11:27:06 PM8/10/16
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Hi Phil

I have successfully installed rapache and two ravens. But somehow the data is not showing up in TwoRavens. Not sure whether is it a port problem. Can you advise. I have included the screenshot below. 

Thanks and Regards
Venki
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Donald Sizemore II

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Aug 11, 2016, 6:17:49 AM8/11/16
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I have successfully installed rapache and two ravens. But somehow the data is not showing up in TwoRavens.

Hello,

I ran into this. The version of preprocess.R included in the Dataverse warfile isn't quite up to rev. with TwoRavens and I believe the current version will be distributed with Dataverse 4.5.

Assuming you used the default installation paths for Dataverse and TwoRavens, you'd want to

$ (sudo) cp /var/www/html/dataexplore/rook/preprocess/preprocess.R /usr/local/glassfish4/glassfish/domains/domain1/applications/dataverse-4.4/WEB-INF/classes/edu/harvard/iq/dataverse/rserve/scripts/preprocess.R

then look in your glassfish/Dataverse files/ hierarchy for any .prep files automatically created by TwoRavens (in the study directory alongside the source data) and delete them.

In addition to setting the :TwoRavensUrl Dataverse option, I also had to
$ curl -X PUT -d true http://localhost:8080/api/admin/settings/:TwoRavensTabularView​

I hope this helps?
Donald

Venkatachalam Kannadasan

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Aug 14, 2016, 10:13:23 PM8/14/16
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Dear Donald

Thank you for the reply and for the tips to get this working. I have copied the said file to the correct directory but couldnt find and .prep file. Infact I couldnt locate the study folder. Can you please help to give me the actual path where i should look for .prep files?

I am still having the problem. I think it could be because of the old .prep files.

Regards
Venki

don sizemore

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Aug 15, 2016, 7:21:12 AM8/15/16
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Hello,

The study folder is set by the config.files.dir option in /usr/local/glassfish4/glassfish/domains/domain1/config/domain.xml

Unless you've changed the default I think it's /usr/local/glassfish4/glassfish/domains/domain1/files

Something like:

$ find /usr/local/glassfish4/glassfish/domains/domain1 -type f -name \*.prep

should return a list of them. Please let me know if that doesn't do the trick?

Donald

painstakingly pecked on my iPhone.
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Venkatachalam Kannadasan

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Aug 24, 2016, 11:02:31 PM8/24/16
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Dear Donald

Sorry for the late reply. I couldnt find any files under the directory files with the extension .prep. I am not sure whether is this to do with the configuration? We are running apache on port 80 and 443 and use apache as front end to access dataverse. Glassfish is running on the default ports 8080 and 8181.

Thanks and Regards
Venki
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Don Sizemore

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Aug 25, 2016, 8:07:13 AM8/25/16
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Hello,

Next you might look at the URLs you're passing in the TwoRavens
source. Like you, I'm fronting Glassfish with Apache and am using the
below successfully:

rook/rookutils.R: url <-
paste("https://dataverse-test.irss.unc.edu/custom/preprocess_dir/preprocessSubset_",sessionid,".txt",sep="")
rook/rookutils.R:
imageVector[[qicount]]<<-paste("https://dataverse-test.irss.unc.edu/custom/pic_dir/",
mysessionid,"_",mymodelcount,qicount,".png", sep = "")
app_ddi.js: dataverseurl="https://dataverse-test.irss.unc.edu";
app_ddi.js: var rappURL = "https://dataverse-test.irss.unc.edu/custom/";
tworavens/app_ddi.js: hostname="localhost:8080";

You might also double-check:
app_ddi.js:var production=true;

and ensure that rook/*.R set production<-TRUE (they're set to FALSE
out of the box).

Have you tried turning on your browser's javascript console to look
for any errors on page load/execution?

Donald


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