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13:11 rebecabarros
hey pdurbin, thanks for answer again. I'm following the documentation (http://guides.dataverse.org/en/latest/installation/r-rapache-tworavens.html) but I'm getting error when try to run the script for extra R packages.
13:12 pdurbin
rebecabarros: so step 2
13:15 rebecabarros
pdurbin: yes. the script fail in the first package (Rcpp 0.12.9), the download is successful but when it try to install, I get 'Fatal error: unable to open the base package' in the log.
13:16 pdurbin
rebecabarros: this is when you're running the `r-setup.sh` script?
13:17 rebecabarros
pdurbin: yes
13:18 pdurbin
I'm taking a look at the script now. This: https://github.com/IQSS/TwoRavens/blob/a6869eb28693d6df529e7cb3888c40de5f302b66/r-setup/r-setup.sh
13:19 pdurbin
I'm seeing "Rcpp 0.12.9" in package-versions.txt
13:23 pdurbin
rebecabarros: when you type just `R` at the command line an hit enter, do you see output similar to this? https://paste.fedoraproject.org/paste/YTBjyvuOrD7B9L~7yTtxAg/raw
13:28 rebecabarros
pdurbin: I do not, I get the same error: 'Fatal error: unable to open the base package'. So the problem is R installation in my computer.
13:29 pdurbin
I think you're right. Someone wrote that the fix was to reinstall R at https://apple.stackexchange.com/questions/251249/r-programming-language-breaks-and-must-be-reinstalled
13:30 pdurbin
rebecabarros: are you using CentOS? Which version?
13:31 rebecabarros
pburbin: yes. CentOS 7
13:32 pdurbin
Ok. Should work. What version does it show when you run `rpm -q R`?
13:33 pdurbin
(On my CentOS 6 server I see "R-3.4.1-1.el6.x86_64".)
13:34 rebecabarros
R-3.4.1-1.el7.x86_64
13:35 pdurbin
Ok, thanks. Well, I think the next step is to be able to run just the `R` command and not have it give that error you're seeing.
13:53 rebecabarros
Strange thing is, I uninstall the R package (following the tips from the two ravens tutorial), then I ran 'rpm -q R' and ok, it gives that I do not have R installed. But when I type 'R' in my command line I get the same erro 'unable to open...'
13:53 rebecabarros
I will try to look into this, thanks for the help, pdurbin.
13:54 pdurbin
rebecabarros: sure. You might want to try asking at https://serverfault.com
14:58 pdurbin
rebecabarros: I'm asking at https://irclog.perlgeek.de/crimsonfu/2017-09-13#i_15157265
15:02 rebecabarros
pdurbin: I have solved. I uninstall all R packages (including R-core, that I did not knew about) following this tip: https://stackoverflow.com/a/29439091/5881002 and then installed R again. Know the 'R' command works in my command line and the r-setup script is running without errors so far.
15:06 pdurbin
rebecabarros: fantastic! Good job.
15:07 pdurbin
rebecabarros: is there anything you think we should improve in the Dataverse Installation Guide?
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15:13 rebecabarros
I guess we should point out about R-core package when is recommended for the user reinstall R before start a new installation/upgrade of Two Ravens and RApache.
15:15 pdurbin
rebecabarros: ok. Can you please create an issue about this at https://github.com/IQSS/dataverse/issues ?
15:16 rebecabarros
Yes, for sure. Thanks again for all the help.
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15:24 mdehollander
Question: I am running Dataverse in a VM using Vagrant. I am trying the file upload via the browser, and I am not able to upload several filetypes like PDF, GZ, TAB. They stay with a full blue bar in the upload area. Other files like tsv, docx appear with a M5 checksum in the box below. Is there a default restricting on supported file formats?
15:38 pdurbin
mdehollander: what does the blue bar say?
15:40 mdehollander
it shows the filename, the filesize, then the blue bar, and then a cross. Nothing else, no message
15:41 mdehollander
Is there a dataverse logfile I could check?
15:43 pdurbin
mdehollander: yes. server.log. Can you please upload a screenshot to https://imgur.com or similar?
15:43 pdurbin
/usr/local/glassfish4/glassfish/​domains/domain1/logs/server.log
15:46 pdurbin
rebecabarros: thanks!
15:53 mdehollander
https://imgur.com/a/PvdMT
15:53 mdehollander
Now on a Ubuntu laptop with Firefox it sometimes allows upload of for example PDF, and sometimes it hangs
15:54 mdehollander
Before I tried it on a windows desktop using firefox
15:54 mdehollander
Can it be a configuration issues when running the Vagrantfile from the github repo?
15:55 pdurbin
I don't think so. It should work. Anything interesting in server.log?
15:56 mdehollander
The server.log does not contain any relevant information, at least no new messages based on the timestamp
15:57 pdurbin
mdehollander: do you might emailing the server.log file to support
15:57 mdehollander
here are the last lines: https://paste.ubuntu.com/25528206/ . Not that the timestamps are not correct because the time of the vm is wrong
15:59 pdurbin
mdehollander: which commit are you on? 9d319bd?
16:01 pdurbin
mdehollander: one thing you could try is `vagrant destroy` to kill the VM , then switch to a tagged release, such as v4.7.1 with `git checkout`, then run `vagrant up` and see if you observe the same behavior in a tagged release.
16:03 mdehollander
Indeed. I just notice that I am on develop (9d319bd83b1d63df70c6d1e839d32ae2df53aa95). I will send the server.log anyways and give it a try on a tagged release. Thanks! (have to go now ;)
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16:47 Thalia_UM
Hello
16:47 Thalia_UM
Good morning
16:47 Thalia_UM
Hi Philip
16:47 Thalia_UM
I have a cuestion about DOIs
16:49 Thalia_UM
Do you know, What is the cost for DOI?
16:49 Thalia_UM
for each identifier
17:24 pdurbin
Thalia_UM: I don't know. You would need to ask DataCite. Please see http://guides.dataverse.org/en/4.7.1/installation/config.html#persistent-identifiers-and-publishing-datasets for their website.
17:47 Thalia_UM
Thank you Philip :)
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