Can't find the registration

[lankiszhang]

Dear all,

I am trying to use nblast on Ubuntu. After solving a lot of dependency problem, I was finally at the step of xform_brain. I got an error retrun from the function:

`Error in value[[3L]](cond) : 
  Unable to find bridging registration between JRC2018F and JRCFIB2018F`

I reinstall the nat.jrcbrain and download saalfeldlab_registrations, but it only finish the 6 downloads without re-do the registration.
So I tried register_saalfeldlab_registrations() manually, and it returns:

`Adding h5reg in forward direction
Adding h5reg in reverse direction
Adding h5reg in forward direction
Adding h5reg in reverse direction
Adding h5reg in forward direction
Adding h5reg in reverse direction
Adding h5reg in forward direction
Adding h5reg in reverse direction
Adding h5reg in forward direction
Adding h5reg in reverse direction
Adding h5reg in forward direction
Adding h5reg in reverse direction

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018F_FAFB
TRUE

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018F_FCWB
TRUE

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018F_JFRC2010
TRUE

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018F_JFRC2013
TRUE

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018F_JRCFIB2018F
TRUE

/home/jiajun/.local/share/R/nat.jrcbrains/JRC2018U_JRC2018F
TRUE

Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
display list redraw incomplete
2: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
3: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state`

I also tried plot(bridging_graph(),vertex.size=15,edge.arrow.size =.5), the figure looks pretty normal.

I also got a notification when I do library(nat.jrcbrains) that I don't have extra transformation. And I got a no TLS stream available error when I tried download_jefferislab_registrations().

I really don't know what to do now. Could you give me any advice on my problem? Thank you in advance!

Best,
Jiajun

[jefferis]

Dear Jiajun,

Thanks again for your interest in the natverse. A few things

1. If you're on mac or ubuntu, you can always try the docker image if you want to get a ready to go image. https://github.com/jefferis/r-natverse#quick-start
2. We welcome any information about dependency install problems. We made the natmanager package to try to work around things that we are aware of (including limiatation of using github to distribute packages). You could raise an issue with details.
3. download_jefferislab_registrations uses git2r to download registrations from github. It seems that there is a problem with the link between libgit2 and openssl. See e.g. no TLS stream available ropensci/git2r#410. Do you want to try installing git2r from source?
4. now for the main problem, I am a bit puzzled from the description. It sounds like you have done the right things. Could you run a couple of things and tell me the results?

nat.templatebrains::allreg_dataframe()
nat.templatebrains::shortest_bridging_seq(sample = 'JRC2018F', reference = "JRCFIB2018F")
devtools::session_info()

My best guess right now is that you have an old version of the nat.templatebrains package installed, perhaps via CRAN, rather than via github and the natmanager package as recommended by http://natverse.org.

With best wishes,

Greg.

[lankiszhang]

Dear Greg, Thank you for your kindly help and sorry for my late reply. Due to the strike of public transport in Cologne last two days, I could only get access to our server today. We have found natverse really helpful for our project. I will try with the docker images on our server. I would also like to re-install natverse by the natmanager packages later on my server, to see if I could get rid of those dependency issues. If I still get something, I would like to raise an issue on natmanager. I got the SSL issue again today, and it seems due to the server is not yet permanently connected to internet. I will check it with the IT department of our university again. The results of the three lines of codes are like this: All_reg_dataframe Shortest bridging seq: Session info: As the results are quiet long lists, I also add them in the attachment. Best wishes, Jiajun 发送自 Windows 10 版邮件应用 发件人: Gregory Jefferis 发送时间: 2020年10月18日 17:59 收件人: natverse/nat.jrcbrains 抄送: lankiszhang; Author 主题: Re: [natverse/nat.jrcbrains] Can't find the registration (#12) Dear Jiajun, Thanks again for your interest in the natverse. A few things 1. If you're on mac or ubuntu, you can always try the docker image if you want to get a ready to go image. https://github.com/jefferis/r-natverse#quick-start 2. We welcome any information about dependency install problems. We made the natmanager package to try to work around things that we are aware of (including limiatation of using github to distribute packages). You could raise an issue with details. 3. download_jefferislab_registrations uses git2r to download registrations from github. It seems that there is a problem with the link between libgit2 and openssl. See e.g. ropensci/git2r#410. Do you want to try installing git2r from source? 4. now for the main problem, I am a bit puzzled from the description. It sounds like you have done the right things. Could you run a couple of things and tell me the results? nat.templatebrains::allreg_dataframe() nat.templatebrains::shortest_bridging_seq(sample = 'JRC2018F', reference = "JRCFIB2018F") devtools::session_info() My best guess right now is that you have an old version of the nat.templatebrains package installed, perhaps via CRAN, rather than via github and the natmanager package as recommended by http://natverse.org. With best wishes, Greg. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[jefferis]

Dear @lankiszhang,

As the results are quiet long lists, I also add them in the attachment.

I think you need to add attachments via the github site not via email. If you have trouble you can contact me directly by email.

Best,

Greg.

[lankiszhang]

Dear Greg,

Sorry, I didn't realize that the file wouldn't be attached by replying via email. Here are the results.

debug_report.zip

Best wishes,
Jiajun