isuuses in download_registrations and loss of JRCFIB2018F and JRCFIB2018Fraw

[mxdidi]

1. When I use "nat.flybrains::download_jefferislab_registrations()" function, there is an error. "Error in git2r::pull(repo):branch is NULL". I think maybe there is a loss of the file?
2. Here I get one bodyID in the neuprint and find and plot this neuron in natverse. I want to show it in the templatebrain. However, I can't use the two files: JRCFIB2018F and JRCFIB2018Fraw. It return "Error in get(paste0(as.character(x), ".surf")) : can't find the object 'JRCFIB2018Fraw.surf'". And also I can't use the xform_brain form JRCFIB2018Fraw to JFRC2.
   Could anyone answer these questions and give me some instructions to show this known neuron in hemibrain dataset in another template brain? Thanks a lot!

[jefferis]

Dear Xun Ma, thanks for your interest in the natverse and sorry you are having trouble. These are two quite separate problems.

For problem 1, I have just tried and I have no problem running

> nat.flybrains::download_jefferislab_registrations()
Loading required namespace: git2r
$`https://github.com/jefferislab/BridgingRegistrations`
Already up-to-date

$`https://github.com/jefferislab/MirrorRegistrations`
Already up-to-date

$`https://github.com/jefferislab/DrosophilidBridgingRegistrations`
Already up-to-date

Can you do e.g.

natverse::natverse_deps()

and paste the status.

Can you also do:

nat.jrcbrains:::list_saalfeldlab_registrations()

and

R.version

for good measure?

[jefferis]

For the second problem can you give the actual code you are trying? See https://natverse.org/help/ for some ideas about asking questions that are easier to answer.

[mxdidi]

Thank you very much for answering me. It's really nice. :)
For the first question, I used another code in the example: download_jefferislab_registrations("Mirror"). It worked for the mirror and drosophilabridging. Actually, I have downloaded these files before. Now I try to put the folder to the path for the nat:flybrains.
I have ran the codes in your answer.
` > natverse::natverse_deps()
The following packages are either locally installed or information about them is missing!

XML, plotly, brotli, qs, dracor, fafbsegdata, reticulate, RcppMsgPack, httptest, RSQLite, dbplyr, arrow, tidyr, nat.ants

Please install them manually from their appropriate source locations

The following natverse dependencies are out-of-date, see details below:

We recommend updating them by running:
natverse_update(update=TRUE)

package remote local source repo status

---

commonmark 1.8.1 1.8.0 CRAN https://cran.rstudio.com/ ✖
lpSolve 5.6.17 5.6.16 CRAN https://cran.rstudio.com/ ✖
lubridate 1.9.0 1.8.0 CRAN https://cran.rstudio.com/ ✖
magic 1.6-1 1.6-0 CRAN https://cran.rstudio.com/ ✖
pkgload 1.3.2 1.3.0 CRAN https://cran.rstudio.com/ ✖
processx 3.8.0 3.7.0 CRAN https://cran.rstudio.com/ ✖
RCurl 1.98-1.9 1.98-1.8 CRAN https://cran.rstudio.com/ ✖ `

For the jrcbrains:
[1] "/Users/max/Library/Application Support/R/nat.jrcbrains/JRC2018F_FAFB"
[2] "/Users/max/Library/Application Support/R/nat.jrcbrains/JRC2018F_FCWB"
[3] "/Users/max/Library/Application Support/R/nat.jrcbrains/JRC2018F_JFRC2013"
[4] "/Users/max/Library/Application Support/R/nat.jrcbrains/JRC2018F_JRCFIB2018F"
[5] "/Users/max/Library/Application Support/R/nat.jrcbrains/JRC2018U_JRC2018F"

R_version
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 2.1
year 2022
month 06
day 23
svn rev 82513
language R
version.string R version 4.2.1 (2022-06-23)
nickname Funny-Looking Kid

I will update those packages and install needed packages.

[mxdidi]

For the second question, here are my codes.
'plot3d(JRCFIB2018F)' returns Error in get(paste0(as.character(x), ".surf")) : can't find 'JRCFIB2018F.surf'

'n1 = neuprint_read_neurons(1139667240)
n1.jrc2018=xform_brain(n1, sample = JRCFIB2018F, reference=JRC2018F)'
returns
Transforming neurons using the sequence: JRCFIB2018F->JRC2018F
Error in myjcall(mytransform, "V", "apply", points[i, ], q) :
method apply with signature ([I[D)V not found

[mxdidi]

Dear Dr. Jefferis,

I think I have fixed these questions. I found the saalfeldlab registrations path was not added successfully. And the second question (do the transform and plot the neuron) is now fixed.
The function in the first question still doesn't work in my computer. I will check the R and related packages to find the problems.
Thank you very much for investing your time to provide these clear explanations.

All the best,
Xun Ma