fail to download flycircuit data

jefferislab / NBLAST_on-the-fly

Web application demonstrating NBLAST neuron similarity/search

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fail to download flycircuit data #100

Open H-Chiu opened 5 years ago

H-Chiu commented 5 years ago

When I executed the commend "source("download_data.R")" under NBLAST_on-the-fly-master, an error showed: Error in library(flycircuit) : there is no package called ‘flycircuit’. Would you mind letting me know how to fix this? Any help would be very appreciated!

jefferis commented 5 years ago

Thanks for your interest. Please see https://github.com/jefferis/flycircuit for install instructions and further details.

H-Chiu commented 5 years ago

Thank you so much for your quick response! I am sorry that I have to bother you with two more problems: (1) When I installed the flycircuit package, the compilation for package 'igraph' failed, the complete error message is as below, make: gfortran-4.8: No such file or directory make: *** [AMD/Source/amd.o] Error 1 ERROR: compilation failed for package ‘igraph’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/igraph’
restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/igraph’ Error in i.p(...) : (converted from warning) installation of package ‘igraph’ had non-zero exit status

(2) When I tried to run "library(shiny)" (, another error is shown, "Error in library: there is no package called ‘shinyURL’"

Would you mind letting me know how to fix them? Thank you very very much!

jefferis commented 5 years ago

First a note, you appear to have a rather old install of R (3.3.x). If you have a sufficiently recent version of macosx (>=10.11), I would recommend upgrading to R 3.5.3. See https://cran.r-project.org/bin/macosx/. If you use the current version of R, then you should not need to compile any packages.

If you cannot upgrade R, you need to install fortran in order to compile igraph from source. see https://cran.r-project.org/bin/macosx/ and https://cran.r-project.org/bin/macosx/tools

You can install like so:

devtools::install_github("aoles/shinyURL")

jefferis commented 5 years ago

Also can I just ask which installation instructions you are following? If you follow the instructions in the https://github.com/jefferislab/NBLAST_on-the-fly README, then in theory you should not have had the missing package errors mentioned above.

H-Chiu commented 5 years ago

Dear Dr. Jefferis, Thank you so much again for your time and help! I had successfully run NBlast on my esktop after upgrading my os system. I was hesitant to do so because of the compatibility issue for other softwares. Just in case it would help any other programming kindergartner like me, after upgrading the os and installing R3.5.3, I still need to install Xcode for running the package install code. I really appreciate your help and the super useful tools you kindly share with the community!