In Julia Studio 0.4.4 on Mac OS X 10.9, I am unable to load the Distance package.
When I run:
julia> using Distance
Julia studio terminal do not respond, it never goes back to the prompt. I have tried to reinstall the package as well as to remove the ~/.julia folder, but the problem persists.
julia> Pkg.status()
Required packages:
- DataFrames 0.4.3
- Distance 0.2.6
- IJulia 0.1.11 55b60c47 (dirty)
- RDatasets 0.1.1
Additional packages:
- BinDeps 0.2.12
- Blocks 0.0.4
- DataArrays 0.0.3
- GZip 0.2.12
- Homebrew 0.0.6
- JSON 0.3.5
- Nettle 0.1.3
- NumericExtensions 0.3.6
- REPLCompletions 0.0.1
- SortingAlgorithms 0.0.1
- StatsBase 0.3.8
- URIParser 0.0.2
- ZMQ 0.1.11
Thank you very much!
Related
When I try to update to the latest version of the tibble package, I am unable to access the binary version 3.1.0 from CRAN. I am given the option to install 3.1.0 from source, but I am running MacOS and unfortunately do not have sufficient hard drive space to install xcode, meaning that I get an error every time I try to install from source. The CRAN tibble page indicates that 3.1.0 should be available as a binary package. Does anyone know why I'm not able to install tibble 3.1.0 as a binary package? Here is what I see when I try to install:
> install.packages('tibble')
There are binary versions available but the source versions are later:
binary source needs_compilation
rlang 0.4.5 0.4.10 TRUE
vctrs 0.2.4 0.3.6 TRUE
tibble 2.1.3 3.1.0 TRUE
Hello stackoverflow community,
I upgraded to the latest version of R and R studio this week, and have my R sessions encountering fatal error whenever I try to load the package raster.
I tried looking at the dependencies of the package, and re-installed all of them just to be sure.
# Install dependencies
db <- available.packages()
(deps <- tools::package_dependencies("raster", db)$raster)
# [1] "sp" "Rcpp" "methods"
install.packages(deps)
Any ideas?
Below are my session infos.
devtools::session_info("raster")
─ Session info ───────────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os macOS Mojave 10.14.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-04-17
─ Packages ───────────────────────────────────────────────────────────────────────
package * version date lib source
lattice * 0.20-41 2020-04-02 [1] CRAN (R 3.6.2)
raster 3.0-12 2020-01-30 [1] CRAN (R 3.6.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)
sp 1.4-1 2020-02-28 [1] CRAN (R 3.6.0)
[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
While looking for a solution, I also found out that my Makevars file is incomplete. I used the solution described in here, which asks RStudio to ensure it always saves files with a trailing newline, but it doesn't work here.
Problem is I don't know if I have had this issue for a long time, or whether it is related to the raster issue.
I tried loading >50 other packages, and the error seems to be tied to the raster library.
> writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
##CC=clang
##CXX=clang++
CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
CC = gcc
CXX=/usr/local/bin/g++-9
CXX1X=/usr/local/clang6/bin/clang++
CXX98=/usr/local/clang6/bin/clang++
CXX11=/usr/local/clang6/bin/clang++
CXX14=/usr/local/clang6/bin/clang++
CXX17=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib
Warning message:
In readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")) :
incomplete final line found on '/Users/Rosalie/.R/Makevars'
Thanks a lot in advance for any help you may be able to provide. I really have no idea what to test next!
Best,
Rosalie
The issue was with clang.
I first updated to macOS Catalina 10.15.4, then uninstalled the R development toolchain I had for previous version using this code. Then, I used some here:
In the terminal, I used the code xcode-select --install, that open a pop-up window. Press "Install", and follow the steps to install xcode.
Verify installation by taping in gcc --version.
Then, download and install the appropriate gfortran binary find correct version here.
In R, I re-installed Rcpp and raster install.packages("Rcpp", "raster").
I am now able to load the raster without the session abording!
I'm setting up R/RStudio on a new Windows 10 machine; first time setting it up in a non-UNIX environment, so bear with me.
From my previous experience with R/RStudio under Linux and macOS, I wanted to setup separate libraries for system and user, i.e., that the Packages pane in RStudio would show both a User Library AND a System Library.
I specified the R_LIBS_USER environment variable for my account as C:\Users\[user name]\Documents\R\win-library\3.5.
When running R/RStudio, the .libPaths() are as follows:
> .libPaths()
[1] "C:/Users/[user name]/Documents/R/win-library/3.5"
[2] "C:/Program Files/R/R-3.5.0/library"
This is pretty much what I wanted: the first library path being the default User Library, and the second path being the System Library. I'm able to install packages at will, and they are per default located inside the User Library.
HOWEVER, the Packages pane in RStudio does NOT show two separate libraries for the User Library and the System Library. Instead, all packages (aside from base) are shown under System Library; including the packages from my User Library. My question now is:
Is there a way to tell R/RStudio that my User Library and my System Library are two separate entities, which should be visually separated in RStudio's Packages pane?
Note: I'm aware this is likely a mere "cosmetic" issue; but it still bothers me! Also, I'm not sure if this is a pure R or an RStudio issue, so I tagged both.
EDIT: I also noticed that the System Library (C:/Program Files/R/R-3.5.0/library) is not available as drop-down option when installing new packages inside the Packages pane.
--
> devtools::session_info()
Session info --------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
system x86_64, mingw32
ui RStudio (1.1.453)
language (EN)
collate Nothing to worry about
tz This neither
date 2018-06-08
Packages ------------------------------------------------------------------
package * version date source
base * 3.5.0 2018-04-23 local
compiler 3.5.0 2018-04-23 local
datasets * 3.5.0 2018-04-23 local
devtools 1.13.5 2018-02-18 CRAN (R 3.5.0)
digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
graphics * 3.5.0 2018-04-23 local
grDevices * 3.5.0 2018-04-23 local
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.0 2018-04-23 local
stats * 3.5.0 2018-04-23 local
tools 3.5.0 2018-04-23 local
utils * 3.5.0 2018-04-23 local
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
yaml 2.1.19 2018-05-01 CRAN (R 3.5.0)
I had exactly the same issue. In my case the cause was using a substituted drive for the user libraries:
> subst
F:\: => C:\data\flash drive
Setting R_LIBS_USER to F:/[...] shows the cosmetic error, using C:/data/flash drive/[...] works.
In my case, Sys.getenv("R_LIBS_USER") is as follow:
"C:\\Users\\USERNAME\\AppData\\Local/R/win-library/4.2"
This path includes two backslashes, so this was causing the environment variable to not be recognized correctly.
Next I searched for a place to put .Renviron as follows
R.home(component = "etc")
I created .Renviron (or Renviro.site) in that folder and saved it with the following in the contents and it worked.
R_LIBS_USER=C:/Users/${USERNAME}/AppData/Local/R/win-library/%v
After intalling NetCDF in julia,
julia> Pkg.status()
1 required packages:
- NetCDF 0.3.0
7 additional packages:
- BinDeps 0.3.19
- Compat 0.7.8
- Conda 0.1.8
- Formatting 0.1.4
- JSON 0.5.0
- SHA 0.1.2
- URIParser 0.1.1
I try simple things like
julia> ncinfo("/home/idf/Downloads/air.sig995.2012.nc")
ERROR: UndefVarError: ncinfo not defined
julia>
I must be missing a step?
Julia packages are git repositories, one could clone a repository directly or by Pkg.add(), it's not equals to loading it, therefore after adding a package and before using it you must load it's contents, and using is the right command to do this task,
So:
using NetCDF; is the missing statement.
I just upgraded to Meteor 1.2 from 1.1.
It did not upgrade and this is what it output
MacBook-Pro:ProjectX Nearpoint$ meteor update
Update to release METEOR#1.2.0.1 is impossible:
While selecting package versions:
error: Conflict: Constraint less#1.0.11 is not satisfied by less 2.5.0_2.
Constraints on package "less":
* less#=2.5.0_2 <- top level
* less#1.0.11 <- multiply:iron-router-progress 1.0.1
* less#1.0.0||2.0.0 <- matteodem:easy-search 1.6.3
* less#1.0.0||2.0.0 <- mdg:camera 1.1.5
This project is at the latest release which is compatible with your current package constraints.
npm-container: updating npm dependencies -- beagle, validator, async...
Changes to your project's package version selections from updating package versions:
cfs:http-methods upgraded from 0.0.29 to 0.0.30
ian:accounts-ui-bootstrap-3 upgraded from 1.2.79 to 1.2.80
matteodem:easy-search upgraded from 1.6.3 to 1.6.4
meteorhacks:kadira upgraded from 2.23.2 to 2.23.4
The following top-level dependencies were not updated to the very latest version available:
* kevohagan:sweetalert 0.5.0 (1.0.0 is available)
* mdg:camera 1.1.5 (1.2.0 is available)
* natestrauser:filepicker-plus 1.2.3 (2.0.0 is available)
* natestrauser:select2 3.5.1 (4.0.0_1 is available)
* zimme:iron-router-active 1.0.4 (2.0.1 is available)
Newer versions of the following indirect dependencies are available:
* babrahams:editable-json 0.4.3 (0.6.0 is available)
* matb33:collection-hooks 0.7.15 (0.8.0 is available)
* meteorhacks:aggregate 1.2.1 (1.3.0 is available)
* meteortoys:hotreload 0.2.0 (0.3.0 is available)
* meteortoys:listen 0.3.0 (0.4.0 is available)
* meteortoys:pub 0.3.1 (0.4.0 is available)
* meteortoys:status 0.1.0 (0.2.0 is available)
* meteortoys:toypro 0.4.2 (0.5.0 is available)
* softwarerero:accounts-t9n 1.0.9 (1.1.4 is available)
* tap:i18n 1.5.1 (1.6.1 is available)
* underscorestring:underscore.string 3.0.3_1 (3.2.2 is available)
To update one or more of these packages, pass their names to `meteor update`.
What should I do to fix this now? I currently cannot start my server after upgrading.
I am getting the error
=> Started proxy.
=> Started MongoDB.
=> Errors prevented startup:
While selecting package versions:
error: Potentially incompatible change required to top-level dependency: matteodem:easy-search 1.6.3,
was 1.6.4.
Constraints on package "matteodem:easy-search":
To allow potentially incompatible changes to top-level dependencies, you must pass
--allow-incompatible-update on the command line.
=> Your application has errors. Waiting for file change.