I was trying to install emmeans using install_github and it required that I install rtools and after attempting this I not only was unsuccessful in installing emmeans with the following code:
devtools::install_github("rvlenth/emmeans", dependencies = TRUE, build_opts = "")
Received this:
Error: Failed to install 'emmeans' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr:
checking for file 'C:\Users\jmb827\AppData\Local\Temp\RtmpYrGInN\remotes387066d354e0\rvlenth-emmeans-32bf444/DESCRIPTION' ... OK
preparing 'emmeans':
checking DESCRIPTION meta-information ... OK
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories
looking to see if a 'data/datalist' file should be added
* building 'emmeans_1.4.5.009003.tar.gz'
ERROR
cannot change to directory ''
but now can not load ggplot2 among other packages with error:
package �ggplot2� was built under R version 3.6.3Error: package or namespace load failed for ‘ggplot2’:
package ‘tibble’ does not have a namespace
Related
I'm running into the following error when trying to install the headless chrom crrri package on Mac OS using remotes::install_github('rlesur/crrri'):
Downloading GitHub repo rlesur/crrri#HEAD Running R CMD build...
checking for file ‘/private/var/folders/6q/k8llt_rd5d3cc2tgx1fy8vth0000gn/T/RtmpinLlHt/remotes2f540ee01d2/RLesur-crrri-69c54e6/DESCRIPTION’
... OK
preparing ‘crrri’:
checking DESCRIPTION meta-information ... OK
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION
building ‘crrri_0.0.13.tar.gz’ Warning: invalid package ‘/var/folders/6q/k8llt_rd5d3cc2tgx1fy8vth0000gn/T//RtmpinLlHt/file2f549b9a34b/*
building ‘crrri_0.0.13.tar.gz’’ Error: ERROR: no packages specified
Warning message: In i.p(...) : installation of package
'/var/folders/6q/k8llt_rd5d3cc2tgx1fy8vth0000gn/T//RtmpinLlHt/file2f549b9a34b/*
building ‘crrri_0.0.13.tar.gz’' had non-zero exit status
Don't know what the issue was but used devtools::install_github instead of remotes and that worked.
When I run the command install_github("chrchang/plink-ng", subdir="/2.0/cindex") in Rstudio, I get the following error message:
Downloading GitHub repo chrchang/plink-ng#HEAD
chrchang-plink-ng-b39d989/2.0/cindex/src/include: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\cindex\\src\\include'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/include: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\include'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/libdeflate: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\libdeflate'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/pgenlib_ffi_support.cpp: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\pgenlib_ffi_support.cpp'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/pgenlib_ffi_support.h: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\pgenlib_ffi_support.h'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/pvar_ffi_support.cpp: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\pvar_ffi_support.cpp'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/pvar_ffi_support.h: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\pvar_ffi_support.h'
chrchang-plink-ng-b39d989/2.0/pgenlibr/src/zstd: Can't create '\\\\?\\C:\\Users\\xxx\\AppData\\Local\\Temp\\Rtmp6PucTt\\remotes68581e00563b\\chrchang-plink-ng-b39d989\\2.0\\pgenlibr\\src\\zstd'
tar.exe: Error exit delayed from previous errors.
√ checking for file 'C:\Users\xxx\AppData\Local\Temp\Rtmp6PucTt\remotes68581e00563b\chrchang-plink-ng-b39d989\2.0\cindex/DESCRIPTION' ...
- preparing 'cindex':
√ checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'cindex_0.2.tar.gz'
Installing package into ‘C:/Users/xxx/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'cindex' ...
** using staged installation
** libs
*** arch - i386
make: *** No rule to make target 'include/plink2_base.o', needed by 'cindex.dll'. Stop.
ERROR: compilation failed for package 'cindex'
* removing 'C:/Users/xxx/Documents/R/win-library/4.0/cindex'
错误: Failed to install 'cindex' from GitHub:
(由警告转换成)installation of package ‘C:/Users/xxx/AppData/Local/Temp/Rtmp6PucTt/file685860d615b0/cindex_0.2.tar.gz’ had non-zero exit status
此外: Warning message:
In utils::untar(tarfile, ...) :
‘tar.exe -xf "C:\Users\xxx\AppData\Local\Temp\Rtmp6PucTt\file68583f07ec.tar.gz" -C "C:/Users/xxx/AppData/Local/Temp/Rtmp6PucTt/remotes68581e00563b"’ returned error code 1*
install_github() on Windows 10 R does not seem to handle Git symlinks correctly. A workaround is to clone the repository and manually expand the symlinks in your copy.
I am using RStudio with R (Version 4.0.2) and I am trying to install this climate package from github: https://github.com/SantanderMetGroup/climate4R
when I type: install_github("SantanderMetGroup/climate4R")
I get this error:
Error: Failed to install 'unknown package' from GitHub:
HTTP error 404.
Not Found
Did you spell the repo owner (`SantanderMetGroup`) and repo name (`climate4R`) correctly?
- If spelling is correct, check that you have the required permissions to access the repo.
I also downloaded the zipped package and tried to manually install the package within rstudio and got this error:
Installing package into ‘C:/Users/...../Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open compressed file 'climate4R-master/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection
Why is it not installing? I have downloaded packages from github before with no problems.
UPDATED HERE:
I had already tried what is suggested below, but it also didn't work. I wanted to check first if I had missed something and it was possible to download the package all at once. When I input this:
library(devtools)
install_github(c("SantanderMetGroup/loadeR.java",
"SantanderMetGroup/climate4R.UDG",
"SantanderMetGroup/loadeR",
"SantanderMetGroup/transformeR",
"SantanderMetGroup/visualizeR",
"SantanderMetGroup/downscaleR"))
I get the following error:
Downloading GitHub repo SantanderMetGroup/loadeR.java#HEAD
√ checking for file 'C:\Users\...\AppData\Local\Temp\RtmpCAqAGF\remotes39b87d2f4f9\SantanderMetGroup-loadeR.java-88da23e/DESCRIPTION' ...
- preparing 'loadeR.java':
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'loadeR.java_1.1.1.tar.gz'
Installing package into ‘C:/Users/.../Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)
* installing *source* package 'loadeR.java' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading Error: package or namespace load failed for 'rJava': .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: JAVA_HOME cannot be determined from the Registry Error: package 'rJava' could not be loaded Execution halted ERROR: lazy loading failed for package 'loadeR.java'
* removing 'C:/Users/.../Documents/R/win-library/4.0/loadeR.java' Error: Failed to install 'loadeR.java' from GitHub: (converted from warning) installation of package ‘C:/Users/.../AppData/Local/Temp/RtmpCAqAGF/file39b86ae96acb/loadeR.java_1.1.1.tar.gz’ had non-zero exit status
As already pointed out, the GitHub Repo is not an R package by itself.
Here from their GitHub Readme how to install their collection of packages that form the climate4R toolset.
library(devtools)
install_github(c("SantanderMetGroup/loadeR.java",
"SantanderMetGroup/climate4R.UDG",
"SantanderMetGroup/loadeR",
"SantanderMetGroup/transformeR",
"SantanderMetGroup/visualizeR",
"SantanderMetGroup/downscaleR"))
In order to install this package, I had to install this:JDK 13
https://www.oracle.com/java/technologies/javase-jdk13-downloads.html
This allowed each of the packages to be installed correctly.
I'm trying to install the package gbm.auto via github, but the download does not seem to work. How can I solve this? I am working on a windows 10 Pro (R version 3.6.1, Rstudio version 1.2.5042). This is the error I get:
remotes::install_github("SimonDedman/gbm.auto")
Downloading GitHub repo SimonDedman/gbm.auto#master
√ checking for file 'C:\Users\Ststrubb\AppData\Local\Temp\RtmpOcwGGZ\remotes1d5c7c774f2a\SimonDedman-gbm.auto-96328bf/DESCRIPTION' ...
- preparing 'gbm.auto': (359ms)
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- looking to see if a 'data/datalist' file should be added
- building 'gbm.auto_1.2.4.tar.gz'
Installing package into ‘C:/Users/Ststrubb/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'gbm.auto' ...
** using staged installation
** R
Error in parse(outFile) :
C:/Users/Ststrubb/AppData/Local/Temp/RtmpALsbRt/R.INSTALL7320575e5a03/gbm.auto/R/gbm.valuemap.R:462:0: unexpected end of input
460: beep(8)} # notify user & close function
461:
^
ERROR: unable to collate and parse R files for package 'gbm.auto'
* removing 'C:/Users/***/Documents/R/win-library/3.6/gbm.auto'
Error: Failed to install 'gbm.auto' from GitHub:
(converted from warning) installation of package ‘C:/Users/***/AppData/Local/Temp/RtmpOcwGGZ/file1d5c40b85311/gbm.auto_1.2.4.tar.gz’ had non-zero exit status
I get the same error when I used
githubinstall or remotes::install_github.
I want to install "qdap" package to run a text mining project. I tried installing the package in many different ways:
1. intsall.packages("qdap")
2. Downloading the file locally then installing
3. Using devtools
library(devtools)
install_github("trinker/qdapDictionaries")
install_github("trinker/qdapRegex")
install_github("trinker/qdapTools")
install_github("trinker/qdap")
I always had the same problem. It seems to be related to rJava package. I tried to install rJava but I wasn't successful.
I'm more of a data analyst than a developer so I don't have much experience with development (using terminal commands or fixing java on my mac).
I'd really like to use this "qdap" package. Could you please help me figure out in a simple manner?
Here's the error message after I install the package:
The downloaded source packages are in
‘/private/var/folders/hk/r0tjy0t57n79lvkh2_fc7snm0000gn/T/RtmpsSJ6Mg/downloaded_packages’
✓ checking for file ‘/private/var/folders/hk/r0tjy0t57n79lvkh2_fc7snm0000gn/T/RtmpsSJ6Mg/remotes42b1730aa4f/trinker-qdap-7f390f7/DESCRIPTION’ (437ms)
─ preparing ‘qdap’: (1.1s)
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (1.3s)
─ checking for empty or unneeded directories
Removed empty directory ‘qdap/tools’
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘qdap_2.4.2.tar.gz’
* installing *source* package ‘qdap’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Warning in system("/usr/libexec/java_home", intern = TRUE) :
running command '/usr/libexec/java_home' had status 1
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
ERROR: lazy loading failed for package ‘qdap’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/qdap’
Error: Failed to install 'qdap' from GitHub:
(converted from warning) installation of package ‘/var/folders/hk/r0tjy0t57n79lvkh2_fc7snm0000gn/T//RtmpsSJ6Mg/file42b3e031f25/qdap_2.4.2.tar.gz’ had non-zero exit status
Maybe the key is in the following
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
and
Warning in system("/usr/libexec/java_home", intern = TRUE) :
running command '/usr/libexec/java_home' had status 1
Are you sure you have installed a JVM? And if yes, the correct one? Because it seems to not find it.
You can download JVM from here.
I hope this helps!