A package that I previously used, "mlogit", is now not unpacking in R. I have manually typed it in as well as using the install packages tool. Although it says "successfully installed", it is not unpacked and does not show up in the Rstudio list of packages. This is what I get in the console:
<U+2714> Package 'mlogit' successfully installed.
Warning messages:
1: In utils::install.packages("Rdpack", repos = "https://cran.rstudio.com/") :
installation of package 'Rdpack' had non-zero exit status
2: In utils::install.packages("mlogit", repos = "https://cran.rstudio.com/") :
installation of package 'Rdpack' had non-zero exit status
3: In utils::install.packages("mlogit", repos = "https://cran.rstudio.com/") :
installation of package 'mlogit' had non-zero exit status
I had not updated R or switched computers, and all my files associated with this script are in the exact same place. I've run it a million times. Not sure what's different now. All other packages I've tried work. There are not alternative packages I can use for this purpose.
Related
hi i am trying to install package for experiment designs like this
install.packages("daewr", dependencies = T)
but it returns the following
configure: error: GNU MP not found, or not 4.1.4 or up, see http://gmplib.org
ERROR: configuration failed for package ‘gmp’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/gmp’
Warning in install.packages :
installation of package ‘gmp’ had non-zero exit status
ERROR: dependency ‘gmp’ is not available for package ‘partitions’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/partitions’
Warning in install.packages :
installation of package ‘partitions’ had non-zero exit status
ERROR: dependency ‘partitions’ is not available for package ‘DoE.base’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/DoE.base’
Warning in install.packages :
installation of package ‘DoE.base’ had non-zero exit status
ERROR: dependency ‘DoE.base’ is not available for package ‘FrF2’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/FrF2’
Warning in install.packages :
installation of package ‘FrF2’ had non-zero exit status
ERROR: dependency ‘FrF2’ is not available for package ‘daewr’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/daewr’
Warning in install.packages :
installation of package ‘daewr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpB1bSe0/downloaded_packages’
so i decided to download the file from https://cran.r-project.org/web/packages/daewr/index.html
after trying to install it returns me
also installing the dependencies ‘gmp’, ‘partitions’, ‘DoE.base’, ‘FrF2.catlg128’
I try to install the first one but it asks for a Bessel package and it still gives me problems
I solved it by installing dependency one by one, many answer you install the dependencies but they do not say how I will explain them for the new ones in linux and in R to install the daerw package with the aforementioned problems, install the following in the linux console
sudo apt-get install libgsl-dev
with that install libraries now I can open R and install
install.packages('gsl')
then I opened the linux console again and installed
sudo apt-get install libgmp-dev
I go back to R and install
install.packages("gmp", dependencies = T)
now I can install the package without problems
install.packages("daewr", dependencies = T)
library(daewr)
I hope that any comment is welcome.
I just installed R using anaconda, and I am following this tutorial:
https://www.analyticsvidhya.com/blog/2016/03/tutorial-powerful-packages-imputing-missing-values/
I learned that I need to install some package by using:
if(!require(Hmisc)) install.packages("Hmisc",repos = "http://cran.us.r-project.org")
There are some warning message i am not sure whether it means successful or not:
Loading required package: Hmisc
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'Hmisc'also installing the dependencies 'survival', 'ggplot2'
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'survival' had non-zero exit status
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'ggplot2' had non-zero exit status
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'Hmisc' had non-zero exit status
The downloaded source packages are in
'/tmp/Rtmpcf6rZ9/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Then I tried to load the library with
library(Hmisc)
But I got the error,
Error in library(Hmisc): there is no package called 'Hmisc'
Does anyone know what might has happened? Thanks.
Edit:
I am suggested to try a few more ways, but they all have various error:
install.packages("Hmisc")
Error in contrib.url(repos, type): trying to use CRAN without setting a mirror
If I do:
install.packages("Hmisc",repos = "http://cran.us.r-project.org")
I got:
also installing the dependencies 'survival', 'ggplot2'
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'survival' had non-zero exit status
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'ggplot2' had non-zero exit status
Warning message:
In install.packages("Hmisc", repos = "http://cran.us.r-project.org"): installation of package 'Hmisc' had non-zero exit status
The downloaded source packages are in
'/tmp/Rtmpcf6rZ9/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
I am suggested not to use Anaconda R, but because I mostly use rpy2 and jupiter notebook the most. I think using the Anaconda R may be the most straight forward method to get my jupiter notebook and python to work seamlessly with R.
I had a similar issue, solved it by installing "acepack" directly install.packages('acepack')
This is mysterious, regardless. I do an update of all packages in Conda. Then, I install Rstudio using anaconda. Then the error does not exist anymore...
I come across this problem when I install the package
"TxDb.Hsapiens.UCSC.hg19.knownGene" from Bioclite on RStudio v.1.1442. Below is the error message:
Warning messages:
/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz' had status 3
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
I also tried to install this package, but it did not work either:
Warning in install.packages :
package ‘parallel’ is not available (for R version 3.4.3)
Warning in install.packages :
package ‘parallel’ is a base package, and should not be updated
I do not understand what the warnings mean and can someone please help me with resolving this issue?
Thank you.
Some further details would be very helpful - especially the code that you actually used.
What OS are you working on?
Is this a fresh install of R?
Have you previously had TxDB.... installed?
Are you working in a conda environment or similar?
Why did you download the gzipped version of the package?
In a fresh R-3.4.3 environment on Ubuntu I get the following
source("http://www.bioconductor.org/biocLite.R")
## installing source BiocInstaller blah blah success
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘RMySQL’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
This suggests that if I wanted to install TxDB... I'd have to get RMySQL installed first, and then GenomicFeatures and then ....
Could you post all the code you used and all the contents of the warning messages that you received, please.
I have been trying over the weekend to install mosaic, car and some other packages on an R kernel (3.4.2) in Jupyter Notebook running Ubuntu 16.04. I have tried install.packages('car', '/home/jayaramdas/anaconda3/lib/R/library/', repos='http://cran.us.r-project.org'): it returns:
also installing the dependency ‘pbkrtest’
Warning message in install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
“installation of package ‘pbkrtest’ had non-zero exit status”Warning message in install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
“installation of package ‘car’ had non-zero exit status”
I've tried installing it in the original R package and I get this:
Warning messages:
1: In install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
installation of package ‘pbkrtest’ had non-zero exit status
2: In install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
installation of package ‘car’ had non-zero exit status
I tried using Rstudio to install it, but it won't let me write the file. I also tried downloading the zip file for Ubuntu and it still gave the 'non-zero exiterror. Is this a usual problem that people have withcar` and other R packages? I am just trying to figure how to add some packages to my jupyter notebook.
You are on Ubuntu. You want to use a package manager (conda).
May I suggest you use the native one?
sudo apt-get install r-cran-car
will install car and all its dependencies. If not, file an Ubuntu bug report.
Similarly, you can get many more packages from Ubuntu: apt-cache search 'r-cran-*'. And once you consider the Rutter PPAs you have a large part of CRAN prebuilt.
I'm running R 3.4.2 and R Studio 1.0.153. I want to install the prob package in R. The prob package in an archived file. It is located here. I am trying to install the prob_1.0-0.tar.gz package. I have no problem downloading and opening the package archive file. The code is below, it seems I need to install the fAsianOptions package.
ERROR: dependency 'fAsianOptions' is not available for package 'prob'
* removing 'C:/Users/blake_000/Documents/R/win-library/3.4/prob' Warning in install.packages : running command
'"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" CMD INSTALL -l
"C:\Users\blake_000\Documents\R\win-library\3.4"
"C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/prob_1.0-0.tar.gz"'
had status 1 Warning in install.packages : installation of package
‘C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/prob_1.0-0.tar.gz’
had non-zero exit status
Unfortunately, the fAsianOptions package is also archived. It is located here and I downloaded version fAsianOptions_3010.79.tar.gz. There were a number of dependencies but I installed the required packages (timeDate, timeSeries, etc.)
However, the fAsianOptions package is not installing. The error code reads as follows:
install.packages("C:/Users/blake_000/Google Drive/Life/CSUEB/Fall
2017/6204- Probability/R Code/fAsianOptions_3010.79.tar.gz", repos =
NULL, type = "source") Installing package into
‘C:/Users/blake_000/Documents/R/win-library/3.4’ (as ‘lib’ is
unspecified)
* installing source package 'fAsianOptions' ...
** package 'fAsianOptions' successfully unpacked and MD5 sums checked
** libs
*** arch - i386 Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-34~1.2/etc/i386/Makeconf" -f
"C:/PROGRA~1/R/R-34~1.2/share/make/winshlib.mk"
SHLIB="fAsianOptions.dll" SHLIB_LIBADD='$(FLIBS)'
OBJECTS="EBMAsianOptions.o GammaFunctions.o
HypergeometricFunctions.o"' had status 127 ERROR: compilation failed
for package 'fAsianOptions'
* removing 'C:/Users/blake_000/Documents/R/win-library/3.4/fAsianOptions' Warning
in install.packages : running command
'"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" CMD INSTALL -l
"C:\Users\blake_000\Documents\R\win-library\3.4"
"C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/fAsianOptions_3010.79.tar.gz"'
had status 1 Warning in install.packages : installation of package
‘C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/fAsianOptions_3010.79.tar.gz’
had non-zero exit status
I'm hoping that someone can help me to install the fAsianOptions dependency so I can install the prob package. Or, if there's an easier way, please let me know!
I had the same problem. I solved it by installing lower version of R -2.9. prob is available in repository for this version.