When I want to install the package mclust, I get the following error:
> install.packages("mclust")
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is
later:
binary source needs_compilation
mclust 5.2.3 5.3 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘mclust’
trying URL 'https://cran.rstudio.com/src/contrib/mclust_5.3.tar.gz'
Content type 'application/x-gzip' length 2792962 bytes (2.7 MB)
downloaded 2.7 MB
* installing *source* package 'mclust' ...
** package 'mclust' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
gfortran -m32 -O3 -mtune=core2 -c mclust.f -o mclust.o
make: gfortran: Command not found
C:/PROGRA~1/R/R-32~1.3/etc/i386/Makeconf:206: recipe for target 'mclust.o' failed
make: *** [mclust.o] Error 127
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-32~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-32~1.3/share/make/winshlib.mk" SHLIB="mclust.dll" SHLIB_LIBADD='$(FLIBS)' OBJECTS="init.o mclust.o mclustaddson.o"' had status 2
ERROR: compilation failed for package 'mclust'
* removing 'C:/Users/hp1/Documents/R/win-library/3.2/mclust'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\hp1\Documents\R\win-library\3.2" C:\Users\hp1\AppData\Local\Temp\RtmpiAzB7h/downloaded_packages/mclust_5.3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘mclust’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\hp1\AppData\Local\Temp\RtmpiAzB7h\downloaded_packages’
When digging for solutions on how to fix it, I came across this where the OP says in a comment that the issue was arising due to missing llpack and lblas libraries, which they fixed by installing lapackdev and blasdev packages. But when I try to install these packages, I get error. I checked all my 12 repositories and tried again, but same result.
> install.packages("lapackdev")
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘lapackdev’ is not available (for R version 3.2.3)
> setRepositories(graphics = getOption("menu.graphics"),
+ ind = NULL, addURLs = character())
--- Please select repositories for use in this session ---
1: + CRAN 2: BioC software
3: BioC annotation 4: BioC experiment
5: BioC extra 6: + CRAN (extras)
7: Omegahat 8: R-Forge
9: rforge.net 10: CRAN (extras, https)
11: R-Forge [https] 12: rforge.net [https]
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1 2 3 4 5 6 7 8 9 10 11 12
> install.packages("lapackdev")
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Warning in install.packages :
package ‘lapackdev’ is not available (for R version 3.2.3)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/bin/windows/contrib/3.2:
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/bin/windows/contrib/3.2:
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Same with blasdev:
> install.packages("blasdev")
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Warning in install.packages :
package ‘blasdev’ is not available (for R version 3.2.3)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/bin/windows/contrib/3.2:
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/bin/windows/contrib/3.2:
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
What is going on and how do I get mclust to install?
I am answering my own question as the following solved the issue (i.e., mclust was installed successfully) without needing to install the 2 packages I mention in the question. So, this might help someone facing difficulty install mclust.
I updated R version from 3.25 to 3.4, and R studio version from 0.9 to the latest (1.0.143 at the time of writing this answer), and this seems to have solved the issue.
Related
Good afternoon. Recently I have encountered the problem with installing "mxnet" package. I have tried several variants of code, but neither of their actually installs this package.
1.
cran <- getOption("repos")
cran["dmlc"] <- "https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/15"
options(repos = cran)
install.packages("mxnet")
library(mxnet)
And get the error like this:
Error: package or namespace load failed for ‘mxnet’: package ‘mxnet’
was installed before R 4.0.0: please re-install it
install.packages("https://github.com/jeremiedb/mxnet_winbin/raw/master/mxnet.zip", repos = NULL)
Then I type library(mxnet) and get the error message as in p.1.
3.
cran <- getOption("repos")
cran["dmlc"] <- "https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23"
options(repos = cran)
library(devtools)
require(devtools)
install_version("DiagrammeR", version = "0.9.0", repos = "http://cran.us.r-project.org")
require(DiagrammeR)
install.packages("mxnet")
library(mxnet)
After executing this code I get the following error:
ERROR: failed to lock directory 'C:/Users/user/Documents/R/win-library/4.0' for modifying
Try removing 'C:/Users/user/Documents/R/win-library/4.0/00LOCK-rlang'
Error: Failed to install 'unknown package' from URL:
(converted from warning) installation of package ‘rlang’ had non-zero exit status
> install.packages("mxnet")
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib:
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES'
Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib:
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/src/contrib/PACKAGES'
Warning in install.packages :
package ‘mxnet’ is not available (for R version 4.0.2)
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/bin/windows/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/bin/windows/contrib/4.0/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/bin/windows/contrib/4.0/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/bin/windows/contrib/4.0:
cannot open URL 'https://apache-mxnet.s3-accelerate.dualstack.amazonaws.com/R/CRAN/23/bin/windows/contrib/4.0/PACKAGES'
In the end, mxnet package hasn't been installed in RStudio yet.
I have familizrized myself with MXNet package installation in R , but some of the instructions, given there, didn't bring any help. Other coincide with my code.
Could you, please, tell me, how to successfully install this package? What code should I run?
Thank you for your effort.
As there is no prebuilt MXNet binary available for the version of R that you are using, you will need to follow the build from source instructions. Please see https://mxnet.apache.org/versions/1.7.0/get_started/build_from_source
You can follow these instructions but use the 1.8.0rc2 release archive instead of 1.7.0 if you like.
This question is duplicate of R: namespace load failed for ‘mxnet’: package ‘mxnet’ was installed before R 4.0.0: please re-install it but can't be flagged as duplicate as there are no accepted answers.
My work laptop has no internet access and I am trying to download the package rgdal.
I have downloaded rgdal_1.4-8.tar.gz, gdal-3.0.4.tar.gz and proj-6.3.2.tar.gz. I tried intalling them via source separately using:
install.packages('.../...tar.gz', type='source', repos=NULL)
but it did not work. Here are the error messages
ERROR: cannot extract package from 'D:/Users/sn/Documents/R source packages/gdal-3.0.4.tar.gz'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/gdal-3.0.4.tar.gz’ had non-zero exit status
ERROR: cannot extract package from 'D:/Users/sn/Documents/R source packages/proj-6.3.2.tar.gz'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/proj-6.3.2.tar.gz’ had non-zero exit status
Error in download.file(sprintf("https://github.com/rwinlib/gdal2/archive/v%s.zip", :
cannot open URL 'https://github.com/rwinlib/gdal2/archive/v2.2.3.zip'
In addition: Warning message:
In download.file(sprintf("https://github.com/rwinlib/gdal2/archive/v%s.zip", :
InternetOpenUrl failed: 'A connection with the server could not be established'
Execution halted
make: *** [Makevars.win:27: winlibs] Error 1
ERROR: compilation failed for package 'rgdal'
* removing 'D:/Users/sn/Documents/R/win-library/3.6/rgdal'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/rgdal_1.4-8.tar.gz’ had non-zero exit status
I have a problem to install package 'swirl' on my Rstudio. I tried several cran in China and it cannot connect to server every time. Does anyone know any possible reason? *ps:since the stackoverflow does not allow me to post more than one URL link so I cut off a 'h' of from 'http'
install.packages("swirl")
Warning in install.packages :
URL
'http://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES.rds':
status was 'Couldn't connect to server' Warning in install.packages :
URL 'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES.gz':
status was 'Couldn't connect to server' Warning in install.packages :
URL 'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES':
status was 'Couldn't connect to server' Warning in install.packages :
unable to access index for repository
ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib: cannot open URL
'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES' Warning
in install.packages : URL
'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES.rds':
status was 'Couldn't connect to server' Warning in install.packages :
URL 'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES.gz':
status was 'Couldn't connect to server' Warning in install.packages :
URL 'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES':
status was 'Couldn't connect to server' Warning in install.packages :
unable to access index for repository
ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib: cannot open URL
'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES' Warning
in install.packages : package 'swirl' is not available (for R
version 3.4.0) Warning in install.packages : URL
'ttp://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.4/PACKAGES.rds':
status was 'Couldn't connect to server'
Try:
install.packages("swirl", repos="http://cran.rstudio.com/", dependencies=TRUE)
Where does one get jsonlite? Apparently it is missing from CRAN?
> install.packages('jsonlite')
Gives:
Installing package into ‘C:/Users/cbusch/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/jsonlite_0.9.20.zip'
Warning in install.packages :
cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/jsonlite_0.9.20.zip': HTTP status was '404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/jsonlite_0.9.20.zip'
Warning in install.packages :
download of package ‘jsonlite’ failed
Any suggestions?
Like #user5249203 said:
install.packages('jsonlite', dependencies=TRUE, repos='http://cran.rstudio.com/')
I have to work with shapefiles and to convert these to rasters the package rgdal is recommended, however the package is not recognized (R v2.11, RStudio 0.98.501, Mac OS X 10_7_5). How could I still install rgdal or omit this package?
To clarify my question more, the error messages are:
> install.packages("rgdal")
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.11
Warning in install.packages :
argument 'lib' is missing: using '/Users/myname/Library/R/2.11/library'
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.11
Warning in install.packages :
package ‘rgdal’ is not available