Unable to install xlsx package in Rstudio - r

I tried installing xlsx package in R.
install.packages("xlsx")
installing *source* package 'xlsx' ...
** package 'xlsx' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: fun(libname, pkgname)
error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures.
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/hi/Documents/R/win-library/3.3/xlsx'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\hi\Documents\R\win-library\3.3" C:\Users\hi\AppData\Local\Temp\RtmpSGp15V/downloaded_packages/xlsx_0.6.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘xlsx’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\hi\AppData\Local\Temp\RtmpSGp15V\downloaded_packages’
Then I ran the library function too
library(xlsx)
Error in library(xlsx) : there is no package called ‘xlsx’
To ensure that whether the package has been installed itself or not I ran
grepl("xlsx",installed.packages())
# It returns "FALSE" 649 times in a row.
I read online about how some rjava packages need to be installed as well so I tried to
install.packages('rJava')
install.packages("xlsxjars")
package ‘rJava’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\hi\AppData\Local\Temp\RtmpSGp15V\downloaded_packages
To ensure grepl("rJava",installed.packages())
Again I got "FALSE" 649 times.

I recently had a similar problem with another package and have had loads of headaches with R and Java integration. My understanding is that you have to install Java for each architecture you're using. If R is trying to install xlsx for both architectures and you've only got the 64-bit java installed, it would cause a failure like the one you got. You could try:
install.packages("xlsx", INSTALL_opts=c("--no-multiarch"))
This would keep it from trying to install the xlsx for the 32-bit architecture.

I had the same problem a few months ago. In my case, the solution was installing both versions of java (32-bit and 64-bit architecture). On windows 10 the 32-bit architecture should be installed on path ./programfiles (x86)/... and the 64-bit architecture should be installed on ./programfiles/... Both java installer can be found on the official web page.
After installing both architectures of java, it is necessary to make sure that JAVA HOME environtment is declared as empty string. Sys.getenv("JAVA HOME") = "".
This steps works for me. I hope that my solution works for you.

Related

package installation C++ compiler does not work R

I would like to install a package from my local environment. I have a mac and tried with both R 4.0.0 and R 3.6.3 and encounter the same issues with both R versions. When installing the package I get the following error and I do not know what to make out of this. Can anyone help interpreting it and suggest possible sources for this problem?
* installing *source* package ‘package’ ...
** using staged installation
checking whether the C++ compiler works... no
configure: error: in `/private/tmp/RtmpCtsuxn/R.INSTALL3d701f92995/goldfish':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘package’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/package’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/package’
Warning in install.packages :
installation of package ‘/Users/simon/Downloads/package_1.4.1.tar’ had non-zero exit status

Can't install package 'Liszt' (not in CRAN) in R 3.6.3

I want to install a package that is not found in CRAN.
Below is a downloadlink to the package.
The package makes use of JAGS, of which i have the 64 bit 4.3.0 version of.
rjags and r2jags packages are installed. Rtools is connected to the pathway. I checked this using
Sys.which("make")
## "C:\\rtools40\\usr\\bin\\make.exe"
Connection to path was done with devtools from this Stacklink:
How to add Rtools\bin to the system path in R
I use the following code to install the downloaded .tar.gz package:
install.packages("C:/Program Files/R/R-3.6.3/Liszt_0.8-5_1.tar.gz", repos=NULL,
type="source")
The package won't installl, instead i get the following error:
* installing *source* package 'Liszt' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Liszt'
finding HTML links ... done
A3ModelFun html
A5ModelFun html
Caterpillar html
LL html
Liszt-package html
extract html
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'rjags':
.onLoad failed in loadNamespace() for 'rjags', details:
call: fun(libname, pkgname)
error: Failed to locate any version of JAGS version 4
The rjags package is just an interface to the JAGS library
Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
http://www.sourceforge.net/projects/mcmc-jags/files
Error : package 'rjags' could not be loaded
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/Sneve/Documents/R/win-library/3.6/Liszt'
Warning in install.packages :
installation of package ‘C:/PROGRA~1/R/R-36~1.3/Liszt_0.8-5_1.tar.gz’ had non-zero exit status
I am trying for a while no, but no success. Any help is much appreciated.
Website providing the package:
http://www.possinghamlab.org/2016-05-30-04-33-10/list-length-analysis.html
package is available here:
http://www.possinghamlab.org/images/LLA/Liszt_0.8-5_1.tar.gz
I installed the 64 Bit version of JAGS. Appearently, the package needs both the 32 and the 64 bit version installed on the PC to be able to work. After i installed also the 32 bit version of JAGS, package installed with no problem.

Trouble with installing r2excel package in R

I am trying to install r2excel package in R via install_github but I get this error
> install_github("kassambara/r2excel")
several lines appearing in the console and I get
* installing *source* package 'r2excel' ...
** R
** preparing package for lazy loading
Warning: package 'xlsx' was built under R version 3.4.4
** help
*** installing help indices
converting help for package 'r2excel'
finding HTML links ... done
getOS html
r2excel-package html
xlsx.addHeader html
xlsx.addHyperlink html
xlsx.addLineBreak html
xlsx.addParagraph html
xlsx.addPlot html
xlsx.addTable html
xlsx.openFile html
xlsx.readFile html
xlsx.writeFile html
xlsx.writeMultipleData html
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'xlsx' was built under R version 3.4.4
Error: package or namespace load failed for 'xlsx':
.onLoad failed in loadNamespace() for 'rJava', details:
call: fun(libname, pkgname)
error: No CurrentVersion entry in Software/JavaSoft registry! Try re- installing Java and make sure R and Java have matching architectures.
Error : package 'xlsx' could not be loaded
Error: loading failed
Execution halted
*** arch - x64
Warning: package 'xlsx' was built under R version 3.4.4
ERROR: loading failed for 'i386'
* removing 'C:/Users/myusername/Documents/R/win-library/3.4/r2excel'
In R CMD INSTALL
Installation failed: Command failed (1)
So I get this error on 'xlsx' loading
What is weird is that I have no trouble loading 'xlsx' and 'rJava' individually with
library(xlsx)
I have a x64 java installed (build 1.8.0_161-b12) and a x64 rStudio running so I really don't know where the problem is coming from.
According to liuyanguu in https://github.com/kassambara/r2excel/issues/6:
"This package was not built in 64 bits system so we cannot install it this way. But you can still use all the functions by clone the repo and source or just copy-paste "/R/r2excel.r". There is actually no need to install the package."

'termstrc' was removed from CRAN, tried installing from .tar file - how do I install 'termstrc' I need it for another program

* installing *source* package 'termstrc' ...
** libs
*** arch - i386
Warning in system(cmd) : 'make' not found
ERROR: compilation failed for package 'termstrc'
* removing 'C:/Program Files/R/R-3.5.1/library/termstrc'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘C:/Users/DANIEL~1/DOWNLO~1/termstrc_1.3.7 (1).tar.gz’ had non-zero exit status
If you want to build R packages from source, you need to have the proper tools like compiler etc. installed. You seem to be using Windows, which is particularly difficult in that respect. The necessary tools have therefore been collected as Rtools package: https://cran.r-project.org/bin/windows/Rtools/. You will have to install that in order to build the package.

Installing xml2 in R in Fedora 27

I'm having trouble installing xml2 in RStudio, running Fedora 27. On running install.packages('xml2'), I get the following error:
installing to /home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2/libs
** R
** inst
** preparing package for lazy loading
** help
Error : /tmp/Rtmp2sKZQZ/R.INSTALL689b37bd918d/xml2/man/read_xml.Rd:47: unable to load shared object '/home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2/libs/xml2.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
ERROR: installing Rd objects failed for package ‘xml2’
* removing ‘/home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpPs5Gzi/downloaded_packages’
I noticed in my /usr/lib64/, I have libicui18n.so.57 only, so I tried copying a libicui18n.so.58 there, and I got the following error:
installing to /home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2/libs
** R
** inst
** preparing package for lazy loading
** help
Error : /tmp/Rtmp908Ecf/R.INSTALL653812e0e41f/xml2/man/read_xml.Rd:47: unable to load shared object '/home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2/libs/xml2.so':
libicuuc.so.58: cannot open shared object file: No such file or directory
ERROR: installing Rd objects failed for package ‘xml2’
* removing ‘/home/ryi/R/x86_64-redhat-linux-gnu-library/3.4/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpPs5Gzi/downloaded_packages’
And I noticed the same problem -- I have version .57, not version .58 of this library as well. Before I repeat this over and over, is this in fact a shared library problem? Or, is there a way to fix this all at once?
I have xml2 installed (libxml2-devel-2.9.5-2.fc27.x86_64) already.
Since no one answered this yet and I've found a hacky solution, I thought I'd give an update on what worked.
It appears that my issue was that, even upon installing libxml2-devel, the version of the libraries I had in /usr/lib64 were not the same version required by RStudio's xml2 package. For example, regarding the particular package being mentioned in my question above, libicuuc.so.58, only libicuuc.so.57 could be found in /usr/lib64.
Running locate libicuuc.so.58, I found that anaconda3 has the correct versions of the libraries, so I got around the above problem temporarily by simply adding ~/anaconda3/lib to $LD_LIBRARY_PATH, roughly following instructions here.
This is a bit hacky, but led to successful installation.
Edit (IMPORTANT): Adding ~/anaconda3/lib to LD_LIBRARY_PATH in .bashrc caused a login loop, presumably because Fedora was trying to use the wrong libraries. To fix this, I added the lines:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/ryi/anaconda3/lib/
export LD_LIBRARY_PATH
to R_HOME/etc/ldpaths.
I have solved this problem by install the ICU4C by source:
downloading ICU4C 58.2 from: ICU-Project
compiled
added the library location to $LD_LIBRARY_PATH,
the install will be work.

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