Error in installing Tabulizer - r

Using the instructions described in github and installing Java accordingly with Chocolatey -- plus installing rJava and setting the path in R with Sys.setenv(JAVA_HOME = "C:/Program Files/Java/jdk1.8.0_131")-- I've done the following in R:
library(ghit)
library(git2r)
ghit::install_github(c("leeper/tabulizerjars", "leeper/tabulizer"), INSTALL_opts = "--no-multiarch", dependencies = c("Depends", "Imports"))
Which is the solution provided in this answer. I get the following error:
Error in git2r::init(d) :
Error in 'git2r_repository_init': Unable to init repository
Setting the option VERBOSE = TRUE in install_github I get the following additional output:
Parsing reponame for 'leeper/tabulizerjars'...
Creating local git repository for tabulizerjars in C:\Users\JOOCAR~1\AppData\Local\Temp\RtmpgnitDP\tabulizerjars1643e0126f5...
Error in git2r::init(d) :
Error in 'git2r_repository_init': Unable to init repository
I read this answer and it seems that it has to do with my username, which is spaced and has accents. But how do I configure this?
edit: 6/4/2017 1:57 am
Following user #jaySf answer, I run part of the code of his answer (since I've already installed rJava and devtools):
library(rJava) # load and attach 'rJava' now
devtools::install_github("ropensci/tabulizer", args="--no-multiarch")
And got the following error:
> library(rJava) # load and attach 'rJava' now
> devtools::install_github("ropensci/tabulizer", args="--no-multiarch")
Downloading GitHub repo ropensci/tabulizer#master
from URL https://api.github.com/repos/ropensci/tabulizer/zipball/master
Installing tabulizer
Downloading GitHub repo ropensci/tabulizerjars#master
from URL https://api.github.com/repos/ropensci/tabulizerjars/zipball/master
Installing tabulizerjars
"C:/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL "C:/Users/Joo \
Caos/AppData/Local/Temp/Rtmpgh9eJi/devtoolsb3c50925145/ropensci-tabulizerjars-c6cc40e" --library="C:/R-3.4.0/library" --install-tests
* installing *source* package 'tabulizerjars' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error: package or namespace load failed for 'tabulizerjars':
.onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/R-3.4.0/library/rJava/libs/i386/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/R-3.4.0/library/tabulizerjars'
Installation failed: Command failed (1)
"C:/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL "C:/Users/Joo \
Caos/AppData/Local/Temp/Rtmpgh9eJi/devtoolsb3c4a2835ec/ropensci-tabulizer-a38d957" --library="C:/R-3.4.0/library" --install-tests --no-multiarch
ERROR: dependency 'tabulizerjars' is not available for package 'tabulizer'
* removing 'C:/R-3.4.0/library/tabulizer'
Installation failed: Command failed (1)
I believe that I might have a problem with my username in the file directory path, but I'm not sure. I tried using install_github with ggplot2 --`install_github("wch/ggplot2") -- and it worked fine. If my guess is correct, how can I edit the file path?
Problem solved
I was running R with both 32 bit and 64 bit files installed. I cannot clearly state what were the problems in doing this, since as I ran Sys.getenv("R_ARCH") it returned x64 previously, but when I uninstalled the 32 bit files, it ran perfectly well with #jaySf code.

Follow these steps in given order should work:
install.packages("rJava")
library(rJava) # load and attach 'rJava' now
install.packages("devtools")
devtools::install_github("ropensci/tabulizer", args="--no-multiarch")
I'm using R 3.4.0 on win64, and described the procedure in a former answer.

install.packages("rJava")
library(rJava) # load and attach 'rJava' now
install.packages("devtools")
#run below package first..
devtools::install_github("ropensci/tabulizerjars", args="--no-multiarch")
devtools::install_github("ropensci/tabulizer", args="--no-multiarch")

You might try:
devtools::install_github("ropensci/tabulizerjars", INSTALL_opts = c("--no-multiarch"))
devtools::install_github("ropensci/tabulizer", INSTALL_opts = c("--no-multiarch"))

Related

Trouble Installing qdap package into R

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!

loading failed in installing R package fdaPDE from github

Good morning,
I am trying to install the R package fdaPDE from GitHub repository "NegriLuca/fdaPDE-manifold" via RStudio1.4, using the package devtools. My OS is Windows 10, I am using Rtools35 and R3.5.1. The package has to be compiled from source. I have typed the following:
install.packages('devtools')
library(devtools)
install_github("NegriLuca/fdaPDE-manifold")
and got the following:
[… I omit the long compilation part …]
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error: package or namespace load failed for 'fdaPDE'inlibrary.dynam(lib, package, package.lib):
DLL 'fdaPDE' not found: maybe not installed for this architecture?
Errore: loading failed
Esecuzione interrotta
*** arch - x64
Error: package or namespace load failed for 'fdaPDE' in library.dynam(lib, package, package.lib):
DLL 'fdaPDE' not found: maybe not installed for this architecture?
Errore: loading failed
Esecuzione interrotta
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Gianmaria/Documents/R/win-library/3.5/fdaPDE'
In R CMD INSTALL
Error in i.p(...) :
(converted from warning) installation of package ‘C:/Users/GIANMA~1/AppData/Local/Temp/RtmpwDxgqJ/file466865be7d8c/fdaPDE_0.1-5.tar.gz’ had non-zero exit status
What can I do to fix this?
I have finally managed to install the package. What I did was the following:
-REMOVE previous installations (I had supposed that to be done automatically but it was not, and I had an older version installed) by typing in Rstudio
remove.packages("fdaPDE")
-In Windows cmd, after having downloaded the code from Github, type
"Path/to/Rfolder/R" CMD BUILD <path to folder fdaPDE>
"Path/to/Rfolder/R" CMD INSTALL -l <path name of the R library tree> <path name of the package to be installed>
Hope that this may be useful for other people who faces similar errors.

Wrong version of Java is loaded during installation

I have a weird issue while trying to install packages which depend on Java/rJava on my 64-bit Windows 10:
> devtools::install_github("ropensci/tabulizer", INSTALL_opts = "--no-multiarch")
Downloading GitHub repo ropensci/tabulizer#master
from URL https://api.github.com/repos/ropensci/tabulizer/zipball/master
Installing tabulizer
Downloading GitHub repo ropensci/tabulizerjars#master
from URL https://api.github.com/repos/ropensci/tabulizerjars/zipball/master
Installing tabulizerjars
"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/binis/AppData/Local/Temp/Rtmpiw2khr/devtools4d7472ae39f9/ropensci-tabulizerjars-60b7cec" \
--library="C:/Users/binis/Documents/R/win-library/3.4" --install-tests
* installing *source* package 'tabulizerjars' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error: package or namespace load failed for 'tabulizerjars':
.onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/binis/Documents/R/win-library/3.4/rJava/libs/i386/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/binis/Documents/R/win-library/3.4/tabulizerjars'
Installation failed: Command failed (1)
"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/binis/AppData/Local/Temp/Rtmpiw2khr/devtools4d744e067cae/ropensci-tabulizer-3aad163" \
--library="C:/Users/binis/Documents/R/win-library/3.4" --install-tests
ERROR: dependency 'tabulizerjars' is not available for package 'tabulizer'
* removing 'C:/Users/binis/Documents/R/win-library/3.4/tabulizer'
Installation failed: Command failed (1)
Now I'm aware that this looks like I messed up with Java versions or path information. But that's not the case (as far as I'm aware):
> library(rJava)
> .jinit()
> .jcall("java/lang/System", "S", "getProperty", "java.version")
[1] "1.8.0_151"
> .jcall("java/lang/System", "S", "getProperty", "java.home")
[1] "C:\\Program Files\\Java\\jre1.8.0_151"
> .jcall("java/lang/System", "S", "getProperty", "sun.arch.data.model")
[1] "64"
> .jcall("java/lang/System", "S", "getProperty", "os.arch")
[1] "amd64"
This shows that os architecture and Java architecture match (R is 64-bit as well), that java.home is set correctly and also that rJava works nicely on my machine.
Now I'm not sure I understand the error message correctly but it seems that R is trying to load the 32-bit version of rJava during installation which fails. I tested this by changing java home to a 32-bit installation on my machine:
> options(java.home="C:/Program Files (x86)/Java/jre1.8.0_151") #32-bit version
> library(rJava)
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/binis/Documents/R/win-library/3.4/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
The error is the same which supports my assumption. However, I do not understand why R would try to use a different Java version during installtion or how I could stop that. I already tested if INSTALL_opts = c("--no-multiarch", "--no-test-load"), type="source" will do anything but the error remains the same...
After I spent some more time on google/stackoverflow, I found that the syntax of install_github is apparently slightly different from install.packages. Instead of ´INSTALL_opts´, options are invoked with ´args´. The follwing command, therefore, installs the example package without "complaints":
devtools::install_github("ropensci/tabulizer",
args = c("--no-multiarch", "--no-test-load"))
I leave this here in case others run into the same issue.

coreNLP & rJava installation issue from gitbub in R

fellow stackoverflowers!
I was trying to install coreNLP from github as there is a bug in the coreNLP package that comes with R.
Now while installing the coreNLP from github using below
To download the R library and corresponding CoreNLP java library, run the following in R:
devtools::install_github("statsmaths/coreNLP")
coreNLP::downloadCoreNLP()
I got an error
installing source package 'coreNLP' ...
** R
** data
* moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
* installing help indices
** building package indices
** testing if installed package can be loaded
* arch - i386
Error: package or namespace load failed for 'coreNLP':
.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/animshru/Documents/R/win-library/3.4/coreNLP'
Installation failed: Command failed (1)
After looking at many suggestions what I understood was
i) I was missing the class file path for Java Home and added the same and tried installing coreNLP again.
Sys.setenv(JAVA_HOME='C:/Program Files/Java/jre1.8.0_121')
devtools::install_github("statsmaths/coreNLP")
This time the error generated relates to the package/library rJava as seen below
Downloading GitHub repo statsmaths/coreNLP#master
from URL https://api.github.com/repos/statsmaths/coreNLP/zipball/master
Installing coreNLP
"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/XYZ/AppData/Local/Temp/RtmpieUxG6/devtools3c0456877ca/statsmaths-coreNLP-caee22e" \
--library="C:/Users/XYZ/Documents/R/win-library/3.4" --install-tests
installing source package 'coreNLP' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/XYZ/Documents/R/win-library/3.4/rJava/libs/x64/rJava.dll':
LoadLibrary failure: The specified module could not be found.
ERROR: lazy loading failed for package 'coreNLP'
* removing 'C:/Users/XYZ/Documents/R/win-library/3.4/coreNLP'
Installation failed: Command failed (1)
I have installed the rJava package successfully and able to access the library for the same. Now I need to understand why I am getting this error of access issue to a rjava.dll file inside the package rJava.?
Has anyone encountered the same problem already??
I have double and triple checked the java version is 64bit same as the R.
Any hints folks??
Thanks

Error in installing R Package "SqlRender"

I am new to R - Programming, I am trying to run "install_github("ohdsi/SqlRender")" on windows 7, 64-bit with jdk 7 (64- bit) and R version 3.1.2 and R-GUI (64-bit).
I am getting the following error:
> library("devtools")
Warning message:
package ‘devtools’ was built under R version 3.1.3
> install_github("ohdsi/SqlRender")
Downloading github repo ohdsi/SqlRender#master
Installing SqlRender
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --no-site-file --no-environ --no-save -- no-restore CMD INSTALL \
"C:/Users/PPingali/AppData/Local/Temp/RtmpMtqVJl/devtools1318104472eb/OHDSI- SqlRender-cc551a2" \
--library="C:/Users/PPingali/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'SqlRender' ...
** R
** inst
** tests
** 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: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/PPingali/Documents/R/win- library/3.1/rJava/libs/i386/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/PPingali/Documents/R/win-library/3.1/SqlRender'
Error: Command failed (1)
Please help me out in fixing this issue...
Thanks in advance.....
....................................................................
rJava package got installed perfectly...
when i run
library(rJava)
gives me no error.....
install.packages("SqlRender",INSTALL_opts = "--no-multiarch")
for some reason checks bost 32 and 64bit versions. even though I have correct x64 version of Java 1.8, R it still failed check i386 step. the INSTALL_opts flaf seems to bypass and then no issue

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