Im trying to update the Rmarkdown package in RStudio but am getting the following error
Warning messages:
1: running command '"C:/Program Files/R/R-3.2.3/bin/x64/R" CMD INSTALL -l "C:\Users\foo\Documents\R\win-library\3.2" C:\Users\foo\AppData\Local\Temp\RtmpUdFXnp/downloaded_packages/rmarkdown_0.9.2.tar.gz' had status 1
2: In utils::install.packages(c("rmarkdown"), repos = "https://cran.rstudio.com/", :
installation of package 'rmarkdown' had non-zero exit status
My Session Information is below
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.2.3`
I do not have admin rights on my PC in work but have installed other libraries into the mydocuments section of my PC without issue
Related
I am unable to install "google-cloud-sdk" and seeing this error
and I followed instructions from https://cloud.google.com/sdk/docs/install#deb
ubuntu#ubuntu:~$ cat /etc/issue
Ubuntu 14.04.5 LTS
ubuntu#ubuntu:~$ sudo apt-get install google-cloud-sdk
Reading package lists... Done
Building dependency tree
Reading state information... Done
google-cloud-sdk is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 172 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] Y
Setting up google-cloud-sdk (356.0.0-0) ...
ERROR: gcloud failed to load: No module named 'typing'
gcloud_main = _import_gcloud_main()
import googlecloudsdk.gcloud_main
from googlecloudsdk.calliope import base
from googlecloudsdk.calliope import display
from googlecloudsdk.calliope import display_taps
from googlecloudsdk.core.resource import resource_printer_base
from googlecloudsdk.core.resource import resource_projector
import proto # pylint: disable=g-import-not-at-top
from .enums import Enum
from proto.marshal.rules.enums import EnumRule
from typing import Type
This usually indicates corruption in your gcloud installation or problems with your Python interpreter.
Please verify that the following is the path to a working Python 2.7 or 3.5+ executable:
/usr/bin/python3
If it is not, please set the CLOUDSDK_PYTHON environment variable to point to a working Python 2.7 or 3.5+ executable.
If you are still experiencing problems, please reinstall the Cloud SDK using the instructions here:
https://cloud.google.com/sdk/
dpkg: error processing package google-cloud-sdk (--configure):
subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
google-cloud-sdk
E: Sub-process /usr/bin/dpkg returned an error code (1)
"typing" module is present as shown below:
ubuntu#ubuntu:~$ python3
Python 3.4.3 (default, Nov 12 2018, 22:25:49)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
> import typing
> >>> from typing import Type
> >>> print(typing.__file__)
> /usr/local/lib/python3.4/dist-packages/typing.py
> >>>
Why it is not working?
Setting up "CLOUDSDK_PYTHON_SITEPACKAGES=1" environment variable worked
ubuntu#ubuntu:~$ export CLOUDSDK_PYTHON_SITEPACKAGES=1
ubuntu#ubuntu:~$ sudo -E apt-get install google-cloud-sdk
Reading package lists... Done
Building dependency tree
Reading state information... Done
google-cloud-sdk is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 172 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] Y
Setting up google-cloud-sdk (356.0.0-0) ...
components post-process --force-recompile
WARNING: Python 3.4.x is no longer officially supported by the Google Cloud SDK
and may not function correctly. Please use Python version 2.7.x or 3.5 and up.
If you have a compatible Python interpreter installed, you can use it by setting
the CLOUDSDK_PYTHON environment variable to point to it.
ubuntu#ubuntu:~$ which gcloud
/usr/bin/gcloud
Please, trying to rebuild IJulia given I am not able to launch it via Anaconda navigator (I receive the red kernel error). With the command Pkg.build("IJulia"), below is the output:
INFO: Building Conda
INFO: Building MbedTLS
===============================[ ERROR: MbedTLS]============================
LoadError: unlink: operation not permitted (EPERM)
while loading C:\Users\s1364322\.julia\v0.6\MbedTLS\deps\build.jl, in expression starting on line 40
==============================================================================
INFO: Building ZMQ
INFO: Building IJulia
INFO: Installing Jupyter via the Conda package.
INFO: Found Jupyter version 4.3.0:
C:\Users\s1364322\.julia\v0.6\Conda\deps\usr\Scripts\jupyter
INFO: Installing Julia kernelspec julia-0.6
Error executing Jupyter command 'kernelspec': [Errno 'jupyter-kernelspec' not found] 2
[InstallKernelSpec] Removing existing kernelspec in
C:\Users\s1364322\AppData\Roaming\jupyter\kernels\julia-0.6
[InstallKernelSpec] Installed kernelspec julia-0.6 in
C:\Users\s1364322\AppData\Roaming\jupyter\kernels\julia-0.6
================================[ BUILD ERRORS]=============================
WARNING: MbedTLS had build errors.
- packages with build errors remain installed in C:\Users\s1364322\.julia\v0.6
- build the package(s) and all dependencies with Pkg.build("MbedTLS")
- build a single package by running its deps/build.jl script
===============================================================================
When I try Pkg.build("MbedTLS"), the output is:
LoadError: unlink: operation not permitted (EPERM)
while loading C:\Users\s1364322\.julia\v0.6\MbedTLS\deps\build.jl, in expression starting on line 40
Please, how can I get the way around?
This is my version info:
Julia Version 0.6.0
Commit 903644385b* (2017-06-19 13:05 UTC)
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: Intel(R) Core(TM) i5-6300U CPU # 2.40GHz
WORD_SIZE: 64
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
LAPACK: libopenblas64_
LIBM: libopenlibm
LLVM: libLLVM-3.9.1 (ORCJIT, skylake)
Thanks for your help!
I install graphviz and pydot from the anaconda console
conda install graphviz
pip install git+https://github.com/nlhepler/pydot.git
And i I was no longer able to launch Anaconda, so I type these commands
conda install anaconda-navigator
I can launch Ananconda but I am offered to update the software, i click yes and i have this message
C:\Users\user\Anaconda3\python.exe C:\Users\user\Anaconda3\Scripts\conda-script.py
install --yes --json --force-pscheck --name root anaconda-navigator=1.6.4: HTTP 000
CONNECTION FAILED for url <https://repo.continuum.io/pkgs/main/win-64/repodata.json.bz2><br>
Elapsed: -<br><br>An HTTP error occurred when trying to retrieve this URL.<br>HTTP errors are
often intermittent, and a simple retry will get you on your way.<br>ConnectionError(
MaxRetryError("HTTPSConnectionPool(host='repo.continuum.io', port=443): Max retries exceeded
with url: /pkgs/main/win-64/repodata.json.bz2 (Caused by NewConnectionError('<
requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x0000000005F6B940>:
Failed to establish a new connection: [Errno 11001] getaddrinfo failed',))",),)<br>
When i want to run RStudio i have this message
rstudio.exe - The procedure entry point was not found
?toLocal8Bit#QString##QEGBA?AVQByteArray##XY can not be found in the dynamic link library
C:\Users\user\Anaconda3\Library\bin\rstudio.exe
library(tensorflow)
install_tensorflow() # success i have now i folder *r-tensorflow* in *C:\Anaconda3\envs\r-tensorflow*
sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.2 R6_2.2.2 tools_3.4.2 withr_2.0.0 curl_3.0 yaml_2.1.14
[8] memoise_1.1.0 git2r_0.19.0 digest_0.6.12 devtools_1.13.4
reticulate::conda_list()
name python
1 r-tensorflow C:\\Anaconda3\\envs\\r-tensorflow\\python.exe
reticulate::py_config()
python: C:\ANACON~1\python.exe
libpython: C:/ANACON~1/python36.dll
pythonhome: C:\ANACON~1
version: 3.6.3 |Anaconda, Inc.| (default, Oct 15 2017, 03:27:45) [MSC v.1900 64 bit (AMD64)]
Architecture: 64bit
numpy: C:\ANACON~1\lib\site-packages\numpy
numpy_version: 1.13.3
python versions found:
C:\ANACON~1\python.exe
C:\Anaconda3\envs\r-tensorflow\python.exe
I reuninstall Rtools, in my system path: Path
C:\Anaconda3\R\bin
C:\Anaconda3\R\bin\x64
C:\Anaconda3\Scripts
C:\Rtools\bin
C:\Rtools\mingw_32\bin
I have a clean install of RStudio Server (Pro) on clean Ubuntu 14.04. Install was smooth only problem I have is with rJava. Everything else appears to be working fine.
To install the rJava package I installed the package from the R (running as sudo) from the console. This is what I have always done when setting up RStudio Servers. Once installed rJava works fine from the R console as sudo or normal user.
From the RStudio IDE I can load the rJava package, but when I call .jinit() I get errors:
library(rJava)
.jinit()
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error in .jinit() : Cannot create Java virtual machine (-4)
This is contrary to what happens if I ssh onto the server directly as same user and run the same commands from R console - this does not generata any error.
Any idea what is going on here? I have searched around and not found anything that helps. I tried completely uninstalling openjdk, tried reinstalling the package. Nothing seems to work - and because I get different behavior between the R console on the terminal and the R console in RStudio Server I am slightly puzzled.
The version of R on the console is:
$platform
[1] "x86_64-pc-linux-gnu"
$arch
[1] "x86_64"
$os
[1] "linux-gnu"
$system
[1] "x86_64, linux-gnu"
$status
[1] ""
$major
[1] "3"
$minor
[1] "1.2"
$year
[1] "2014"
$month
[1] "10"
$day
[1] "31"
$`svn rev`
[1] "66913"
$language
[1] "R"
$version.string
[1] "R version 3.1.2 (2014-10-31)"
$nickname
[1] "Pumpkin Helmet"
This is the same as the version that R Studio Server is using.
JAVA_HOME is the same from R console on terminal and R console in RStudio Server
> Sys.getenv('JAVA_HOME')
[1] "/usr/lib/jvm/java-1.7.0-openjdk-amd64/jre"
This is the same as the JAVA_HOME I get from the shell.
I have the following java version:
java -version
java version "1.7.0_75"
OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)
Would love some suggestions or input from folks who have struggled with this same problem.
Cheers,
Matt
Have you check how much memory you set up for the JVM? I had the same issue as initially I set it up as 8g.
You can set up the size of JVM's memory using the following command:
options( java.parameters = "-Xmx8g" )
I have Aptana version 3.4.2.201308081805 on Linux Mint 15 64bit
was open just once and now anytime when I want to start the Aptana crash
here is the one from a few crash log:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0x7) at pc=0x00007fab6e08a938, pid=4403, tid=140373276522240
#
# JRE version: 7.0_25-b30
# Java VM: OpenJDK 64-Bit Server VM (23.7-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libzip.so+0x4938] Java_java_util_zip_ZipFile_getZipMessage+0x8d8
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please include
# instructions on how to reproduce the bug and visit:
# https://bugs.launchpad.net/ubuntu/+source/openjdk-7/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Don't use OpenJDK
Use Java 7 from the wbupd8 repository
sudo apt-add-repository ppa:webupd8team/java
Prerequirements
sudo apt-get install software-properties-common
If you got problems with SWT take a look at
Eclipse cannot load SWT libraries
I managed to fix this issue by removing openjdk and installing oracle jdk.
The step by step instruction is provided in the following article
http://www.wikihow.com/Install-Oracle-Java-on-Ubuntu-Linux
so far no crash in aptana.
FYI: I am using lubuntu