R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> install.packages('devtools')
Installing package into ‘/home/kingslee/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘xml2’ is not available
also installing the dependency ‘rversions’
--2015-07-29 12:02:27--
https://cran.rstudio.com/src/contrib/rversions_1.0.2.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 54.230.188.51
Connecting to cran.rstudio.com (cran.rstudio.com)|54.230.188.51|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4654 (4.5K) [application/x-gzip]
Saving to: ‘/tmp/Rtmpcd8fcf/downloaded_packages/rversions_1.0.2.tar.gz’
0K .... 100%
540M=0s
2015-07-29 12:02:29 (540 MB/s) -
‘/tmp/Rtmpcd8fcf/downloaded_packages/rversions_1.0.2.tar.gz’ saved [4654/4654]
--2015-07-29 12:02:29-- https://cran.rstudio.com/src/contrib/devtools_1.8.0.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 54.230.188.51
Connecting to cran.rstudio.com (cran.rstudio.com)|54.230.188.51|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 141487 (138K) [application/x-gzip]
Saving to: ‘/tmp/Rtmpcd8fcf/downloaded_packages/devtools_1.8.0.tar.gz’
0K .......... .......... .......... .......... .......... 36% 388K 0s
50K .......... .......... .......... .......... .......... 72% 487K 0s
100K .......... .......... .......... ........ 100% 440K=0.3s
2015-07-29 12:02:30 (434 KB/s) -
‘/tmp/Rtmpcd8fcf/downloaded_packages/devtools_1.8.0.tar.gz’ saved [141487/141487]
ERROR: dependency ‘xml2’ is not available for package ‘rversions’
* removing ‘/home/kingslee/R/x86_64-pc-linux-gnu-library/3.0/rversions’
Warning in install.packages :
installation of package ‘rversions’ had non-zero exit status
ERROR: dependency ‘rversions’ is not available for package ‘devtools’
* removing ‘/home/kingslee/R/x86_64-pc-linux-gnu-library/3.0/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpcd8fcf/downloaded_packages’
You might to install that xml tool on the machine.
sudo apt-get -y install libxml2-dev
If that does indeed get rid of your error, you should follow this post for more instructions on how to get R properly set up on Ubuntu
Related
I am trying to install dlib in Anaconda so as to use it inside jupyter-notebook.
I tried using conda install -c menpo dlib and then dlib doesn't get installed rather it then says :
Downloading and Extracting Packages
py-boost-1.67.0 | 318 KB | ################################################################# | 100%
widgetsnbextension-1 | 1.1 MB | | 0%
ipywidgets-5.1.5 | 61 KB | | 0%
boost-1.59.0 | 11.9 MB | | 0%
dlib-19.9 | 2.3 MB | | 0%
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/menpo/osx-64/widgetsnbextension-1.2.3-py35_1.tar.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/menpo/osx-64/ipywidgets-5.1.5-py35_0.tar.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/menpo/osx-64/boost-1.59.0-py35_0.tar.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/menpo/osx-64/dlib-19.9-py35_0.tar.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
Then, I downloaded the dlib-19.16.0.tar.gz from here and saved it in /anaconda3/lib/python3.6/site-packages and then ran conda install -c conda-forge dlib-19.16.0.tar.gz but it shows :
PackagesNotFoundError: The following packages are not available from current channels:
- dlib-19.16.0.tar.gz
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/osx-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/pro/osx-64
- https://repo.anaconda.com/pkgs/pro/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
The first error is just saying you are not able to connect to the menpo repository of libraries. I recommend to check your proxy/internet connection.
In the second case you are trying to install a tar.gz file, that's a compressed file. Decompressed it(unzip it) first and then try to install it.
I'm trying to execute Jest on Ubuntu 14.04.02, in a virtual machine with 4gb of RAM. node version 0.12.2, npm 2.0.0-alpha-5
free shows me:
total used free shared buffers cached
Mem: 3.8G 199M 3.6G 976K 1.1M 18M
When I run npm test, I keep getting a variety of out of memory errors:
Error: FATAL ERROR: CALL_AND_RETRY_LAST Allocation failed - process out of memory
FATAL ERROR: Committing semi space failed. Allocation failed - process out of memory
# Fatal error in ../deps/v8/src/heap/store-buffer.cc, line 132
# CHECK(old_virtual_memory_->Commit(reinterpret_cast<void*>(old_limit_), grow * kPointerSize, false)) failed
Any idea what the minimum memory requirement is...or if I have misconfiguration something that is leading to this?
It turns out downgrading to node version 0.10.32, installed via npm, healed the issue.
I have a rhel 5.2 machine and I am trying to mount a ntfs file system harddisk. I know that we need ntfs and fuse rpms to mount it. By installing those rpms I mounted it in my rhel 5.4 machine. But in 5.2 I followed the same steps but failed to mount. Then after googling I found that 5.2 kernel doesn't support or have fuse kernel by default and then I followed this link.
Below is the output after doing the steps said in this link.
[root#racdb1 ~]# wget http://packages.sw.be/rpmforge-release/rpmforge-release-0. 3.6-1.el5.rf.i386.rpm
--14:14:20-- http://packages.sw.be/rpmforge-release/rpmforge-release-0.3.6-1.el 5.rf.i386.rpm
Resolving packages.sw.be... 78.46.17.228
Connecting to packages.sw.be|78.46.17.228|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.3.6-1.el 5.rf.i386.rpm [following]
--14:14:32-- http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.3.6- 1.el5.rf.i386.rpm
Resolving pkgs.repoforge.org... 78.46.17.228
Connecting to pkgs.repoforge.org|78.46.17.228|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://rpmforge.sw.be/redhat/el5/en/i386/rpmforge/RPMS/rpmforge-releas e-0.3.6-1.el5.rf.i386.rpm [following]
--14:14:39-- http://rpmforge.sw.be/redhat/el5/en/i386/rpmforge/RPMS/rpmforge-re lease-0.3.6-1.el5.rf.i386.rpm
Resolving rpmforge.sw.be... 78.46.17.228
Connecting to rpmforge.sw.be|78.46.17.228|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://tree.repoforge.org/redhat/el5/en/i386/rpmforge/RPMS/rpmforge-re lease-0.3.6-1.el5.rf.i386.rpm [following]
--14:14:51-- http://tree.repoforge.org/redhat/el5/en/i386/rpmforge/RPMS/rpmforg e-release-0.3.6-1.el5.rf.i386.rpm
Resolving tree.repoforge.org... 78.46.17.228
Connecting to tree.repoforge.org|78.46.17.228|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://apt.sw.be/redhat/el5/en/i386/rpmforge/RPMS/rpmforge-release-0.3 .6-1.el5.rf.i386.rpm [following]
--14:14:59-- http://apt.sw.be/redhat/el5/en/i386/rpmforge/RPMS/rpmforge-release -0.3.6-1.el5.rf.i386.rpm
Resolving apt.sw.be... 193.1.193.67
Connecting to apt.sw.be|193.1.193.67|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 16698 (16K) [application/x-redhat-package-manager]
Saving to: `rpmforge-release-0.3.6-1.el5.rf.i386.rpm'
100%[=======================================>] 16,698 14.4K/s in 1.1s
14:15:09 (14.4 KB/s) - `rpmforge-release-0.3.6-1.el5.rf.i386.rpm' saved [16698/1 6698]
[root#racdb1 ~]# rpm -Uhv rpmforge-release-0.3.6-1.el5.rf.i386.rpm
warning: rpmforge-release-0.3.6-1.el5.rf.i386.rpm: Header V3 DSA signature: NOKE Y, key ID 6b8d79e6
Preparing... ########################################### [100%]
1:rpmforge-release ########################################### [100%]
[root#racdb1 ~]# yum install fuse fuse-ntfs-3g dkms dkms-fuse
Loading "security" plugin
Loading "rhnplugin" plugin
This system is not registered with RHN.
RHN support will be disabled.
rpmforge 100% |=========================| 1.9 kB 00:00
primary.sqlite.bz2 100% |=========================| 7.3 MB 01:20
Setting up Install Process
Parsing package install arguments
No package fuse available.
No package dkms-fuse available.
Resolving Dependencies
--> Running transaction check
---> Package fuse-ntfs-3g.i386 0:2013.1.13-2.el5.rf set to be updated
--> Processing Dependency: fuse >= 2.6.3 for package: fuse-ntfs-3g
---> Package dkms.noarch 0:2.1.1.2-1.el5.rf set to be updated
--> Finished Dependency Resolution
**Error: Missing Dependency: fuse >= 2.6.3 is needed by package fuse-ntfs-3g**
I don't know what to do from the above error which I got. I searched in google but I didn't get the solution anywhere. How to solve the above issue?
I finally found the process to use ntfs file system in rhel 5.2. I followed the link.
http://oliphauntz.blogspot.in/2011/03/fix-how-to-mount-ntfs-filesystem-on.html#comment-form
In the above link the step " wget http://pbxinaflash.net/source/pogoplug/fuse-2.6.0.tar.gz" is not working. So I manually downloaded fuse-2.6.0 from internet and then installed and configured it. Try the same if anyone is facing the same problem which I faced.
I'm trying to take a script I have that updates my sytstem for me, and have it output it's text to a file, and the screen. This is fairly simple using tee, except my update manager, pacman, outputs the same kind of text like wget. Here's some sample output.
core 107.0 KiB 392K/s 00:00 [################################################################] 100%
extra 1531.8 KiB 719K/s 00:02 [################################################################] 100%
community 2.1 MiB 818K/s 00:03 [################################################################] 100%
When I try to redirect that kind of output to a file using tee, this is the output I get to my screen and file.
:: Synchronizing package databases...
downloading core.db...
downloading extra.db...
downloading community.db...
I understand this is because pacman uses a buffer to output to the screen, but I'm still hoping there's a way I can output the status to the screen and the file, and not just the "downloading xyz...".
Thank you in advance for any help.
Edit:
I have no current updates, but here's some sample output that's very similar of me installing the Opera browser. The lines with the percentages and the pound signs are buffers that update with the progress of the download.
resolving dependencies...
looking for inter-conflicts...
Packages (1): opera-12.16.1860-2
Total Download Size: 10.49 MiB
Total Installed Size: 45.03 MiB
:: Proceed with installation? [Y/n] y
:: Retrieving packages ...
opera-12.16.1860-2-x86_64 13.4 MiB 1151K/s 00:12 [################################################################] 100%
(1/1) checking keys in keyring [################################################################] 100%
(1/1) checking package integrity [################################################################] 100%
(1/1) loading package files [################################################################] 100%
(1/1) checking for file conflicts [################################################################] 100%
(1/1) checking available disk space [################################################################] 100%
(1/1) installing opera [################################################################] 100%
Optional dependencies for opera
gstreamer0.10-base-plugins: HTML5 Video support
gstreamer0.10-good: HTML5 Video support
This is what the above output looks like when redirected through tee.
warning: opera-12.16.1860-2 is up to date -- reinstalling
resolving dependencies...
looking for inter-conflicts...
Packages (1): opera-12.16.1860-2
Total Installed Size: 45.03 MiB
Net Upgrade Size: 0.00 MiB
:: Proceed with installation? [Y/n] y
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
reinstalling opera...
As you can see, the download progess isn't shown. Just three periods.
Note sure if I fully understand the question, but I think possibly your script outputs to both stdout and stderr and you want both to be captured to file as well displayed on the terminal. In which case, you could do this by redirecting stderr of your script to stderr, before piping the whole thing to tee:
./myscript.sh 2>&1 | tee output.log
So I think you also want all the output with respect to progress bars, etc. You can use the script command to get this:
script -e -q -c "./myscript.sh" output.log
This works for me with wget:
Terminal output:
ubuntu#ubuntu:~$ script -e -q -c "wget http://stackoverflow.com" output.log
--2014-02-21 20:01:31-- http://stackoverflow.com/
Resolving stackoverflow.com (stackoverflow.com)... 198.252.206.140
Connecting to stackoverflow.com (stackoverflow.com)|198.252.206.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 214108 (209K) [text/html]
Saving to: `index.html.5'
100%[======================================>] 214,108 7.59K/s in 38s
Last-modified header invalid -- time-stamp ignored.
2014-02-21 20:02:13 (5.55 KB/s) - `index.html.5' saved [214108/214108]
ubuntu#ubuntu:~$
Contents of output.log:
Script started on Fri 21 Feb 2014 08:01:31 PM PST
--2014-02-21 20:01:31-- http://stackoverflow.com/
Resolving stackoverflow.com (stackoverflow.com)... 198.252.206.140
Connecting to stackoverflow.com (stackoverflow.com)|198.252.206.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 214108 (209K) [text/html]
Saving to: `index.html.5'
0% [ ] 0 --.-K/s
1% [ ] 3,367 3.66K/s
2% [> ] 5,863 5.09K/s
3% [> ] 7,111 3.54K/s
5% [> ] 10,855 3.73K/s
### Output omitted - I have a slow connection right now ###
97% [=====================================> ] 209,806 7.84K/s eta 1s
99% [=====================================> ] 212,302 7.44K/s eta 1s
100%[======================================>] 214,108 7.59K/s in 38s
Last-modified header invalid -- time-stamp ignored.
2014-02-21 20:02:13 (5.55 KB/s) - `index.html.5' saved [214108/214108]
I just installed Oracle Coherence 3.6 on RHEL 5.5. When I execute cache-server.sh I get a lot of GC warnings about allocating large blocks and then it fails with a segmentation fault. Suggestions? Here is the stack:
GC Warning: Repeated allocation of very large block (appr. size 1024000):
May lead to memory leak and poor performance.
GC Warning: Repeated allocation of very large block (appr. size 1024000):
May lead to memory leak and poor performance.
./bin/cache-server.sh: line 24: 6142 Segmentation fault $JAVAEXEC -server -showversion $JAVA_OPTS -cp "$COHERENCE_HOME/lib/coherence.jar" com.tangosol.net.DefaultCacheServer $1
[root#localhost coherence_3.6]# swapon -s
Filename Type Size Used Priority
/dev/mapper/VolGroup00-LogVol01 partition 2097144 0 -1
[root#localhost coherence_3.6]# free
total used free shared buffers cached
Mem: 3631880 662792 2969088 0 142636 353244
-/+ buffers/cache: 166912 3464968
Swap: 2097144 0 2097144
[root#localhost coherence_3.6]# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/VolGroup00-LogVol00
147G 6.7G 133G 5% /
/dev/sda1 99M 12M 82M 13% /boot
tmpfs 1.8G 0 1.8G 0% /dev/shm
/dev/hdb 2.8G 2.8G 0 100% /media/RHEL_5.5 Source
/dev/hda 57M 57M 0 100% /media/VBOXADDITIONS_4.2.16_86992
[root#localhost coherence_3.6]#
I haven't seen this issue before, but to start, I'd suggest the following:
Check for Linux updates. The JVMs for example now try to use large pages, and there have been some bugs in RH related to large pages that are fixed in the latest versions.
Download the latest Java 7 JDK. While no JDK is entirely bug-free, we have done extensive testing with JDK 7 patch levels 15, 21 and 40.
Download the latest version of Coherence. Coherence 12.1.2 is now out, but if you don't want to go for the very latest, then Coherence 3.7.1 is the suggested version. (The release after 3.7.1 is called 12.1.2. That is to align with Oracle versioning.)
I would check your space allocation on disk and memory/swap. You are probably running out of space somewhere.
df -h
free
You could also check your Java version - make sure that you are well patched.
Are you using Java 6 or Java 7?
There are Oracle forums for Coherence - you should try and ask the question there - thats where the real experts hang out.