Open Anemone95 opened 6 years ago
Hi @Anemone0! I am not sure what is happening here. Maybe it is a (temporary) connectivity issue with your virtual machine in Vagrant? Can you try once more? Just make sure to remove any leftovers of this broken VM.
I tried going vagrant up
on my machine, and this is how the process ends:
default: installing packages ...
default: building HTML index ...
default: make[3]: Leaving directory `/vagrant/tmp/R-3.1.1/src/library'
default: make[2]: Leaving directory `/vagrant/tmp/R-3.1.1/src'
default: make[2]: Entering directory `/vagrant/tmp/R-3.1.1/tests'
default: make[2]: Nothing to be done for `install'.
default: make[2]: Leaving directory `/vagrant/tmp/R-3.1.1/tests'
default: make[1]: Leaving directory `/vagrant/tmp/R-3.1.1'
I suspect that means that everything got installed properly.
Ok, on my Windows 10 machine running the latest versions of vagrant and VirtualBox, I do get the same exact error as @Anemone0. If I scroll back in the log, I also noticed these:
default: R-3.1.1/src/library/Recommended/boot.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/boot.tgz: Cannot create symlink to `boot_1.3-11.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/boot_1.3-11.tar.gz
default: R-3.1.1/src/library/Recommended/class.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/class.tgz: Cannot create symlink to `class_7.3-10.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/class_7.3-10.tar.gz
default: R-3.1.1/src/library/Recommended/cluster.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/cluster.tgz: Cannot create symlink to `cluster_1.15.2.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/cluster_1.15.2.tar.gz
default: R-3.1.1/src/library/Recommended/codetools.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/codetools.tgz: Cannot create symlink to `codetools_0.2-8.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/codetools_0.2-8.tar.gz
default: R-3.1.1/src/library/Recommended/foreign.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/foreign.tgz: Cannot create symlink to `foreign_0.8-61.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/foreign_0.8-61.tar.gz
default: R-3.1.1/src/library/Recommended/KernSmooth.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/KernSmooth.tgz: Cannot create symlink to `KernSmooth_2.23-12.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/KernSmooth_2.23-12.tar.gz
default: R-3.1.1/src/library/Recommended/lattice.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/lattice.tgz: Cannot create symlink to `lattice_0.20-29.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/lattice_0.20-29.tar.gz
default: R-3.1.1/src/library/Recommended/Makefile.in
default: R-3.1.1/src/library/Recommended/Makefile.win
default: R-3.1.1/src/library/Recommended/MASS.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/MASS.tgz: Cannot create symlink to `MASS_7.3-33.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/MASS_7.3-33.tar.gz
default: R-3.1.1/src/library/Recommended/Matrix.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/Matrix.tgz: Cannot create symlink to `Matrix_1.1-4.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/Matrix_1.1-4.tar.gz
default: R-3.1.1/src/library/Recommended/mgcv.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/mgcv.tgz: Cannot create symlink to `mgcv_1.8-0.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/mgcv_1.8-0.tar.gz
default: R-3.1.1/src/library/Recommended/nlme.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/nlme.tgz: Cannot create symlink to `nlme_3.1-117.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/nlme_3.1-117.tar.gz
default: R-3.1.1/src/library/Recommended/nnet.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/nnet.tgz: Cannot create symlink to `nnet_7.3-8.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/nnet_7.3-8.tar.gz
default: R-3.1.1/src/library/Recommended/rpart.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/rpart.tgz: Cannot create symlink to `rpart_4.1-8.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/rpart_4.1-8.tar.gz
default: R-3.1.1/src/library/Recommended/spatial.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/spatial.tgz: Cannot create symlink to `spatial_7.3-8.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/spatial_7.3-8.tar.gz
default: R-3.1.1/src/library/Recommended/survival.tgz
default: tar:
default: R-3.1.1/src/library/Recommended/survival.tgz: Cannot create symlink to `survival_2.37-7.tar.gz'
default: : Protocol error
default: R-3.1.1/src/library/Recommended/survival_2.37-7.tar.gz
I am not sure if this is the root cause or not. Btw, my hunch is also that this problem is not related to ssh, but rather to unpacking/installing R. I am not sure though. It also seems to be happening only in newer versions of vagrant/VirtualBox. It could also be that Ubuntu 12.04 is not well-supported in these new versions. So maybe updating to 14.04 would help. Just brainstorming.
It seems to maybe be related to this: https://stackoverflow.com/questions/17895256/creating-symbolic-link-protocol-error
@zvonimir is right. When vagrant up
, the project directory is mounted to VirtualBox. Build scripts need to hard link to compile R-3.1.1, but NTFS does not support this. (You can see this process in env/emulab/prepare-dataanalysis.sh
):
cd ${MALINE}
mkdir tmp opt
cd tmp
# get the source code for R-3.1.1
wget http://cran.at.r-project.org/src/base/R-3/R-3.1.1.tar.gz
if [ $? -ne 0 ]; then
echo "Error while downloading the source code for R-3.1.1"
exit 101
fi
tar -xvf R-3.1.1.tar.gz
if [ $? -ne 0 ]; then
echo "Error while extracting the source code for R-3.1.1"
exit 102
fi
cd R-3.1.1
./configure --with-x=no --prefix=${MALINE}/opt/R-3.1.1/
if [ $? -ne 0 ]; then
echo "Error while configuring R-3.1.1"
exit 103
fi
make
if [ $? -ne 0 ]; then
echo "Error during the make process for-R 3.1.1"
exit 104
fi
So I changed the compilation path to the user's home directory and succeeded.
Line 5- 7 in env/emulab/prepare-dataanalysis.sh
:
cd /home/vagrant
mkdir tmp opt
cd tmp
However, I am not sure if such changes will affect the normal operation of the program.
After I run the command
vagrant up
, I get an error like this:The error seems to happen in compiling R-3.1.1. By the way, I use Windows 10.0.16299, and Vagrant 2.0.1. Is there any solutions?