Rstudio Hangs while installing packages [not able to install nlopt-2.4.2]

[Venkatesh6840]

** building package indices
** installing vignettes
** testing if installed package can be loaded

• DONE (webshot)
• installing source package ‘nloptr’ ...
  ** package ‘nloptr’ successfully unpacked and MD5 sums checked
  checking for g++... g++
  checking whether the C++ compiler works... yes
  checking for C++ compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C++ compiler... yes
  checking whether g++ accepts -g... yes
  checking how to run the C++ preprocessor... g++ -E
  checking whether we are using the GNU C++ compiler... (cached) yes
  checking whether g++ accepts -g... (cached) yes
  checking for pkg-config... yes
  configure: Now testing for NLopt header file.
  checking for grep that handles long lines and -e... /bin/grep
  checking for egrep... /bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking nlopt.h usability... no
  checking nlopt.h presence... no
  checking for nlopt.h... no
  configure: Need to download and build NLopt
  trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
  Error in download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz", :
  cannot open URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
  Execution halted
  /usr/bin/gtar: This does not look like a tar archive

gzip: stdin: unexpected end of file
/usr/bin/gtar: Child returned status 1
/usr/bin/gtar: Error is not recoverable: exiting now
Warning message:
In untar(tarfile = "nlopt-2.4.2.tar.gz") :
'/usr/bin/gtar -xf 'nlopt-2.4.2.tar.gz'' returned error code 2
configure: Starting to install library to /tmp/RtmpRwvLJS/R.INSTALL26ca3850fac/nloptr/nlopt-2.4.2
./configure: line 3325: cd: nlopt-2.4.2: No such file or directory
./configure: line 3325: ed: command not found
./configure: line 3327: ed: command not found
./configure: line 3331: ed: command not found

[jerry1100]

Hey @Venkatesh6840, I'm not very familiar with RStudio but I'll try to help.

First it'll help if you list down the steps you took to produce this issue, so I can reproduce it on my end.

[jerry1100]

Played around and got something similar. Did you just run install.packages("nloptr") in RStudio?

[Venkatesh6840]

1)Open Rstudio from IBM Data Science Experience Desktop
2)File->New File-> R Script
3)install.packages("car", dependencies=TRUE, INSTALL_opts = c('--no-lock'))
4)press ctrl+enter on the above statement
5)a pop-up box is displayed "updating loaded packages"
do you want to restart R prior to installing?
6)Clicked on Yes -> again and again the pop-up box displayed many times
7)Clicked on No -> it tried to install car packaged , but the above error will be displayed "nlopt-2.4.2" not installed

[jerry1100]

It seems like

Error in download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz", :
cannot open URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'

might be what's causing the error. For some reason we can't download that file from inside R, but doing it via the browser works fine.

Try it yourself. Start an R session and enter:
download.file("http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz", "./"), which somehow results in a 403 Forbidden status code.

I'll keep investigating.

[jerry1100]

After some digging around, it seems like it's an issue with R's download.file() not setting the proper headers when making the request, specifically the User-Agent HTTP header (more info).

Here's a StackOverflow post which describes a similar problem, as well as a workaround for downloading the file.

I'll see if it's possible to download the file manually and install it.

[jerry1100]

I made some progress by manually downloading nloptr, building it, then trying to install "car", but I don't know if it was successful or not. I saw some error messages but it seemed like the install finished. You'll have to try it for yourself.

Here are the instructions:

1. Launch RStudio
2. Open a terminal and enter docker ps --format "{{.Names}}" | grep "rstudio"
   • If you see more than one result, go to the runtimes page (click "Runtimes" on the DSX sidebar) and shutdown all the instances of RStudio except one (the project that you're interested in)
3. Start a bash session inside the rstudio container: docker exec -it $(docker ps --format "{{.Names}}" | grep "rstudio") bash
4. Download and extract the nlopt package: curl -L http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz | tar -xz
5. Go to nlopt directory: cd nlopt-2.4.2
6. Build and install: ./configure && make && make install
7. Go back to RStudio and attempt to install "car"

Let me know if the above works.

[Venkatesh6840]

Im not able to recreate the above steps
I opened bash shell in Rstudio and tried to run the command "curl -l http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz | tar -xz"

getting error as
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 373 100 373 0 0 317 0 0:00:01 0:00:01 --:--:-- 317
100 373 100 373 0 0 317 0 0:00:01 0:00:01 --:--:-- 317

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

[jerry1100]

Two things:

1. The '-L' flag in the curl command should be capitalized. Again, the command to download and extract the packages is: curl -L http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz | tar -xz
2. Make sure you create a bash session using the steps I outlined above. Once you get in the container, enter whoami and make sure that you are the root user. If you create a shell session from RStudio (Tools > Shell), you'll be signed in as the rstudio user, not the root user.

[Venkatesh6840]

I tried using the above steps from terminal , install was completed with some error messages , but when i tried to run command "library(car)"
Error in library(car) : there is no package called ‘car’
means installation was not successful

attached the car package installation log
car_error.txt

[jerry1100]

Hey @Venkatesh6840, sorry but I'm not sure how to help you further. Hopefully someone else will come across a similar issue and figures out a way to fix it.