Missing dependencies in pkg installs SOLVED

Wed, Jun 28, 2017 7:15 AM

So apparently (being a linux novice) I didn't realize it was insufficient to simply have the file marked as executable. It turns out the default TMP directory on my machine  is mounted with a noexec flag so no files in that directory are allowed to be executed.  The solution is to set an environment variable TMPDIR=some new directory I created  (eg. /home/myusername/tmp) Then R uses that directory for the installs.  The easiest method then is to use do  

sudo R
Sys.setev(TMPDIR="/home/myusername/tmp") 
install.packages(pkglist)

the sudo R part just ensures I am installing into the global library and not a user specific library

--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK 
T +1 763 417 4545 | M +1 612 567 8287 

-----Original Message-----
From: Conklin, Mike (GfK) 
Sent: Friday, June 23, 2017 4:38 PM
To: Don Cohen; Duncan Murdoch
Cc: Martin Maechler; r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

Checked all the permissions, and it appears that file_test returns a FALSE and system(ls -l) shows it is executable, so the problem seems to be in R and it's relationship to RHEL.  I tried installing R3.3.3 to see if the older version would install stringi and had the same problem so it doesn't appear to be R3.4 related.  I am now reaching out to some other sources who may have installed R on similar systems.

From: Conklin, Mike (GfK)
Sent: Friday, June 23, 2017 8:50 AM
To: Don Cohen; Duncan Murdoch
Cc: Martin Maechler; r-help at r-project.org
Subject: RE: [R] Missing dependencies in pkg installs

I had the same thought in the shower this morning but I was disappointed to find that SElinux was disabled on the system.  My next step will be to install a previous version of R on the system.  My problem is that I am planning a shiny server installation and at least half of the apps on the current system depend on these libraries that will not install.
--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
T +1 763 417 4545 | M +1 612 567 8287

-----Original Message-----
From: Don Cohen [mailto:don-r-help at isis.cs3-inc.com]
Sent: Thursday, June 22, 2017 6:18 PM
To: Duncan Murdoch
Cc: Conklin, Mike (GfK); Martin Maechler; r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

Duncan Murdoch writes:
 > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote:
 > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable.
 >
 > I don't know what is causing this bug.  Perhaps a Linux user can  > reproduce it and fix it.
 >
 > Here's what I see:
 >
 > file_test("-x") calls file.access(filename, 1L).  That in turn calls the  > C library function access(..., X_OK).  The ... is the name of the file,  > translated into the local encoding and expanded.  As far as I can see,  > that means ... should be exactly the string below.
 > >
 > > [1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi"
 >
 > The only thing I can think of is that your system is protecting you from  > executing a newly created file until some sort of virus or other check  > is done.  (This is common on Windows, but I've never heard of it before  > on Linux.)

Just a thought - are you running SELinux ?
Check the log files for refusals to run programs.