subject:"\[R\] Missing dependencies in pkg installs"

Re: [R] Missing dependencies in pkg installs SOLVED

2017-06-28 Thread Conklin, Mike (GfK)

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@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@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-h...@isis.cs3-inc.com]
Sent: Thursday, June 22, 2017 6:18 PM
To: Duncan Murdoch
Cc: Conklin, Mike (GfK); Martin Maechler; r-help@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.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Missing dependencies in pkg installs

2017-06-23 Thread Conklin, Mike (GfK)

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@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-h...@isis.cs3-inc.com]
Sent: Thursday, June 22, 2017 6:18 PM
To: Duncan Murdoch
Cc: Conklin, Mike (GfK); Martin Maechler; r-help@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.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Missing dependencies in pkg installs

2017-06-23 Thread Conklin, Mike (GfK)

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-h...@isis.cs3-inc.com] 
Sent: Thursday, June 22, 2017 6:18 PM
To: Duncan Murdoch
Cc: Conklin, Mike (GfK); Martin Maechler; r-help@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.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Don Cohen

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.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Duncan Murdoch


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.)


Hopefully someone else can help...

Duncan Murdoch


Browse[2]> dir(new)
 [1] "DESCRIPTION"   "INSTALL"   "LICENSE"   "MD5"
 [5] "NAMESPACE" "NEWS"  "R" "cleanup"
 [9] "configure" "configure.win" "inst"  "man"
[13] "src"
Browse[2]> test_file("-x",paste0(new,"/configure")
+ )
Error in test_file("-x", paste0(new, "/configure")) :
  could not find function "test_file"
Browse[2]> file_test("-x",paste0(new,"/configure"))
/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi/configure
  FALSE


However, at the same time, in a separate session I have the system look at the 
very same file and clearly the execution bit is set.


[root@dcex1102shinypr ~]# ls -l /tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi
total 312
-rwxr-xr-x 1 root root 66 Apr  2  2015 cleanup
-rwxr-xr-x 1 root root 173757 Apr  7 11:43 configure
-rw-r--r-- 1 root root669 Jun 23  2015 configure.win
-rw-r--r-- 1 root root   1451 Apr  7 15:08 DESCRIPTION
drwxr-xr-x 2 root root 35 Jun 22 22:26 inst
-rw-r--r-- 1 root root   6207 Apr  7 11:21 INSTALL
-rw-r--r-- 1 root root   3580 Mar 21 13:29 LICENSE
drwxr-xr-x 2 root root   4096 Jun 22 22:26 man
-rw-r--r-- 1 root root  63692 Apr  7 15:08 MD5
-rw-r--r-- 1 root root   6204 Oct 24  2016 NAMESPACE
-rw-r--r-- 1 root root  22407 Apr  7 11:44 NEWS
drwxr-xr-x 2 root root   4096 Jun 22 22:26 R
drwxr-xr-x 3 root root   8192 Jun 22 22:26 src
[root@dcex1102shinypr ~]#


If I CTRL-Z out of R in the first session I confirm the same result - the 
system shows the file as executable

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


-Original Message-----
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Thursday, June 22, 2017 3:06 PM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

On 22/06/2017 3:42 PM, Conklin, Mike (GfK) wrote:

Not much progress. I step through debug and it gets to the do.install() function 
which immediately errors with the same "configuration not executable" error.


I believe that is a locally defined function, which means you can set a 
breakpoint within it but only if R is compiled with source info, or you can 
manually call debug(do_install) after it has been created (typically just 
before it is called is a safe place to do this), and do the usual process.

It's still very mysterious to me why configure is losing its executable bit.  What I would do if I 
could reproduce this would be to run right up to the 
file_test("-x","configure") line, then print my working directory, and ctrl-Z 
out of R to look at the files there.  That should confirm that configure is not executable.

Then the hard part is figuring out why it isn't

Duncan



So, made a tempfunc that was a copy of tools:::.install_packages and
edited the file_test("-x","configure") line to return a TRUE

now I get a Permission Denied error (even if I run as root)


tempfunc("/home/meconk/stringi_1.1.5.tar.gz")

* installing to library '/usr/lib64/R/library'
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
sh: ./configure: Permission denied
ERROR: configuration failed for package 'stringi'
* removing '/usr/lib64/R/library/stringi'
Error in do_exit(status = status) : .install_packages() exit status 1
Error in do_exit(status = status) : .install_packages() exit status 1

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


-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Thursday, June 22, 2017 11:09 AM
To: Conklin,

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Conklin, Mike (GfK)

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.

[1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi"
Browse[2]> dir(new)
 [1] "DESCRIPTION"   "INSTALL"   "LICENSE"   "MD5"
 [5] "NAMESPACE" "NEWS"  "R" "cleanup"
 [9] "configure" "configure.win" "inst"  "man"
[13] "src"
Browse[2]> test_file("-x",paste0(new,"/configure")
+ )
Error in test_file("-x", paste0(new, "/configure")) :
  could not find function "test_file"
Browse[2]> file_test("-x",paste0(new,"/configure"))
/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi/configure
  FALSE


However, at the same time, in a separate session I have the system look at the 
very same file and clearly the execution bit is set.


[root@dcex1102shinypr ~]# ls -l /tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi
total 312
-rwxr-xr-x 1 root root 66 Apr  2  2015 cleanup
-rwxr-xr-x 1 root root 173757 Apr  7 11:43 configure
-rw-r--r-- 1 root root669 Jun 23  2015 configure.win
-rw-r--r-- 1 root root   1451 Apr  7 15:08 DESCRIPTION
drwxr-xr-x 2 root root 35 Jun 22 22:26 inst
-rw-r--r-- 1 root root   6207 Apr  7 11:21 INSTALL
-rw-r--r-- 1 root root   3580 Mar 21 13:29 LICENSE
drwxr-xr-x 2 root root   4096 Jun 22 22:26 man
-rw-r--r-- 1 root root  63692 Apr  7 15:08 MD5
-rw-r--r-- 1 root root   6204 Oct 24  2016 NAMESPACE
-rw-r--r-- 1 root root  22407 Apr  7 11:44 NEWS
drwxr-xr-x 2 root root   4096 Jun 22 22:26 R
drwxr-xr-x 3 root root   8192 Jun 22 22:26 src
[root@dcex1102shinypr ~]#


If I CTRL-Z out of R in the first session I confirm the same result - the 
system shows the file as executable

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


-Original Message-----
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Thursday, June 22, 2017 3:06 PM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

On 22/06/2017 3:42 PM, Conklin, Mike (GfK) wrote:
> Not much progress. I step through debug and it gets to the do.install() 
> function which immediately errors with the same "configuration not 
> executable" error.

I believe that is a locally defined function, which means you can set a 
breakpoint within it but only if R is compiled with source info, or you can 
manually call debug(do_install) after it has been created (typically just 
before it is called is a safe place to do this), and do the usual process.

It's still very mysterious to me why configure is losing its executable bit.  
What I would do if I could reproduce this would be to run right up to the 
file_test("-x","configure") line, then print my working directory, and ctrl-Z 
out of R to look at the files there.  That should confirm that configure is not 
executable.

Then the hard part is figuring out why it isn't

Duncan

>
> So, made a tempfunc that was a copy of tools:::.install_packages and 
> edited the file_test("-x","configure") line to return a TRUE
>
> now I get a Permission Denied error (even if I run as root)
>
>> tempfunc("/home/meconk/stringi_1.1.5.tar.gz")
> * installing to library '/usr/lib64/R/library'
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> sh: ./configure: Permission denied
> ERROR: configuration failed for package 'stringi'
> * removing '/usr/lib64/R/library/stringi'
> Error in do_exit(status = status) : .install_packages() exit status 1 
> Error in do_exit(status = status) : .install_packages() exit status 1
>
> --
> W. Michael Conklin
> EVP Marketing & Data Sciences
> GfK
> T +1 763 417 4545 | M +1 612 567 8287
>
>
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Thursday, June 22, 2017 11:09 AM
> To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
> Cc: r-help@r-project.org
> Subject: Re: [R] Missing dependencies in pkg installs
>
> On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:
>> Following Duncan's instructions I find that the system and R find that 
>> configure IS executable but if trying to install via install.packages I get 
>> the same error.
>> I also tried using R CMD INSTALL from the terminal and install.packages with 
>> a local file pointing to the very same tar.gz file that shows the executable 
>> bit set. All res

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Duncan Murdoch


On 22/06/2017 3:42 PM, Conklin, Mike (GfK) wrote:

Not much progress. I step through debug and it gets to the do.install() function 
which immediately errors with the same "configuration not executable" error.


I believe that is a locally defined function, which means you can set a 
breakpoint within it but only if R is compiled with source info, or you 
can manually call debug(do_install) after it has been created (typically 
just before it is called is a safe place to do this), and do the usual 
process.


It's still very mysterious to me why configure is losing its executable 
bit.  What I would do if I could reproduce this would be to run right up 
to the file_test("-x","configure") line, then print my working 
directory, and ctrl-Z out of R to look at the files there.  That should 
confirm that configure is not executable.


Then the hard part is figuring out why it isn't

Duncan



So, made a tempfunc that was a copy of tools:::.install_packages and edited the 
file_test("-x","configure") line to return a TRUE

now I get a Permission Denied error (even if I run as root)


tempfunc("/home/meconk/stringi_1.1.5.tar.gz")

* installing to library '/usr/lib64/R/library'
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
sh: ./configure: Permission denied
ERROR: configuration failed for package 'stringi'
* removing '/usr/lib64/R/library/stringi'
Error in do_exit(status = status) : .install_packages() exit status 1
Error in do_exit(status = status) : .install_packages() exit status 1

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


-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Thursday, June 22, 2017 11:09 AM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:

Following Duncan's instructions I find that the system and R find that 
configure IS executable but if trying to install via install.packages I get the 
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a local file 
pointing to the very same tar.gz file that shows the executable bit set. All result in 
the same "configure is not executable" result.



That's very mysterious.  This is hard to debug, because R runs a separate 
process to do the installs.  If you want to track this down you can debug the 
code as follows.

1.  Manually download the tarball, using any method (perhaps download.packages("stringi", destdir = 
".", type = "source").

2.  In R, run

debug(tools:::.install_packages)
tools:::.install_packages("stringi_1.1.5.tar.gz")

You can single step until you see the message, and try to diagnose why it is 
happening.

Watch out, this function will exit R at the end.

Duncan Murdoch


[meconk@dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1
meconk meconk 173757 Apr  7 11:43 stringi/configure
[meconk@dcex1102shinypr ~]$ sudo R [sudo] password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and 'citation()' on how to
cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]


getwd()

[1] "/home/meconk"

file_test("-x","stringi/configure")

stringi/configure
 TRUE

install.packages("stringi")   
Installing package into '/usr/lib64/R/library'

(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
==
downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R Installation and 
Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
'/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had no

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Conklin, Mike (GfK)

Not much progress. I step through debug and it gets to the do.install() 
function which immediately errors with the same "configuration not executable" 
error.

So, made a tempfunc that was a copy of tools:::.install_packages and edited the 
file_test("-x","configure") line to return a TRUE

now I get a Permission Denied error (even if I run as root)

> tempfunc("/home/meconk/stringi_1.1.5.tar.gz")
* installing to library '/usr/lib64/R/library'
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
sh: ./configure: Permission denied
ERROR: configuration failed for package 'stringi'
* removing '/usr/lib64/R/library/stringi'
Error in do_exit(status = status) : .install_packages() exit status 1
Error in do_exit(status = status) : .install_packages() exit status 1

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


-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Thursday, June 22, 2017 11:09 AM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:
> Following Duncan's instructions I find that the system and R find that 
> configure IS executable but if trying to install via install.packages I get 
> the same error.
> I also tried using R CMD INSTALL from the terminal and install.packages with 
> a local file pointing to the very same tar.gz file that shows the executable 
> bit set. All result in the same "configure is not executable" result.
>

That's very mysterious.  This is hard to debug, because R runs a separate 
process to do the installs.  If you want to track this down you can debug the 
code as follows.

1.  Manually download the tarball, using any method (perhaps 
download.packages("stringi", destdir = ".", type = "source").

2.  In R, run

debug(tools:::.install_packages)
tools:::.install_packages("stringi_1.1.5.tar.gz")

You can single step until you see the message, and try to diagnose why it is 
happening.

Watch out, this function will exit R at the end.

Duncan Murdoch

> [meconk@dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1 
> meconk meconk 173757 Apr  7 11:43 stringi/configure 
> [meconk@dcex1102shinypr ~]$ sudo R [sudo] password for meconk:
>
> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and 'citation()' on how to 
> cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or 
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
>> getwd()
> [1] "/home/meconk"
>> file_test("-x","stringi/configure")
> stringi/configure
>  TRUE
>> install.packages("stringi")  
>>  Installing package into '/usr/lib64/R/library'
> (as 'lib' is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB) 
> ==
> downloaded 3.5 MB
>
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> ERROR: 'configure' exists but is not executable -- see the 'R Installation 
> and Administration Manual'
> * removing '/usr/lib64/R/library/stringi'
>
> The downloaded source packages are in
> '/tmp/Rtmpxw9twb/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("stringi") :
>   installation of package 'stringi' had non-zero exit status
>
> --
> W. Michael Conklin
> EVP Marketing & Data Sciences
> GfK
> T +1 763 417 4545 | M +1 612 567 8287
>
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan 
> Murdoch
> Sent: Thursday, June 22, 2017 8:23 AM
> To: Martin Maechler; David Winsemius
> Cc: r-help@r-project.org
> Subject: Re: [R] Missing dependencies in pkg installs
>
> The "c

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Duncan Murdoch


On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:

Following Duncan's instructions I find that the system and R find that 
configure IS executable but if trying to install via install.packages I get the 
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a local file 
pointing to the very same tar.gz file that shows the executable bit set. All result in 
the same "configure is not executable" result.



That's very mysterious.  This is hard to debug, because R runs a 
separate process to do the installs.  If you want to track this down you 
can debug the code as follows.


1.  Manually download the tarball, using any method (perhaps 
download.packages("stringi", destdir = ".", type = "source").


2.  In R, run

debug(tools:::.install_packages)
tools:::.install_packages("stringi_1.1.5.tar.gz")

You can single step until you see the message, and try to diagnose why 
it is happening.


Watch out, this function will exit R at the end.

Duncan Murdoch


[meconk@dcex1102shinypr ~]$ ls -l stringi/configure
-rwxr-xr-x 1 meconk meconk 173757 Apr  7 11:43 stringi/configure
[meconk@dcex1102shinypr ~]$ sudo R
[sudo] password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]


getwd()

[1] "/home/meconk"

file_test("-x","stringi/configure")

stringi/configure
 TRUE

install.packages("stringi")   
Installing package into '/usr/lib64/R/library'

(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
==
downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R Installation and 
Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
'/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had non-zero exit status

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

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch
Sent: Thursday, June 22, 2017 8:23 AM
To: Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

The "configure exists but is not executable" problem is somewhat common on 
Windows, because there's usually no such thing as an executable bit there.  (Cygwin does 
something to fake one, but Windows generally
doesn't.)  If you create a tarball there by default you get no executable bits 
marked in it.

For a long time, R CMD build has dealt with this issue by using the internal 
tar() function.  It corrects the executable bit with a warning during the build.

So if people are getting that error, something has gone wrong.  A few
guesses:

  - They are on Linux but using a mount of a Windows volume that doesn't 
preserve the bit.

  - They are using a tarball produced in some strange way on Windows, e.g. by 
calling tar directly instead of R CMD build.

  - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which means 
the second is unlikely (unless it was very recently fixed), but the first is 
still possible.  One test is to manually expand the tarball, then use both ls 
and R's test to see if the executable bit is set and is detected by R.  For 
example, after downloading stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:

David Winsemius <dwinsem...@comcast.net>
on Wed, 21 Jun 2017 18:04:13 -0700 writes:


>> On Jun 21, 2017, at 1

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Conklin, Mike (GfK)

also it seems to be no issue to execute configure from the command line  
./configure

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

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Conklin, Mike 
(GfK)
Sent: Thursday, June 22, 2017 10:15 AM
To: Duncan Murdoch; Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

Following Duncan's instructions I find that the system and R find that 
configure IS executable but if trying to install via install.packages I get the 
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a 
local file pointing to the very same tar.gz file that shows the executable bit 
set. All result in the same "configure is not executable" result.

[meconk@dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1 meconk meconk 
173757 Apr  7 11:43 stringi/configure [meconk@dcex1102shinypr ~]$ sudo R [sudo] 
password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and 'citation()' on how to cite R or 
R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for 
an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> getwd()
[1] "/home/meconk"
> file_test("-x","stringi/configure")
stringi/configure
 TRUE
> install.packages("stringi")   
> Installing package into '/usr/lib64/R/library'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB) 
==
downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R Installation and 
Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
'/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had non-zero exit status

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

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch
Sent: Thursday, June 22, 2017 8:23 AM
To: Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

The "configure exists but is not executable" problem is somewhat common on 
Windows, because there's usually no such thing as an executable bit there.  
(Cygwin does something to fake one, but Windows generally
doesn't.)  If you create a tarball there by default you get no executable bits 
marked in it.

For a long time, R CMD build has dealt with this issue by using the internal 
tar() function.  It corrects the executable bit with a warning during the build.

So if people are getting that error, something has gone wrong.  A few
guesses:

  - They are on Linux but using a mount of a Windows volume that doesn't 
preserve the bit.

  - They are using a tarball produced in some strange way on Windows, e.g. by 
calling tar directly instead of R CMD build.

  - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which means 
the second is unlikely (unless it was very recently fixed), but the first is 
still possible.  One test is to manually expand the tarball, then use both ls 
and R's test to see if the executable bit is set and is detected by R.  For 
example, after downloading stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:
>>>>>> David Winsemius <dwinsem...@comcast.net>
>>>>>> on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>
> >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK) 
> <mike.conk...@gfk.com> wrote:
> >>
> &g

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Conklin, Mike (GfK)

Following Duncan's instructions I find that the system and R find that 
configure IS executable but if trying to install via install.packages I get the 
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a 
local file pointing to the very same tar.gz file that shows the executable bit 
set. All result in the same "configure is not executable" result.

[meconk@dcex1102shinypr ~]$ ls -l stringi/configure
-rwxr-xr-x 1 meconk meconk 173757 Apr  7 11:43 stringi/configure
[meconk@dcex1102shinypr ~]$ sudo R
[sudo] password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> getwd()
[1] "/home/meconk"
> file_test("-x","stringi/configure")
stringi/configure
 TRUE
> install.packages("stringi")   
> Installing package into '/usr/lib64/R/library'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
==
downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R Installation and 
Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
'/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had non-zero exit status

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

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch
Sent: Thursday, June 22, 2017 8:23 AM
To: Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

The "configure exists but is not executable" problem is somewhat common on 
Windows, because there's usually no such thing as an executable bit there.  
(Cygwin does something to fake one, but Windows generally
doesn't.)  If you create a tarball there by default you get no executable bits 
marked in it.

For a long time, R CMD build has dealt with this issue by using the internal 
tar() function.  It corrects the executable bit with a warning during the build.

So if people are getting that error, something has gone wrong.  A few
guesses:

  - They are on Linux but using a mount of a Windows volume that doesn't 
preserve the bit.

  - They are using a tarball produced in some strange way on Windows, e.g. by 
calling tar directly instead of R CMD build.

  - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which means 
the second is unlikely (unless it was very recently fixed), but the first is 
still possible.  One test is to manually expand the tarball, then use both ls 
and R's test to see if the executable bit is set and is detected by R.  For 
example, after downloading stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:
>>>>>> David Winsemius <dwinsem...@comcast.net>
>>>>>> on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>
> >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK) 
> <mike.conk...@gfk.com> wrote:
> >>
> >> I have a Ubuntu server with an R installation that has 384 packages 
> installed.  We are trying to replicate the system on a Red Hat Enterprise 
> server. I downloaded the list of packages from the Ubuntu machine and read it 
> into an R session on the new machine. Then I ran 
> install.packages(listofpackages).  Now I have 352 packages on the new machine 
> but several very common packages (like much of the tidyverse, ggplot2, Hmisc) 
> failed to install

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Duncan Murdoch

The "configure exists but is not executable" problem is somewhat common 
on Windows, because there's usually no such thing as an executable bit 
there.  (Cygwin does something to fake one, but Windows generally 
doesn't.)  If you create a tarball there by default you get no 
executable bits marked in it.

For a long time, R CMD build has dealt with this issue by using the 
internal tar() function.  It corrects the executable bit with a warning 
during the build.

So if people are getting that error, something has gone wrong.  A few 
guesses:

 - They are on Linux but using a mount of a Windows volume that doesn't 
preserve the bit.

 - They are using a tarball produced in some strange way on Windows, 
e.g. by calling tar directly instead of R CMD build.

 - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which 
means the second is unlikely (unless it was very recently fixed), but 
the first is still possible.  One test is to manually expand the 
tarball, then use both ls and R's test to see if the executable bit is 
set and is detected by R.  For example, after downloading 
stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:

David Winsemius 
on Wed, 21 Jun 2017 18:04:13 -0700 writes:

>> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)  
wrote:
>>
>> I have a Ubuntu server with an R installation that has 384 packages 
installed.  We are trying to replicate the system on a Red Hat Enterprise server. I 
downloaded the list of packages from the Ubuntu machine and read it into an R session 
on the new machine. Then I ran install.packages(listofpackages).  Now I have 352 
packages on the new machine but several very common packages (like much of the 
tidyverse, ggplot2, Hmisc) failed to install because of missing dependencies (most of 
which are the other packages that failed to install).
>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-redhat-linux-gnu (64-bit)

> I'd make sure you have reviewed this:

> 
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries

yes,  but see also below ..

> Best;
> David.

>> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>> [9] LC_ADDRESS=C   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> other attached packages:
>> [1] dplyr_0.7.0 shiny_1.0.3
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.0   magrittr_1.5 assertthat_0.2.0 R6_2.2.2
>> [5] htmltools_0.3.6  tools_3.4.0  glue_1.1.1   tibble_1.3.3
>> [9] Rcpp_0.12.11 digest_0.6.12xtable_1.8-2 httpuv_1.3.3
>> [13] mime_0.5 rlang_0.1.1
>>>
>>
>>
>> If I try and install Hmisc for example I get the following errors:
>> for the first error ERROR: 'configure' exists but is not executable --
>> see the 'R Installation and dministration Manual'  I did
>> not find the R Installation and Administration Manual
>> helpful.

why?  It does assume you spend some time understanding what it
is talking about.
OTOH, it is  *THE*  official document on the topic, written and
constantly updated by the  R core team.

Anyway:   " ERROR: 'configure' exists but is not executable "

is I think a crucial piece of information .. it's from stringi's
installation failure, and the top level directory of stringi (1.1-5)
in a Unix like (ls -l with user group names removed) looks like:

  -rw-r--r--. 1451 Apr  7 15:08 DESCRIPTION
  -rw-r--r--. 6207 Apr  7 11:21 INSTALL
  -rw-r--r--. 3580 Mar 21 13:29 LICENSE
  -rw-r--r--.63692 Apr  7 15:08 MD5
  -rw-r--r--. 6204 Oct 24  2016 NAMESPACE
  -rw-r--r--.22407 Apr  7 11:44 NEWS
  drwxr-xr-x. 8192 Mar 28 10:26 R
  -rwxr-xr-x.   66 Apr  2  2015 cleanup
  -rw-rw-r--.32193 Apr  8 05:46 config.log
  -rwxrwxr-x.40648 Apr  8 05:46 config.status
  -rwxr-xr-x.   173757 Apr  7 11:43 configure
  -rw-r--r--.  669 Jun 23  2015 configure.win
  drwxr-xr-x.  512 Apr  7 11:50 inst
  drwxr-xr-x. 8192 Mar 28 10:26 man
  drwxr-xr-x.16384 Apr  8 05:47 src

Note the

Re: [R] Missing dependencies in pkg installs

2017-06-22 Thread Martin Maechler

> David Winsemius 
> on Wed, 21 Jun 2017 18:04:13 -0700 writes:

>> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)  
wrote:
>> 
>> I have a Ubuntu server with an R installation that has 384 packages 
installed.  We are trying to replicate the system on a Red Hat Enterprise 
server. I downloaded the list of packages from the Ubuntu machine and read it 
into an R session on the new machine. Then I ran 
install.packages(listofpackages).  Now I have 352 packages on the new machine 
but several very common packages (like much of the tidyverse, ggplot2, Hmisc) 
failed to install because of missing dependencies (most of which are the other 
packages that failed to install).
>> 
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-redhat-linux-gnu (64-bit)

> I'd make sure you have reviewed this:

> 
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries

yes,  but see also below ..

> Best;
> David.

>> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>> 
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>> 
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>> [9] LC_ADDRESS=C   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> other attached packages:
>> [1] dplyr_0.7.0 shiny_1.0.3
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.0   magrittr_1.5 assertthat_0.2.0 R6_2.2.2
>> [5] htmltools_0.3.6  tools_3.4.0  glue_1.1.1   tibble_1.3.3
>> [9] Rcpp_0.12.11 digest_0.6.12xtable_1.8-2 httpuv_1.3.3
>> [13] mime_0.5 rlang_0.1.1
>>> 
>> 
>> 
>> If I try and install Hmisc for example I get the following errors:
>> for the first error ERROR: 'configure' exists but is not executable -- 
>> see the 'R Installation and dministration Manual'  I did
>> not find the R Installation and Administration Manual
>> helpful.

why?  It does assume you spend some time understanding what it
is talking about.
OTOH, it is  *THE*  official document on the topic, written and
constantly updated by the  R core team.

Anyway:   " ERROR: 'configure' exists but is not executable "

is I think a crucial piece of information .. it's from stringi's
installation failure, and the top level directory of stringi (1.1-5)
in a Unix like (ls -l with user group names removed) looks like:

  -rw-r--r--. 1451 Apr  7 15:08 DESCRIPTION
  -rw-r--r--. 6207 Apr  7 11:21 INSTALL
  -rw-r--r--. 3580 Mar 21 13:29 LICENSE
  -rw-r--r--.63692 Apr  7 15:08 MD5
  -rw-r--r--. 6204 Oct 24  2016 NAMESPACE
  -rw-r--r--.22407 Apr  7 11:44 NEWS
  drwxr-xr-x. 8192 Mar 28 10:26 R
  -rwxr-xr-x.   66 Apr  2  2015 cleanup
  -rw-rw-r--.32193 Apr  8 05:46 config.log
  -rwxrwxr-x.40648 Apr  8 05:46 config.status
  -rwxr-xr-x.   173757 Apr  7 11:43 configure
  -rw-r--r--.  669 Jun 23  2015 configure.win
  drwxr-xr-x.  512 Apr  7 11:50 inst
  drwxr-xr-x. 8192 Mar 28 10:26 man
  drwxr-xr-x.16384 Apr  8 05:47 src

Note the "x"s  in the 'configure' line's " -rwxr-xr-x. ": 
This means the file is executable and a reasonable shell can
just "call the file" and it will be executed, but that's the
part which failed for you.

.. this *is* peculiar as it looks like some of the standard Unix
tools may be misbehaving for you .. I assume it could be some OS
security "feature" playing against you..

>> 
>> 
>>> install.packages("Hmisc")
>> Installing package into '/usr/lib64/R/library'
>> (as 'lib' is unspecified)
>> also installing the dependencies 'stringi', 'evaluate', 'reshape2', 
'stringr', knitr', 'ggplot2', 'htmlTable', 'viridis'
>> 
>> trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
>> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
>> ==
>> downloaded 3.5 MB
>> 
>> trying URL 'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
>> Content type 'application/x-gzip' length 21914 bytes (21 KB)
>> ==
>> downloaded 21 KB
>> 
>> trying URL 
'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
>> Content type 'application/x-gzip' length 34688 bytes (33 KB)
>> ==
>> downloaded 33 KB
>> 
>> trying URL

Re: [R] Missing dependencies in pkg installs

2017-06-21 Thread David Winsemius


> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)  wrote:
> 
> I have a Ubuntu server with an R installation that has 384 packages 
> installed.  We are trying to replicate the system on a Red Hat Enterprise 
> server. I downloaded the list of packages from the Ubuntu machine and read it 
> into an R session on the new machine. Then I ran 
> install.packages(listofpackages).  Now I have 352 packages on the new machine 
> but several very common packages (like much of the tidyverse, ggplot2, Hmisc) 
> failed to install because of missing dependencies (most of which are the 
> other packages that failed to install).
> 
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-redhat-linux-gnu (64-bit)

I'd make sure you have reviewed this:

https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries

Best;
David.

> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
> 
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> other attached packages:
> [1] dplyr_0.7.0 shiny_1.0.3
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0   magrittr_1.5 assertthat_0.2.0 R6_2.2.2
> [5] htmltools_0.3.6  tools_3.4.0  glue_1.1.1   tibble_1.3.3
> [9] Rcpp_0.12.11 digest_0.6.12xtable_1.8-2 httpuv_1.3.3
> [13] mime_0.5 rlang_0.1.1
>> 
> 
> 
> If I try and install Hmisc for example I get the following errors:
> for the first error ERROR: 'configure' exists but is not executable -- see 
> the 'R Installation and dministration Manual'  I did not find the R 
> Installation and Administration Manual helpful.
> 
> 
>> install.packages("Hmisc")
> Installing package into '/usr/lib64/R/library'
> (as 'lib' is unspecified)
> also installing the dependencies 'stringi', 'evaluate', 'reshape2', 
> 'stringr', knitr', 'ggplot2', 'htmlTable', 'viridis'
> 
> trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
> ==
> downloaded 3.5 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
> Content type 'application/x-gzip' length 21914 bytes (21 KB)
> ==
> downloaded 21 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
> Content type 'application/x-gzip' length 34688 bytes (33 KB)
> ==
> downloaded 33 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 94095 bytes (91 KB)
> ==
> downloaded 91 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
> Content type 'application/x-gzip' length 1031259 bytes (1007 KB)
> ==
> downloaded 1007 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
> Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
> ==
> downloaded 2.1 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
> Content type 'application/x-gzip' length 152095 bytes (148 KB)
> ==
> downloaded 148 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
> Content type 'application/x-gzip' length 1787731 bytes (1.7 MB)
> ==
> downloaded 1.7 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
> Content type 'application/x-gzip' length 702759 bytes (686 KB)
> ==
> downloaded 686 KB
> 
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> ERROR: 'configure' exists but is not executable -- see the 'R Installation 
> and dministration Manual'
> * removing '/usr/lib64/R/library/stringi'
> ERROR: dependency 'stringi' is not available for package 'stringr'
> * removing '/usr/lib64/R/library/stringr'
> ERROR: dependency 'stringr' is not available for package 'evaluate'
> * removing '/usr/lib64/R/library/evaluate'
> ERROR: dependency 'stringr' is not available for package 'reshape2'
> * removing '/usr/lib64/R/library/reshape2'
> ERROR: dependencies 'evaluate', 'stringr' are not available for package 
> 'knitr'
> * removing '/usr/lib64/R/library/knitr'
> ERROR: dependency

[R] Missing dependencies in pkg installs

2017-06-21 Thread Conklin, Mike (GfK)

I have a Ubuntu server with an R installation that has 384 packages installed.  
We are trying to replicate the system on a Red Hat Enterprise server. I 
downloaded the list of packages from the Ubuntu machine and read it into an R 
session on the new machine. Then I ran install.packages(listofpackages).  Now I 
have 352 packages on the new machine but several very common packages (like 
much of the tidyverse, ggplot2, Hmisc) failed to install because of missing 
dependencies (most of which are the other packages that failed to install).

R version 3.4.0 (2017-04-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8   LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] dplyr_0.7.0 shiny_1.0.3

loaded via a namespace (and not attached):
[1] compiler_3.4.0   magrittr_1.5 assertthat_0.2.0 R6_2.2.2
[5] htmltools_0.3.6  tools_3.4.0  glue_1.1.1   tibble_1.3.3
[9] Rcpp_0.12.11 digest_0.6.12xtable_1.8-2 httpuv_1.3.3
[13] mime_0.5 rlang_0.1.1
>


If I try and install Hmisc for example I get the following errors:
for the first error ERROR: 'configure' exists but is not executable -- see the 
'R Installation and dministration Manual'  I did not find the R Installation 
and Administration Manual helpful.


> install.packages("Hmisc")
Installing package into '/usr/lib64/R/library'
(as 'lib' is unspecified)
also installing the dependencies 'stringi', 'evaluate', 'reshape2', 'stringr', 
knitr', 'ggplot2', 'htmlTable', 'viridis'

trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
==
downloaded 3.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
Content type 'application/x-gzip' length 21914 bytes (21 KB)
==
downloaded 21 KB

trying URL 'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
Content type 'application/x-gzip' length 34688 bytes (33 KB)
==
downloaded 33 KB

trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
Content type 'application/x-gzip' length 94095 bytes (91 KB)
==
downloaded 91 KB

trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
Content type 'application/x-gzip' length 1031259 bytes (1007 KB)
==
downloaded 1007 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
==
downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
Content type 'application/x-gzip' length 152095 bytes (148 KB)
==
downloaded 148 KB

trying URL 'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
Content type 'application/x-gzip' length 1787731 bytes (1.7 MB)
==
downloaded 1.7 MB

trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
Content type 'application/x-gzip' length 702759 bytes (686 KB)
==
downloaded 686 KB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R Installation and 
dministration Manual'
* removing '/usr/lib64/R/library/stringi'
ERROR: dependency 'stringi' is not available for package 'stringr'
* removing '/usr/lib64/R/library/stringr'
ERROR: dependency 'stringr' is not available for package 'evaluate'
* removing '/usr/lib64/R/library/evaluate'
ERROR: dependency 'stringr' is not available for package 'reshape2'
* removing '/usr/lib64/R/library/reshape2'
ERROR: dependencies 'evaluate', 'stringr' are not available for package 'knitr'
* removing '/usr/lib64/R/library/knitr'
ERROR: dependency 'reshape2' is not available for package 'ggplot2'
* removing '/usr/lib64/R/library/ggplot2'
ERROR: dependencies 'stringr', 'knitr' are not available for package 'htmlTable
* removing '/usr/lib64/R/library/htmlTable'
ERROR: dependency 'ggplot2' is not available for package 'viridis'
* removing '/usr/lib64/R/library/viridis'
ERROR: dependencies 'ggplot2', 'htmlTable', 'viridis' are not available for 
pacage 'Hmisc'
* removing '/usr/lib64/R/library/Hmisc'

Re: [R] Missing dependencies in pkg installs SOLVED

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

Re: [R] Missing dependencies in pkg installs

[R] Missing dependencies in pkg installs

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