Testing for an NFS effect on the failure of 'make check':
Try first on /usr/local/
9:42 cd /usr/local/src/
9:42 sudo mkdir R
9:43 sudo chown mdalphin:mdalphin R
9:43 cd R
9:43 gunzip -c /opt/apps/x86_64/R/Archive/R-3.2.5.tar.gz | tar xf -
9:43 cd R-3.2.5/
9:44 ./configure --prefix=/opt/apps/x86_64/R/R-3.2.5 LIBnn=lib
9:44 make
9:57 make check
This PASSES all tests. Exit status of ZERO.
Now try on NFS:
10:04 cd /opt/apps/x86_64/R/src/
10:05 gunzip -c /opt/apps/x86_64/R/Archive/R-3.2.5.tar.gz | tar xf -
10:06 cd R-3.2.5/
10:06 ./configure --prefix=/opt/apps/x86_64/R/R-3.2.5 LIBnn=lib
10:06 make
10:14 make check
This FAILS (see below). Exit status of NON-ZERO:
running code in 'reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1
make[3]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
make: *** [check] Error 2
What might be different?
> ls -ld /opt/apps/x86_64/R/src/R-3.2.5/ /usr/local/src/R/R-3.2.5/
drwxr-xr-x 15 mdalphin mdalphin 4096 Apr 22 09:57
/opt/apps/x86_64/R/src/R-3.2.5/
drwxr-xr-x 15 mdalphin mdalphin 4096 Apr 22 09:50 /usr/local/src/R/R-3.2.5/
> mount | grep /opt/
myHost.science:/mnt/home/opt/apps on /opt/apps type nfs
(rw,soft,bg,nfsvers=3,addr=XXX.XXX.XXX.XXX)
Just the NFS, I guess. This is not good, but not an R-Devel problem.
Thanks for the help.
Cheers,
Mark Dalphin PhD
Director of Bioinformatics
mark.dalp...@pacificedge.co.nz
Ph: +64 3 479 4690
Cell: +64 21 156 7625
Skype: mark.dalphin.pel
________________________________
87 St David St, PO Box 56, Dunedin, New Zealand 9016 www.pacificedgedx.com
________________________________________
From: Mark Dalphin <mark.dalp...@pacificedge.co.nz>
Sent: Friday, 22 April 2016 9:19
To: peter dalgaard; Prof Brian Ripley
Subject: Re: [Rd] Fresh build from source of R-3.2.5 failing "make check" under
64-bit Ubuntu
I have run it both ways; for the purposes of this email, it was easier
to capture both STDOUT and STDERR ( '>&') into one file and have the
process run in the background (second '&'). That way I could more
readily capture the exact commands used and not have them scroll off the
top of the screen (make's output is quite large). The exact same error
occurs when I run the 'make' command as:
./configure PARAMETERS
make
make check
It is on an NFS file system; I'll look into building on a local file
system (/usr/local/) and see if I get the same errors.
Cheers,
Mark Dalphin
On 22/04/16 00:35, peter dalgaard wrote:
> On 21 Apr 2016, at 14:11 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
>
>> On 21/04/2016 12:20, peter dalgaard wrote:
>>> Hmm. I don't think this has been seen by other Ubuntu users, or other
>>> Linuxen for that matter.
>>>
>>> You have a gratuitous use of "&", but I don't really see how that would
>>> give these symptoms, unless you accidentally run a command twice, creating
>>> a race condition between two background processes.
>> He did say he used tcsh, for which >& is legal and far more memorable than
>> (goes to look it up to get the order right) >foo 2>&1
> I know (old tcsh user, before bash got traction[*], in fact). It was the "&"
> at the end that I was talking about:
>
> make check >& make_check.out &
>
> This runs make in the background and redirects stdout/err to a file. As I
> said, it is most likely harmless unless you accidentally get two processes
> running at the same time, but I think I'd try runnning in the foreground,
> just in case.
>
> -pd
>
> [*] That'll be before Linux; the first versions of Slackware used bash (ash
> for boot disks). So... like 1991, 25 years back. Yikes!
>
>>> More likely it is file system related, like NFS directory caching or maybe
>>> permissions, although the latter seems unlikely if one package does install
>>> properly. You might want to recheck whether installed.packages(lib.loc =
>>> "myLib", priority = "NA") gives different results a bit later, and if not,
>>> check that the package descriptions are sane.
>>>
>>> -pd
>>>
>>> On 21 Apr 2016, at 00:50 , Mark Dalphin <mark.dalp...@pacificedge.co.nz>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Let me justify building R from source. While I can obtain R built for me
>>>> under Ubuntu, I tend to build it from scratch as we use a NFS-shared
>>>> build as well as shared R libraries for all the bioinfo staff at this
>>>> company. Only one build and one set of packages to ensure uniformity
>>>> across all workstations.
>>>>
>>>> My problem is that despite using a pretty standard build process, I am
>>>> failing at the "make check" step. I don't see what I might have done
>>>> that is causing the failure.
>>>>
>>>> My platform is:
>>>>
>>>>> uname -a
>>>> Linux littlebourne 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15
>>>> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>>> cat /etc/issue
>>>> Ubuntu 14.04.4 LTS \n \l
>>>>
>>>> I've downloaded the recent R-3.2.5 tar-gz file and gone through the
>>>> standard build, though in a non-standard location. I keep copies of the
>>>> tar-gzipped file in an "Archive" directory.
>>>>
>>>>> gunzip -c Archive/R-3.2.5.tar.gz | tar xf -
>>>>> cd R-3.2.5/
>>>>> ./configure --prefix=/opt/apps/x86_64/R/R-3.2.5 LIBnn=lib
>>>> [ ... much output ...]
>>>> R is now configured for x86_64-pc-linux-gnu
>>>>
>>>> Source directory: .
>>>> Installation directory: /opt/apps/x86_64/R/R-3.2.5
>>>>
>>>> C compiler: gcc -std=gnu99 -g -O2
>>>> Fortran 77 compiler: gfortran -g -O2
>>>>
>>>> C++ compiler: g++ -g -O2
>>>> C++ 11 compiler: g++ -std=c++11 -g -O2
>>>> Fortran 90/95 compiler: gfortran -g -O2
>>>> Obj-C compiler: gcc -g -O2 -fobjc-exceptions
>>>>
>>>> Interfaces supported: X11, tcltk
>>>> External libraries: readline, zlib, bzlib, lzma, PCRE
>>>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
>>>> Options enabled: shared BLAS, R profiling
>>>>
>>>> Capabilities skipped: ICU
>>>> Options not enabled: memory profiling
>>>>
>>>> Recommended packages: yes
>>>>
>>>> # Note: I use tcsh, not bash
>>>>> make >& make.out &
>>>> # There are no obvious errors and the 'make' proceeds finally through
>>>> some Java configuration
>>>> # and then exits with a zero status.
>>>>
>>>>> make check >& make_check.out &
>>>> [ ... much output captured ...]
>>>> make[3]: Entering directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
>>>> running code in 'reg-tests-1a.R' ... OK
>>>> running code in 'reg-tests-1b.R' ... OK
>>>> running code in 'reg-tests-1c.R' ... OK
>>>> running code in 'reg-tests-2.R' ... OK
>>>> comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
>>>> running code in 'reg-examples1.R' ... OK
>>>> running code in 'reg-examples2.R' ... OK
>>>> running code in 'reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error
>>>> 1
>>>> make[3]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
>>>> make[2]: *** [test-Reg] Error 2
>>>> make[2]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
>>>> make[1]: *** [test-all-basics] Error 1
>>>> make[1]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests'
>>>> make: *** [check] Error 2
>>>>
>>>>> cd tests
>>>>> tail -30 reg-packages.Rout.fail
>>>> *** installing help indices
>>>> ** building package indices
>>>> ** testing if installed package can be loaded
>>>> * DONE (pkgB)
>>>> Loading required package: pkgB
>>>> building package exNSS4 ...
>>>>
>>>> installing package exNSS4 using file exNSS4_1.1.tar.gz ...
>>>> * installing *source* package 'exNSS4' ...
>>>> ** R
>>>> ** preparing package for lazy loading
>>>> Creating a generic function for 'plot' from package 'graphics' in
>>>> package 'exNSS4'
>>>> ** help
>>>> No man pages found in package 'exNSS4'
>>>> *** installing help indices
>>>> ** building package indices
>>>> ** testing if installed package can be loaded
>>>> * DONE (exNSS4)
>>>> Loading required package: exNSS4
>>>>> (res <- installed.packages(lib.loc = "myLib", priority = "NA"))
>>>> Package LibPath Version Priority Depends Imports LinkingTo Suggests
>>>> myTst "myTst" "myLib" "1.0" NA "methods" NA NA NA
>>>> Enhances License License_is_FOSS
>>>> myTst NA "What license is it under?" NA
>>>> License_restricts_use OS_type MD5sum NeedsCompilation Built
>>>> myTst NA NA NA NA "3.2.5"
>>>>> stopifnot(identical(res[,"Package"], setNames(,sort(c(p.lis, "myTst")))),
>>>> + res[,"LibPath"] == "myLib")
>>>> Error: identical(res[, "Package"], setNames(, sort(c(p.lis, "myTst"))))
>>>> is not TRUE
>>>> Execution halted
>>>>
>>>>> ls myLib
>>>> exNSS4 myTst pkgA pkgB
>>>>
>>>> So, it looks like the "installed.packages()" is not correctly detecting
>>>> what is present in "myLib".
>>>>
>>>> Has anyone else seen this? Has anyone got any ideas about what is going
>>>> wrong? My environment does not include R_LIBS, LD_LIBRARY, etc. The PATH
>>>> does include an older version of R, 3.1.1.
>>>>
>>>> Regards,
>>>> Mark Dalphin
>>>>
>>>> ______________________________________________
>>>> R-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> --
>> Brian D. Ripley, rip...@stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
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