From pdalgd at gmail.com  Thu Apr 21 13:20:18 2016
From: pdalgd at gmail.com (peter dalgaard)
Date: Thu, 21 Apr 2016 13:20:18 +0200
Subject: [Rd] Fresh build from source of R-3.2.5 failing "make check"
	under 64-bit Ubuntu
In-Reply-To: <571807B7.2070603@pacificedge.co.nz>
References: <571807B7.2070603@pacificedge.co.nz>
Message-ID: <A32AC8B9-F509-4A2C-9DF8-F6E2C4199192@gmail.com>

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. 

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.dalphin at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu
peter dalgaard