[Bioc-devel] svn and building packages under R for Windows 2.12.0

[Gordon K Smyth]

Here's a little mystery with R 2.12.0 and Windows.

I have no trouble building or checking my copy of the limma package 
(version 3.7.1) under R for Windows 2.12.0.  I do get a cygwin warning 
which is new with R 2.12.0, but the package still builds fine.  The output 
from R CMD INSTALL is given below.

However, after I commit limma to the Bioconductor repository, then check 
it out to a new directory, I cannot build or check the checked out version 
using R 2.12.0.  The error message is given below.

I get the same behaviour whether I work with the Bioconductor 2.7 or 
Bioconductor 2.8 versions of limma and the corresponding svn repositories. 
In particular, I cannot build the Biodonductor 2.7 Release of limma 2.6.0 
under R 2.12.0 for Windows.

My version of R tools appears to be up to date, as I re-installed it 7 
October 2010.

I have tried copying non-versioned files from my original version to the 
checked out version to ensure they contain exactly the same files. 
Doesn't help.

If I copy the checked out version to a unix directory, then it builds and 
checks fine using R 2.12.0 for linux.

I've never seen this sort of error before.  All my files have MS-DOS style 
end of lines, except for a file of C source code with Unix style line 
ends.  These all seem to be preserved in the original and checked out 
versions.

Any ideas?
Gordon


COMMAND PROMPT SESSION USING MY ORIGINAL COPY LIMMA:

>R CMD INSTALL --build limma
* installing to library 'c:/lib/R/R-2.12.0/library'
* installing *source* package 'limma' ...
** libs
cygwin warning:
   MS-DOS style path detected: c:/lib/R/R-2.12.0/etc/i386/Makeconf
   Preferred POSIX equivalent is: 
/cygdrive/c/lib/R/R-2.12.0/etc/i386/Makeconf
   CYGWIN environment variable option "nodosfilewarning" turns off this 
warning.
   Consult the user's guide for more details about POSIX paths:
     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
make: Nothing to be done for `all'.
installing to c:/lib/R/R-2.12.0/library/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.7.1.zip

* DONE (limma)



COMMAND PROMPT SESSION AFTER CHECKING LIMMA OUT FROM BIOCONDUCTOR 2.8:

>R CMD INSTALL --build limma
* installing to library 'c:/lib/R/R-2.12.0/library'
* installing *source* package 'limma' ...
** libs
cygwin warning:
   MS-DOS style path detected: c:/lib/R/R-2.12.0/etc/i386/Makeconf
   Preferred POSIX equivalent is: 
/cygdrive/c/lib/R/R-2.12.0/etc/i386/Makeconf
   CYGWIN environment variable option "nodosfilewarning" turns off this 
warning.
   Consult the user's guide for more details about POSIX paths:
     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
gcc -I"c:/lib/R/R-2.12.0/include"         -O3 -Wall  -std=gnu99 -c 
normexp.c -o
normexp.o
     142 [main] make 4420 c:\lib\Rtools\bin\make.exe: *** fatal error - 
couldn't
allocate heap, Win32 error 487, base 0x480000, top 0x520000, reserve_size 
651264
, allocsize 655360, page_const 4096
Stack trace:
Frame     Function  Args
0022E4C0  6102749B  (0022E4C0, 00000000, 00000000, 00000000)
0022E7B0  6102749B  (61177B80, 00008000, 00000000, 61179977)
0022F7E0  61004AFB  (611AF64C, 00480000, 00520000, 0009F000)
0022F810  6106BEB3  (7FFEFFFF, 00000003, 00000002, 7C90DA0A)
0022F900  610BDF9B  (0000078C, 02000000, 61163664, 61163660)
0022F930  61006090  (00000000, 00000000, 00000000, 00000000)
0022F9F0  6106D0E9  (61000000, 00000001, 0022FD30, 6106CE10)
0022FA10  7C90118A  (6106CE10, 61000000, 00000001, 0022FD30)
0022FB18  7C91C4FA  (0022FD30, 7FFDE000, 7FFDF000, 00000000)
0022FC94  7C9211B4  (0022FD30, 7C900000, 0022FCE0, 7C90E900)
0022FD1C  7C9210AF  (0022FD30, 7C900000, 00000000, 00010017)
End of stack trace
      79 [main] make 4780 fork: child -1 - died waiting for longjmp before 
initia
lization, retry 0, exit code 0x100, errno 11
make: vfork: Resource temporarily unavailable
ERROR: compilation failed for package 'limma'
* removing 'c:/lib/R/R-2.12.0/library/limma'
* restoring previous 'c:/lib/R/R-2.12.0/library/limma'


PATH INFORMATION FOR MY COMMAND SESSION:

PATH=c:\lib\Rtools\bin;c:\lib\Rtools\perl\bin;c:\lib\Rtools\MinGW\bin;c:\lib\bin
;c:\lib\R\R-2.12.0\bin;c:\progra~1\HTML Help 
workshop\;C:\WINDOWS\system32;C:\WI
NDOWS;C:\WINDOWS\System32\Wbem;C:\lib\MiKTeX 2.6\miktex\bin;C:\lib\Inno 
Setup 5;

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