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

Fri Oct 22 01:33:40 CEST 2010

Hi Mike,

Yes, your suggestion was correct.  When I remove the executables the error 
is now introduced on my original copy.

My computer is running Sophos Anti-Virus.  Unfortunately, it is corporate 
policy at my institute that anti virus software be active at all times. 
I don't have permission to turn it off.  Even if I could turn it off, I 
wouldn't want to do so on an ongoing basis.

Not sure when to go to from here.

Cheers
Gordon

On Thu, 21 Oct 2010, Mike Smith wrote:

> Hi Gordon,
>
> If you remove the compiled files from your local copy (everything in
> limma/src other than normexp.c)  is the error introduced?  It appears that
> gcc isn't being invoked on your local copy as the source file has all ready
> been compiled, which isn't the case with a fresh bioconductor download.
>
> I'm sure you've done some Googling, but there appear to be loads of posts
> with similar errors that have turned out to be related to various anti-virus
> / malware software preventing cygwin from running - particularly Symantec
> software.  If you have anything like that on the machine, maybe try turning
> it off and running again.
>
> Sorry that's not a more definitive answer,
>
> Mike Smith
>
> On Thu, Oct 21, 2010 at 4:28 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> 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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