Thanks for the help. I tried yours but it didn't work. The following comment is seen in the code, so I guess it's not working on OS X 10.4 and produced the error. //timezone is not portable (is a function, not a long, on OS X Tiger) I finally managed to "fix" it by replacing: utc_offset = - (timezone / 3600); with: utc_offset = -8; IRanges package was installed succesfully after that. Thanks again! -Lilyana On Wed, May 12, 2010 at 9:23 PM, Patrick Aboyoun <paboyoun@fhcrc.org> wrote: > I found a candidate replacement: > > > format(Sys.time(), "%Y-%m-%d %X %z (%a, %d %b %Y)") > [1] "2010-05-12 21:19:17 -0700 (Wed, 12 May 2010)" > > The author of the original C code, Herve Pages, is currently on holiday and > I don't know if he had a reason not to use the built in Sys.time function. > If there are not objections within the next 24 hours by the user community, > I'll check in this this fix. > > > Cheers, > Patrick > > > > > On 5/12/10 9:10 PM, Patrick Aboyoun wrote: > >> Lilyana, >> Steve is right. We added an svn.time function to IRanges that produces a >> time/date stamp in the same format as the BioC Subversion server, e.g. >> "2007-12-07 10:03:15 -0800 (Fri, 07 Dec 2007)", for use by the >> GenomicFeatures package. We implemented a method in C that builds on Linux, >> Windows 32bit& 64bit, and Mac OS X 10.5& 10.6, but not on Mac OS X 10.4 >> (Tiger). Since we dropped support for Mac OS X 10.4, we felt comfortable >> with this decision at the time. We'll explore alternatives to see if we can >> come up with an svn.time solution that doesn't preclude building on Mac OS X >> 10.4. Suggestions by the user community is welcome to speed this process >> along. >> >> >> Cheers, >> >> Patrick >> >> >> On 5/12/10 6:48 PM, Steve Lianoglou wrote: >> >>> Hi, >>> >>> On Wed, May 12, 2010 at 6:28 PM, Lilyana Margaretha<lilyanam@uw.edu> >>> wrote: >>> >>>> Hi, >>>> >>>> I am a beginner user of R and trying to install "IRanges" package. >>>> I have R version 2.11 and running it on Mac OS X 10.4.11. >>>> It always gives out this error: >>>> >>>> gcc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include >>>> -I/sw/include -I/usr/local/include -fPIC -g -O2 -c strutils.c -o >>>> strutils.o >>>> strutils.c: In function ‘get_svn_time’: >>>> strutils.c:167:27: error: invalid operands to binary / (have ‘char * >>>> (*)(int, int)’ and ‘int’) >>>> make: *** [strutils.o] Error 1 >>>> ERROR: compilation failed for package ‘IRanges’ >>>> * removing ‘/Users/lilyanamargaretha/Desktop/IRanges.Rcheck/IRanges’ >>>> >>>> Any suggestion on how to solve this will be very much appreciated. >>>> >>> I guess I shouldn't really respond since I don't know this for a fact, >>> but maybe you need a minimum OS X version of 10.5 (leopard) for >>> everything to work? >>> >>> (I see the that binaries provided online are for Leopard, which is why >>> I'm guessing so) >>> >>> -steve >>> >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- Lilyana Margaretha Graduate student- Blau Lab Molecular and Cellular Biology Program University of Washington Institute for Stem Cell and Regenerative Medicine 815 Mercer Street Room N521 Seattle, WA 98109 USA (206)543-3363 [[alternative HTML version deleted]]

Hi Lilyana, Patrick, Patrick Aboyoun wrote: > I found a candidate replacement: > > > format(Sys.time(), "%Y-%m-%d %X %z (%a, %d %b %Y)") > [1] "2010-05-12 21:19:17 -0700 (Wed, 12 May 2010)" > > The author of the original C code, Herve Pages, is currently on holiday > and I don't know if he had a reason not to use the built in Sys.time > function. I was not aware of the format method for POSIXct objects (format.POSIXct). It's good to know about it. Unfortunately the conversion specification %z is not portable. It seems to work fine on Mac OS X but it produces "+0000" on my Ubuntu 9.04 instead of "-0700" (I'm in Seattle): > format(Sys.time(), "%z") [1] "+0000" I just committed a new version of svn.time() that compiles and behaves consistently on Linux, Windows and Mac OS X (Leopard and Tiger). It will be available in IRanges 1.6.3 (release) and 1.7.4 (devel) thru biocLite() in the next 24 hours. Cheers, H. > If there are not objections within the next 24 hours by the > user community, I'll check in this this fix. > > > Cheers, > Patrick > > > > On 5/12/10 9:10 PM, Patrick Aboyoun wrote: >> Lilyana, >> Steve is right. We added an svn.time function to IRanges that produces >> a time/date stamp in the same format as the BioC Subversion server, >> e.g. "2007-12-07 10:03:15 -0800 (Fri, 07 Dec 2007)", for use by the >> GenomicFeatures package. We implemented a method in C that builds on >> Linux, Windows 32bit& 64bit, and Mac OS X 10.5& 10.6, but not on Mac >> OS X 10.4 (Tiger). Since we dropped support for Mac OS X 10.4, we felt >> comfortable with this decision at the time. We'll explore alternatives >> to see if we can come up with an svn.time solution that doesn't >> preclude building on Mac OS X 10.4. Suggestions by the user community >> is welcome to speed this process along. >> >> >> Cheers, >> >> Patrick >> >> >> On 5/12/10 6:48 PM, Steve Lianoglou wrote: >>> Hi, >>> >>> On Wed, May 12, 2010 at 6:28 PM, Lilyana Margaretha<lilyanam at="" uw.edu=""> >>> wrote: >>>> Hi, >>>> >>>> I am a beginner user of R and trying to install "IRanges" package. >>>> I have R version 2.11 and running it on Mac OS X 10.4.11. >>>> It always gives out this error: >>>> >>>> gcc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include >>>> -I/sw/include -I/usr/local/include -fPIC -g -O2 -c strutils.c -o >>>> strutils.o >>>> strutils.c: In function ?get_svn_time?: >>>> strutils.c:167:27: error: invalid operands to binary / (have ?char * >>>> (*)(int, int)? and ?int?) >>>> make: *** [strutils.o] Error 1 >>>> ERROR: compilation failed for package ?IRanges? >>>> * removing ?/Users/lilyanamargaretha/Desktop/IRanges.Rcheck/IRanges? >>>> >>>> Any suggestion on how to solve this will be very much appreciated. >>> I guess I shouldn't really respond since I don't know this for a fact, >>> but maybe you need a minimum OS X version of 10.5 (leopard) for >>> everything to work? >>> >>> (I see the that binaries provided online are for Leopard, which is why >>> I'm guessing so) >>> >>> -steve >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319