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11.5 years ago by
jason smith50
jason smith50 wrote:
Hi, First I'd like to thank everyone for bioconductor- it has been very useful. I have installed R 2.7.0 GUI 1.24 (5102) on an intel Mac running OS 10.5.3. R seems to be working and when I use biocLite to load packages I get a warning. Then when I try to load the packages everything seems to work except affy (and some related) packages. Here is what I get: > source("http://bioconductor.org/biocLite.R") > biocLite() Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor. Will install the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" "Biobase" "Biostrings" "DynDoc" "gcrma" [10] "genefilter" "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" "multtest" "ROC" "vsn" [19] "xtable" "affyQCReport" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/Users/sjorges2002/Library/R/2.7/library' And later when I try to load affy: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so': dlopen(/Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy. so, 6): Library not loaded: /usr/local/lib/libintl.3.dylib Referenced from: /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so Reason: image not found Error in library(affy) : .First.lib failed for 'affy' What can I do to fix this? Thanks, Jason
gui affy • 1.0k views
modified 11.5 years ago • written 11.5 years ago by jason smith50
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11.5 years ago by
Denali
Steve Lianoglou12k wrote:
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11.5 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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11.5 years ago by
jason smith50
jason smith50 wrote:
Kasper, Yes it is a standard system intel core 2 duo, MacBook 3,1; 2.2GHZ; 4GB RAM. xcode 3.0 installed. I did not install anything 'customized'. In R: > options("pkgType") $pkgType [1] "mac.binary" Here is the result of otool in terminal: jason-smiths-macbook:~ sjorges2002$ otool -L affy.so otool: can't open file: affy.so (No such file or directory) But I can navigate to this file: Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so affy.so is a 100KB Unix executable in i386 Vincent Carey said that they had to install Darwin ports, sudo ports, and gettext to fix this issue. However, since I am not a programmer/developer I don't have a C compiler or know how to use xcode to do this. Thanks Jason I am at a bit of a loss here. My version of affy does not link against that library, but I am on ppc. Could you try to do the following from Terminal # otool -L affy.so (where you have navigated to the folder where affy.so is, see your output). Have you installed the developer tools? And the stuff you get when you click "customize" during the R installation? Still, that should not be necessary. And could you please check (in R) what the pkgType option is set to?
> Kasper, > > Yes it is a standard system intel core 2 duo, MacBook 3,1; 2.2GHZ; 4GB > RAM. xcode 3.0 installed. I did not install anything 'customized'. In R: > >> options("pkgType") > $pkgType > [1] "mac.binary" > > Here is the result of otool in terminal: > jason-smiths-macbook:~ sjorges2002$ otool -L affy.so > otool: can't open file: affy.so (No such file or directory) > > But I can navigate to this file: > Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so > affy.so is a 100KB Unix executable in i386 Could you actually run otool -L on that file in your Library folder? > Vincent Carey said that they had to install Darwin ports, sudo ports, and > gettext to fix this issue. However, since I am not a programmer/developer > I don't have a C compiler or know how to use xcode to do this. Yeah, I saw Vince email. It looks really strange I must say, especially him noting that the problem suddenly appeared. You should not have to install gettext at all and certainly not from Darwinports. I am very bewildered by this. Try to run the otool command. We might have to look into the building process for macs. Kasper > Thanks > Jason > > I am at a bit of a loss here. My version of affy does not link against > that library, but I am on ppc. Could you try to do the following from > Terminal > # otool -L affy.so > (where you have navigated to the folder where affy.so is, see your > output). Have you installed the developer tools? And the stuff you get > when you click "customize" during the R installation? Still, that > should not be necessary. And could you please check (in R) what the > pkgType option is set to? > > > >
0
11.5 years ago by
jason smith50
jason smith50 wrote:
Kasper, Here is what I get when I run otool. I'm not sure if I am doing it right. jason-smiths-macbook:~ sjorges2002$otool -L "affy.so" otool: can't open file: affy.so (No such file or directory) Thanks, Jason ADD COMMENTlink written 11.5 years ago by jason smith50 Hi, On Jun 16, 2008, at 8:14 AM, jason smith wrote: > Kasper, > > Here is what I get when I run otool. I'm not sure if I am doing it > right. > > jason-smiths-macbook:~ sjorges2002$ otool -L "affy.so" > otool: can't open file: affy.so (No such file or directory) You're not doing it right :-) You have to point to the actual affy.so file. From your previous errors, it looks like you should run this from the command line: otool -L /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so Let's see what you get from that. -steve
Thanks Steve, Here is what I get from otool: jason-smiths-macbook:~ sjorges2002$otool -L /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so: affy.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib (compatibility version 2.7.0, current version 2.7.0) /usr/local/lib/libintl.3.dylib (compatibility version 8.0.0, current version 8.3.0) /usr/lib/libiconv.2.dylib (compatibility version 5.0.0, current version 5.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.10) /System/Library/Frameworks/CoreFoundation.framework/Versions/A /CoreFoundation (compatibility version 150.0.0, current version 368.35.0) /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) Best Jason --- On Mon, 6/16/08, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > > You're not doing it right :-) > > otool -L > /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so > > Let's see what you get from that. > > -steve ADD REPLYlink written 11.5 years ago by jason smith50 Ok, I will take this over to the R-SIG-Mac list and cc Herve who is the build manager of Bioconductor. I suspect that something is wrong with the Bioconductor builds. Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook running 10.5.3. He says he has Xcode 3.0 installed. He tries to install the binary version of aff from Bioconductor using the normal biocLite("affy") However, even though the tarball downloads and gets installed, the package won't load. It complains that it needs the library /usr/local/ lib/libintl.3.dylib (and an otool -L really confirms this), but apparently this files does not exists. I am a bit surprised that the binary version links to something in /usr/local. I have this file on my PPC G4 running 10.5.3. As I see it, this should work out of the box with the system Jason is running. Does anyone have any good ideas? My hunch is that something might be up with the binary builds? Vince Carey reports that a student of his had a similar problem. Kasper On Jun 16, 2008, at 6:53 AM, jason smith wrote: > Thanks Steve, > > Here is what I get from otool: > > jason-smiths-macbook:~ sjorges2002$ otool -L /Users/sjorges2002/ > Library/R/2.7/library/affy/libs/i386/affy.so > /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so: > affy.so (compatibility version 0.0.0, current version 0.0.0) > /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version > 1.2.3) > /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/ > libR.dylib (compatibility version 2.7.0, current version 2.7.0) > /usr/local/lib/libintl.3.dylib (compatibility version 8.0.0, current > version 8.3.0) > /usr/lib/libiconv.2.dylib (compatibility version 5.0.0, current > version 5.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 88.3.10) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/ > CoreFoundation (compatibility version 150.0.0, current version > 368.35.0) > /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, > current version 1.0.0) > > Best > Jason > > --- On Mon, 6/16/08, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: > > >> >> You're not doing it right :-) > >> >> otool -L >> /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so >> >> Let's see what you get from that. >> >> -steve > > >
Hi, On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote: > Ok, I will take this over to the R-SIG-Mac list and cc Herve who is > the build manager of Bioconductor. I suspect that something is wrong > with the Bioconductor builds. > > Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook > running 10.5.3. He says he has Xcode 3.0 installed. He tries to > install the binary version of aff from Bioconductor using the normal > biocLite("affy") > However, even though the tarball downloads and gets installed, the > package won't load. It complains that it needs the library /usr/ > local/lib/libintl.3.dylib (and an otool -L really confirms this), > but apparently this files does not exists. I am a bit surprised that > the binary version links to something in /usr/local. I have this > file on my PPC G4 running 10.5.3. As I see it, this should work out > of the box with the system Jason is running. Does anyone have any > good ideas? My hunch is that something might be up with the binary > builds? Just so Jason can get up and running quickly (and not have to wait for this to get sorted out in the builds or whatever), I would recommend as a band-aid procedure to just install gettext for now, as I am fairly certain that this will provide the /usr/local/lib/libintl. 3.dylib that he is missing. I gather that he might not be very comfortable from the command line, so following these steps in a terminal session should do the trick: cd /tmp curl http://mirrors.usc.edu/pub/gnu/gettext/gettext-0.17.tar.gz | tar xz cd gettext-0.17 ./configure make sudo make install HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics, and Systems Biology Weill Medical College, Cornell University http://cbio.mskcc.org/~lianos
Another way Jason can get up and run quickly is to do something like R> options(pkgType = "source") and then do biocLite. That is probably a better solution than trying to install gettext Kasper On Jun 19, 2008, at 10:18 AM, Steve Lianoglou wrote: > Hi, > > On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote: > >> Ok, I will take this over to the R-SIG-Mac list and cc Herve who is >> the build manager of Bioconductor. I suspect that something is >> wrong with the Bioconductor builds. >> >> Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook >> running 10.5.3. He says he has Xcode 3.0 installed. He tries to >> install the binary version of aff from Bioconductor using the normal >> biocLite("affy") >> However, even though the tarball downloads and gets installed, the >> package won't load. It complains that it needs the library /usr/ >> local/lib/libintl.3.dylib (and an otool -L really confirms this), >> but apparently this files does not exists. I am a bit surprised >> that the binary version links to something in /usr/local. I have >> this file on my PPC G4 running 10.5.3. As I see it, this should >> work out of the box with the system Jason is running. Does anyone >> have any good ideas? My hunch is that something might be up with >> the binary builds? > > Just so Jason can get up and running quickly (and not have to wait > for this to get sorted out in the builds or whatever), I would > recommend as a band-aid procedure to just install gettext for now, > as I am fairly certain that this will provide the /usr/local/lib/ > libintl.3.dylib that he is missing. > > I gather that he might not be very comfortable from the command > line, so following these steps in a terminal session should do the > trick: > > cd /tmp > curl http://mirrors.usc.edu/pub/gnu/gettext/gettext-0.17.tar.gz | > tar xz > cd gettext-0.17 > ./configure > make > sudo make install > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics, and Systems Biology > Weill Medical College, Cornell University > > http://cbio.mskcc.org/~lianos
On Jun 19, 2008, at 2:03 PM, Kasper Daniel Hansen wrote: > Another way Jason can get up and run quickly is to do something like > > R> options(pkgType = "source") > > and then do biocLite. That is probably a better solution than trying > to install gettext > Definitely, and especially since it doesn't help (see my comments to Steve below). I wouldn't recommend installing gettext (unless you know what you're doing) simply because it will modify your system such that all future configurations will detect it and behave differently. As long as you don't plan to copy anything to another machine it is not a big deal, but if you do, you'll learn very quickly why that's a bad idea ;). Nonetheless, there are valid cases. However, as Jan pointed out correctly, this is not the only problem that BioC builds have, unfortunately. I can only repeat my plea that I sent while ago to the BioC team to fix their Mac builds. > Kasper > > On Jun 19, 2008, at 10:18 AM, Steve Lianoglou wrote: > >> Hi, >> >> On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote: >> >>> Ok, I will take this over to the R-SIG-Mac list and cc Herve who >>> is the build manager of Bioconductor. I suspect that something is >>> wrong with the Bioconductor builds. >>> >>> Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook >>> running 10.5.3. He says he has Xcode 3.0 installed. He tries to >>> install the binary version of aff from Bioconductor using the normal >>> biocLite("affy") >>> However, even though the tarball downloads and gets installed, the >>> package won't load. It complains that it needs the library /usr/ >>> local/lib/libintl.3.dylib (and an otool -L really confirms this), >>> but apparently this files does not exists. I am a bit surprised >>> that the binary version links to something in /usr/local. I have >>> this file on my PPC G4 running 10.5.3. As I see it, this should >>> work out of the box with the system Jason is running. Does anyone >>> have any good ideas? My hunch is that something might be up with >>> the binary builds? >> >> Just so Jason can get up and running quickly (and not have to wait >> for this to get sorted out in the builds or whatever), I would >> recommend as a band-aid procedure to just install gettext for now, >> as I am fairly certain that this will provide the /usr/local/lib/ >> libintl.3.dylib that he is missing. >> Are you? Did you actually test it? I'm pretty sure that you're wrong, because the commands below compile libintl.8.dylib(!) and thus won't help (that one is fine and part of your Gtk binary). I'm still puzzled at where the BioC team gets libintl.3 ... Cheers, Simon >> I gather that he might not be very comfortable from the command >> line, so following these steps in a terminal session should do the >> trick: >> >> cd /tmp >> curl http://mirrors.usc.edu/pub/gnu/gettext/gettext-0.17.tar.gz | >> tar xz >> cd gettext-0.17 >> ./configure >> make >> sudo make install >> >> HTH, >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Physiology, Biophysics, and Systems Biology >> Weill Medical College, Cornell University >> >> http://cbio.mskcc.org/~lianos > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >
On Jun 19, 2008, at 11:42 AM, Simon Urbanek wrote: > Are you? Did you actually test it? I'm pretty sure that you're > wrong, because the commands below compile libintl.8.dylib(!) and > thus won't help (that one is fine and part of your Gtk binary). I'm > still puzzled at where the BioC team gets libintl.3 ... Well, I have libintl.3 on my Leopard G4 powerbook. It is a fairly recent install and I am pretty sure I have not installed gettext manually - but I could be wrong of course. Neither am I running Darwin ports or Fink. Kasper
> Are you? Did you actually test it? I'm pretty sure that you're > wrong, because the commands below compile libintl.8.dylib(!) and > thus won't help (that one is fine and part of your Gtk binary). Ouch, well I stand corrected then. Sorry for sending out misinformation ... > I'm still puzzled at where the BioC team gets libintl.3 ... Yeah. Even more puzzling (to me) is where mine came from ... as someone else mentioned before, I also have a fairly clean install of leopard (having just replaced my hard drive a few weeks ago) and libnitl.3.dylib is magically there. My apologies once again. -steve
Last night's BioC 2.2 Mac OS X binary packages went well and will soon be available on bioconductor.org. These packages make use of the dynamic libraries (libgcc_s.1.dylib, libgfortran.2.dylib, libreadline.5.2.dylib, and libreadline.dylib) that are distributed with the standard Mac OS X build of R 2.7.x. The new packages have been pushed to the web server behind bioconductor.org, but due to the file caching by the web server, the more popular packages are pulled from the cache rather than the new package set. It can sometimes take a few hours for the cache to be cleared and for the complete set of Mac OS X binary packages to be available. Here is a look at how the affy and affyio packages are now linking to external libraries: [Examination of affy] pitt:~/test biocbuild$otool -L affy/libs/i386/affy.so affy/libs/i386/affy.so: affy.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib (compatibility version 2.7.0, current version 2.7.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFou ndation (compatibility version 150.0.0, current version 368.27.0) /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgcc_s.1. dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) [Examination of affyio] pitt:~/test biocbuild$ otool -L affyio/libs/i386/affyio.so affyio/libs/i386/affyio.so: affyio.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib (compatibility version 2.7.0, current version 2.7.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFou ndation (compatibility version 150.0.0, current version 368.27.0) /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgcc_s.1. dylib (compatibility version 1.0.0, current version 1.0.0) If you experience any other related issues along these lines, please feel free to e-mail me directly. Cheers, Patrick Patrick Aboyoun wrote: > Thanks to all for bringing this issue of the BioC 2.2 Max OS X binary > packages to light, and I apologize for any inconvenience these > non-standard binary packages have caused the BioC user community. If > all goes well with the build system tomorrow morning, the Mac OS X > binary packages will be produced under the standard Mac OS X R > framework. I will send out an e-mail tomorrow morning notifying you on > its status. > > I don't want to get too much into the gory details of the build > system, but I will provide you with a high level synopsis on what > caused the breakdown. Back when the Bioconductor core team released > BioC 2.2 in May, we had a last minute scramble for the Mac OS X binary > packages builds. Up until release time, we were building the packages > on Mac OS X Leopard (10.5.2). It was brought to our attention the week > of the release that those builds were not working on Mac OS X Tiger. > When we switched to a Tiger build machine, we experienced problems > with the png device (type = "quartz", the default, failed to work in > our build environment). In order to be expedient we used a custom > build of R 2.7.0 to get around this issue. This had the unintended > consequence that you discovered. We have since reverted back to using > the standard R 2.7.1 build for the Mac and are using a configuration > file to set options(bitmapType = "cairo") to get around the png device > issue. These new Mac binary package builds will be linking into the > dynamic libraries located in the standard R directory > /Library/Frameworks/R.framework/Resources/lib. > > > Cheers, > Patrick [Removed e-mail trail]
On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote: > Ok, I will take this over to the R-SIG-Mac list and cc Herve who is > the build manager of Bioconductor. I suspect that something is wrong > with the Bioconductor builds. > > Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook > running 10.5.3. He says he has Xcode 3.0 installed. He tries to > install the binary version of aff from Bioconductor using the normal > biocLite("affy") > However, even though the tarball downloads and gets installed, the > package won't load. It complains that it needs the library /usr/ > local/lib/libintl.3.dylib (and an otool -L really confirms this), > but apparently this files does not exists. I am a bit surprised that > the binary version links to something in /usr/local. I have this > file on my PPC G4 running 10.5.3. As I see it, this should work out > of the box with the system Jason is running. Does anyone have any > good ideas? My hunch is that something might be up with the binary > builds? > Yes, that sounds like a problem with the BioC builds (libintl.3.dylib is really strange - we use libintl.8.dylib as a part of optional Gtk on CRAN, but never libintl3.dylib..). I didn't test BioC builds ever since we stopped building it on CRAN, but I have heard complains about their binaries linking various stuff from /usr/local, so I'd suggest to file a bug report with them (BTW: Xcode should not be required from binary installs). Cheers, S > Vince Carey reports that a student of his had a similar problem. > > Kasper > > On Jun 16, 2008, at 6:53 AM, jason smith wrote: > >> Thanks Steve, >> >> Here is what I get from otool: >> >> jason-smiths-macbook:~ sjorges2002$otool -L /Users/sjorges2002/ >> Library/R/2.7/library/affy/libs/i386/affy.so >> /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so: >> affy.so (compatibility version 0.0.0, current version 0.0.0) >> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version >> 1.2.3) >> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/ >> libR.dylib (compatibility version 2.7.0, current version 2.7.0) >> /usr/local/lib/libintl.3.dylib (compatibility version 8.0.0, >> current version 8.3.0) >> /usr/lib/libiconv.2.dylib (compatibility version 5.0.0, current >> version 5.0.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version 88.3.10) >> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/ >> CoreFoundation (compatibility version 150.0.0, current version >> 368.35.0) >> /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, >> current version 1.0.0) >> >> Best >> Jason >> >> --- On Mon, 6/16/08, Steve Lianoglou >> <mailinglist.honeypot at="" gmail.com=""> wrote: >> >> >>> >>> You're not doing it right :-) >> >>> >>> otool -L >>> /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so >>> >>> Let's see what you get from that. >>> >>> -steve >> >> >> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ADD REPLYlink written 11.5 years ago by Simon Urbanek60 Yeah you want to run it on the affy.so file in your library folder. This is what you need to type otool -L /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so Kasper On Jun 16, 2008, at 5:14 AM, jason smith wrote: > Kasper, > > Here is what I get when I run otool. I'm not sure if I am doing it > right. > > jason-smiths-macbook:~ sjorges2002$ otool -L "affy.so" > otool: can't open file: affy.so (No such file or directory) > > Thanks, > Jason > > >