Dear all, Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for Mac OS X 10.5 (Leopard) and higher. Now I wanted to run R CMD check for my BioC package which contains C++ code but got the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no suitable image found. Did find: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o, but wrong architecture ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' Do you have any hint what might be the reason for this error? As far as I understand this message means that Snow Leopard is the wrong architecture, why? Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
R CMD check fails on Snow Leopard
8 messages · Simon Urbanek, Kasper Daniel Hansen, cstrato
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all, Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for Mac OS X 10.5 (Leopard) and higher. Now I wanted to run R CMD check for my BioC package which contains C++ code but got the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no suitable image found. Did find: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o, but wrong architecture ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
Dear Simon,
My package is "xps" which has always worked on Tiger and also on
Leopard, thus I am shocked that it does not work on Snow Leopard. The
problem is not only that I cannot do "R32 CMD check xps-1.9.0.tar.gz"
which results in the error message mentioned, but that the binary which
I have downloaded using "biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
> library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so,
6): Library not loaded: @rpath/libCore.so
Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
Reason: no suitable image found. Did find:
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'
At the moment I have no idea what might be the reason for this:-(
Best regards
Christian
On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all, Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for Mac OS X 10.5 (Leopard) and higher. Now I wanted to run R CMD check for my BioC package which contains C++ code but got the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no suitable image found. Did find: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o, but wrong architecture ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
You can have a look at the library by doing file (otool is also nice to know btw), I get # file affxparser.so affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64 You do this on both the ROOT library and the xps.so library to see what the architectures are. Based on the error message, they are different. Why, is something I think you will have to track down yourself, because that depends on how you compiled R/ROOT. Kasper
On Wed, Apr 28, 2010 at 5:54 PM, cstrato <cstrato at aon.at> wrote:
Dear Simon,
My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) : ?unable to load shared library '/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so': ?dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6): Library not loaded: @rpath/libCore.so ?Referenced from: /Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so ?Reason: no suitable image found. ?Did find: ? ? ? ?/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong architecture ? ? ? ?/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong architecture Error: package/namespace load failed for 'xps' At the moment I have no idea what might be the reason for this:-( Best regards Christian On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all, Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for Mac OS X 10.5 (Leopard) and higher. Now I wanted to run R CMD check for my BioC package which contains C++ code but got the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : ?unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so': ?dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no suitable image found. ?Did find: ? ? ? ?/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o, but wrong architecture ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Dear Kasper, Thank you for this suggestion which was very helpful. As it turns out, at the moment I am not able to compile ROOT for 32 bit on Snow Leopard. I have already contacted the ROOT developers. Best regards Christian
On 4/29/10 5:25 AM, Kasper Daniel Hansen wrote:
You can have a look at the library by doing file (otool is also nice to know btw), I get # file affxparser.so affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64 You do this on both the ROOT library and the xps.so library to see what the architectures are. Based on the error message, they are different. Why, is something I think you will have to track down yourself, because that depends on how you compiled R/ROOT. Kasper On Wed, Apr 28, 2010 at 5:54 PM, cstrato<cstrato at aon.at> wrote:
Dear Simon,
My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6):
Library not loaded: @rpath/libCore.so
Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
Reason: no suitable image found. Did find:
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'
At the moment I have no idea what might be the reason for this:-(
Best regards
Christian
On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all,
Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and
downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for
Mac OS X 10.5 (Leopard) and higher.
Now I wanted to run R CMD check for my BioC package which contains C++
code but got the following error:
installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so':
dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no
suitable image found. Did find:
/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o,
but wrong architecture
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'
Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
1 day later
Dear Simon, dear Kasper, While I could solve the problem with wrong architecture, R CMD check now results in the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so, 6): Symbol not found: __ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc Referenced from: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so Expected in: flat namespace in /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' This time I get this error both on Leopard for "i386" and on Snow Leopard for "x86_64" while the Bioconductor server does not have this problem (to my great relieve), see: http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/pelham-checksrc.html Do you have any idea what might be the reason for this problem? Best regards Christian
On 4/29/10 5:25 AM, Kasper Daniel Hansen wrote:
You can have a look at the library by doing file (otool is also nice to know btw), I get # file affxparser.so affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64 You do this on both the ROOT library and the xps.so library to see what the architectures are. Based on the error message, they are different. Why, is something I think you will have to track down yourself, because that depends on how you compiled R/ROOT. Kasper On Wed, Apr 28, 2010 at 5:54 PM, cstrato<cstrato at aon.at> wrote:
Dear Simon,
My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6):
Library not loaded: @rpath/libCore.so
Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
Reason: no suitable image found. Did find:
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'
At the moment I have no idea what might be the reason for this:-(
Best regards
Christian
On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all,
Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and
downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for
Mac OS X 10.5 (Leopard) and higher.
Now I wanted to run R CMD check for my BioC package which contains C++
code but got the following error:
installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so':
dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no
suitable image found. Did find:
/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o,
but wrong architecture
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'
Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On Apr 30, 2010, at 4:55 PM, cstrato wrote:
Dear Simon, dear Kasper, While I could solve the problem with wrong architecture, R CMD check now results in the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so, 6): Symbol not found: __ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc Referenced from: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so Expected in: flat namespace in /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' This time I get this error both on Leopard for "i386" and on Snow Leopard for "x86_64" while the Bioconductor server does not have this problem (to my great relieve), see: http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/pelham-checksrc.html Do you have any idea what might be the reason for this problem?
Likely xps was not linked against all necessary libraries. Since it is sinked as dynamic library bugs like that are only visible at run-time not at link-time. Cheers, Simon
On 4/29/10 5:25 AM, Kasper Daniel Hansen wrote:
You can have a look at the library by doing file (otool is also nice to know btw), I get # file affxparser.so affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64 You do this on both the ROOT library and the xps.so library to see what the architectures are. Based on the error message, they are different. Why, is something I think you will have to track down yourself, because that depends on how you compiled R/ROOT. Kasper On Wed, Apr 28, 2010 at 5:54 PM, cstrato<cstrato at aon.at> wrote:
Dear Simon,
My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6):
Library not loaded: @rpath/libCore.so
Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
Reason: no suitable image found. Did find:
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'
At the moment I have no idea what might be the reason for this:-(
Best regards
Christian
On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all,
Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and
downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for
Mac OS X 10.5 (Leopard) and higher.
Now I wanted to run R CMD check for my BioC package which contains C++
code but got the following error:
installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so':
dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no
suitable image found. Did find:
/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o,
but wrong architecture
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'
Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Dear Simon, Thank you for your reply. The difference between the code uploaded to BioC and my new code is the "Makefile.arch". I have just run R CMD check using the uploaded "Makefile.arch" where the relevant part is: ifeq ($(ARCH),macosx) # MacOS X with cc (GNU cc 2.95.2 and gcc 3.3) MACOSX_MINOR := $(shell sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2) MACOSXTARGET := MACOSX_DEPLOYMENT_TARGET=10.$(MACOSX_MINOR) ifeq ($(MACOSX_MINOR),5) MACOSX_MINOR = 4 endif CXX = c++ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD = $(MACOSXTARGET) c++ LDFLAGS = $(OPT2) -bind_at_load # The SOFLAGS will be used to create the .dylib, # the .so will be created separately DllSuf = dylib UNDEFOPT = dynamic_lookup ifneq ($(MACOSX_MINOR),4) ifneq ($(MACOSX_MINOR),3) UNDEFOPT = suppress LD = c++ endif endif SOFLAGS = -dynamiclib -single_module -undefined $(UNDEFOPT) endif Using this code I can once again run R CMD check w/o problems, however, since this code does not work on Snow Leopard, I have replaced it with the following code which causes the reported error: ifeq ($(ARCH),macosx) # MacOS X with cc (GNU cc 2.95.2 and gcc 3.3) MACOSX_MINOR := $(shell sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2) ifeq ($(MACOSX_DEPLOYMENT_TARGET),) MACOSXTARGET := MACOSX_DEPLOYMENT_TARGET=10.$(MACOSX_MINOR) else MACOSXTARGET := MACOSX_DEPLOYMENT_TARGET=$(MACOSX_DEPLOYMENT_TARGET) endif CXX = g++ CXXFLAGS = $(OPT2) -pipe -Wall -W -Woverloaded-virtual LD = $(MACOSXTARGET) g++ LDFLAGS = $(OPT2) # The SOFLAGS will be used to create the .dylib, # the .so will be created separately ifeq ($(subst $(MACOSX_MINOR),,1234),1234) DllSuf = so else DllSuf = dylib endif UNDEFOPT = dynamic_lookup ifneq ($(subst $(MACOSX_MINOR),,12),12) UNDEFOPT = suppress LD = g++ endif SOFLAGS = -dynamiclib -single_module -undefined $(UNDEFOPT) -install_name $(CURDIR)/ endif Do you have any hint why this code does not work? Best regards Christian
On 4/30/10 11:00 PM, Simon Urbanek wrote:
On Apr 30, 2010, at 4:55 PM, cstrato wrote:
Dear Simon, dear Kasper, While I could solve the problem with wrong architecture, R CMD check now results in the following error: installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so': dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so, 6): Symbol not found: __ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc Referenced from: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so Expected in: flat namespace in /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so ERROR: loading failed * removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps' This time I get this error both on Leopard for "i386" and on Snow Leopard for "x86_64" while the Bioconductor server does not have this problem (to my great relieve), see: http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/pelham-checksrc.html Do you have any idea what might be the reason for this problem?
Likely xps was not linked against all necessary libraries. Since it is sinked as dynamic library bugs like that are only visible at run-time not at link-time. Cheers, Simon
On 4/29/10 5:25 AM, Kasper Daniel Hansen wrote:
You can have a look at the library by doing file (otool is also nice to know btw), I get # file affxparser.so affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64 You do this on both the ROOT library and the xps.so library to see what the architectures are. Based on the error message, they are different. Why, is something I think you will have to track down yourself, because that depends on how you compiled R/ROOT. Kasper On Wed, Apr 28, 2010 at 5:54 PM, cstrato<cstrato at aon.at> wrote:
Dear Simon,
My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.
When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:
library(xps)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6):
Library not loaded: @rpath/libCore.so
Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
Reason: no suitable image found. Did find:
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
/Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'
At the moment I have no idea what might be the reason for this:-(
Best regards
Christian
On 4/28/10 11:38 PM, Simon Urbanek wrote:
On Apr 28, 2010, at 5:22 PM, cstrato wrote:
Dear all,
Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and
downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for
Mac OS X 10.5 (Leopard) and higher.
Now I wanted to run R CMD check for my BioC package which contains C++
code but got the following error:
installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so':
dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no
suitable image found. Did find:
/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o,
but wrong architecture
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'
Do you have any hint what might be the reason for this error?
Apparently the R and your package have different architectures. The reason is most likely your package - often badly written Makevars or Makefile if some dependencies are used, or stale object files in the sources (failure to clean up) etc. You'd have to show us the package and exactly how you're trying to instal it if we are to help you further.
As far as I understand this message means that Snow Leopard is the wrong architecture, why?
You understand the message incorrectly - it tells you the R (which is the one loading the package) cannot find binary of the same architecture in the package, but it can find another, different, architecture instead. "Snow Leopard" is not an architecture it's an operating system. Cheers, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac