[BioC] affxparser compile error on mac

[Mark Robinson]

Hi all.

Since the upgrade to R 2.5, I cannot get affxparser to compile on my
mac.  There is no compile error, it creates the shared object file  
(affxparser.so), but cannot load it in the end.  I've asked for a gcc  
compiler upgrade (out of my control) as a possible solution,  
currently have:

target=powerpc-apple-darwin8
Thread model: posix
gcc version 4.0.1 (Apple Computer, Inc. build 5367)

Does anyone else have this problem?

Downloaded source and binary from:
http://www.bioconductor.org/packages/2.0/bioc/html/affxparser.html

Few more details below.

Thanks,
Mark


-------
I tried to install the binary, but doesn't seem to like being loaded:
-------
 >
 > library(affxparser)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
	unable to load shared library '/Users/mrobinson/Library/R/2.5/ 
library/affxparser/libs/ppc/affxparser.so':
   dlopen(/Users/mrobinson/Library/R/2.5/library/affxparser/libs/ppc/ 
affxparser.so, 6): Symbol not found:  
__ZN20affymetrix_fusion_io13FusionCELData7GetStdvEi
   Referenced from: /Users/mrobinson/Library/R/2.5/library/affxparser/ 
libs/ppc/affxparser.so
   Expected in: dynamic lookup

Error: package/namespace load failed for 'affxparser'
 >

 >
 > sessionInfo()
R version 2.5.0 (2007-04-23)
powerpc-apple-darwin8.9.1

locale:
en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"   
"methods"   "base"



-------
Below is the compile output ...
-------

R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

(Using the menu ...)

Warning in install.packages(file.choose(), , NULL, type = "source") :
	 argument 'lib' is missing: using '/Users/mrobinson/Library/R/2.5/
library'
WARNING: ignoring environment value of R_HOME
* Installing *source* package 'affxparser' ...
** libs
** arch - i386
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-
precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/
Frameworks/R.framework/Resources/include/i386 -imacros
R_affx_constants.h -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/
calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -
Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/
src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -
Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/
parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/
calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -
Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/
portability -D_USE_MEM_MAPPING_ -msse3    -fPIC  -g -O2 -march=nocona -
O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/
calvin_files/data/src/CDFData.o

(..... edited)

g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-
precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/
Frameworks/R.framework/Resources/include/ppc -imacros
R_affx_constants.h -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/
calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -
Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/
src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -
Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/
parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/
calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -
Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/
portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -g -O2 -
O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o
g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -
single_module -multiply_defined suppress -L/usr/local/lib -o
affxparser.so fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/
calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/
calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/
data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/
CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/
CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o
fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/
data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o
fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/
calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/
GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o
fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/
calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/
calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/
src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/
FusionCELData.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/
GCOSCELDataAdapter.o fusion_sdk/calvin_files/parameter/src/
ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/
CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o
fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/
calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/
parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/
DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/
calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/
calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/
utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/
DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/
calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/
checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/
BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/
CELFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o
R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o
R_affx_bpmap_parser.o   -F/Library/Frameworks/R.framework/.. -
framework R
** R
** inst
** save image
** preparing package for lazy loading
Error in dyn.load(x, as.logical(local), as.logical(now)) :
	unable to load shared library '/Users/mrobinson/Library/R/2.5/library/
affxparser/libs/ppc/affxparser.so':
   dlopen(/Users/mrobinson/Library/R/2.5/library/affxparser/libs/ppc/
affxparser.so, 6): Symbol not found:
__ZN20affymetrix_fusion_io13FusionCELData7GetStdvEi
   Referenced from: /Users/mrobinson/Library/R/2.5/library/affxparser/
libs/ppc/affxparser.so
   Expected in: dynamic lookup
Execution halted
ERROR: lazy loading failed for package 'affxparser'
** Removing '/Users/mrobinson/Library/R/2.5/library/affxparser'