Entering edit mode
Dear all,
I called microRNA package when I tried rtracklayer package on a Mac OS
X 10.4 machine. Errors produced when loading the depended package
Rlibstree (see below).
I tried installed Rlibstree alone from binaries or source, both
failed. Error messages (see below). suggested that R_newStringSet and
R_stringSetAdd functions (in stree.c file) had problem when passing
argument 1 of 'lst_string_new'. This seems to be consistent with the
loading error message, but I am not sure what does it mean. Could
anybody help or give any hints. Thanks a lot!
Weijun
#Loading error
Loading required package: Rlibstree
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resou
rces/library/Rlibstree/libs/ppc/Rlibstree.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/l
ibs/ppc/Rlibstree.so, 6): Symbol not found:
_lst_alg_longest_common_substring
Referenced from: /Library/Frameworks/R.framework/Resources/library/R
libstree/libs/ppc/Rlibstree.so
Expected in: dynamic lookup
Error: package 'Rlibstree' could not be loaded
> sessionInfo()
R version 2.8.0 (2008-10-20)
powerpc-apple-darwin8.11.1
locale:
C
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.1
loaded via a namespace (and not attached):
[1] affyio_1.10.1 preprocessCore_1.4.0
Installing error (from source)
?
gcc -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I../local/include/ -I/usr/local/include -fPIC -g -O2 -c prefix.c
-o prefix.o
gcc -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I../local/include/ -I/usr/local/include -fPIC -g -O2 -c stree.c
-o stree.o
stree.c: In function 'R_newStringSet':
stree.c:100: warning: passing argument 1 of 'lst_string_new' discards
qualifiers from pointer target type
stree.c: In function 'R_stringSetAdd':
stree.c:316: warning: passing argument 1 of 'lst_string_new' discards
qualifiers from pointer target type
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o Rlibstree.so prefix.o
stree.o -L../local/lib -lstree -F/Library/Frameworks/R.framework/..
-framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown
load command 4)
make: *** [Rlibstree.so] Error 1
chmod: /Library/Frameworks/R.framework/Versions/2.8/Resources/library/
Rlibstree/libs/ppc/*: No such file or directory
ERROR: compilation failed for package 'Rlibstree'
** Removing '/Library/Frameworks/R.framework/Versions/2.8/Resources/li
brary/Rlibstree'
** Restoring previous '/Library/Frameworks/R.framework/Versions/2.8/Re
sources/library/Rlibstree'