[Bioc-devel] Troubles with Windows build

Ulrich Bodenhofer bodenho|er @end|ng |rom b|o|n|@jku@@t
Wed Sep 11 16:38:43 CEST 2019

Dear colleagues,

I have two issues with the Windows BUILD BIN of our 'msa' package. (to 
my horror, I figured out that the first problem has existed for quite a 
while; I am deeply sorry for that!)

The main problem can be seen on


It seems that something is wrong with the file 
src/ClustalOmega/src/exceptions4c/e4c_lite.o. Since it does not seem to 
me that e4c_lite.c is freshly compiled (I may be wrong in this point) 
and based on a StackOverflow post 
I have the impression that the build system might still have an on old 
version of some .o files. I can hardly imagine this, but it would 
explain the problem. To be frank, I am quite lost and have no idea what 
else could be the problem. Any hint is gratefully appreciated!

The second issue: the 'msa' package integrates multiple other open 
source packages in one shared library. In order to to so, it uses the 
'ar' tool to compile static libraries of the individual packages and 
then combines them to a shared library. This has always worked fine, and 
on the Bioconductor build servers, too. Now it seems I can no longer run 
the binary build on my Windows system. My Windows makefiles refer to the 
'$(AR)' variable, but it seems this variable is not correctly expanded 
to the actual location of the 'ar' tool (in Rtools 35, it is not in 
Rtools\bin, but in Rtools\mingw_(32|64)\bin) . Any thoughts on this?

Thank you very much in advance and best regards,

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