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Renaming affyio module

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commit f282dd24b68a4c7e51e33581d539b21c91898822 1 parent f17cf2c
@pjotrp authored
Showing with 1,056 additions and 784 deletions.
  1. 0  src/clibs/{affyio-1.8 → affyio}/DESCRIPTION
  2. 0  src/clibs/{affyio-1.8 → affyio}/HISTORY
  3. 0  src/clibs/{affyio-1.8 → affyio}/LICENSE
  4. 0  src/clibs/{affyio-1.8 → affyio}/NAMESPACE
  5. 0  src/clibs/{affyio-1.8 → affyio}/R/check.cdf.type.R
  6. 0  src/clibs/{affyio-1.8 → affyio}/R/read.cdffile.list.R
  7. 0  src/clibs/{affyio-1.8 → affyio}/R/read.celfile.R
  8. 0  src/clibs/{affyio-1.8 → affyio}/R/read.celfile.header.R
  9. 0  src/clibs/{affyio-1.8 → affyio}/R/read.probematrices.R
  10. 0  src/clibs/{affyio-1.8 → affyio}/README_BIOLIB
  11. 0  src/clibs/{affyio-1.8 → affyio}/aclocal.m4
  12. +1,035 −775 src/clibs/{affyio-1.8 → affyio}/configure
  13. +21 −9 src/clibs/{affyio-1.8 → affyio}/configure.in
  14. 0  src/clibs/{affyio-1.8 → affyio}/man/check.cdf.type.Rd
  15. 0  src/clibs/{affyio-1.8 → affyio}/man/read.cdffile.list.Rd
  16. 0  src/clibs/{affyio-1.8 → affyio}/man/read.celfile.Rd
  17. 0  src/clibs/{affyio-1.8 → affyio}/man/read.celfile.header.Rd
  18. 0  src/clibs/{affyio-1.8 → affyio}/man/read.celfile.probeintensity.matrices.Rd
  19. 0  src/clibs/{affyio-1.8 → affyio}/src/CMakeLists.txt
  20. 0  src/clibs/{affyio-1.8 → affyio}/src/Makevars.in
  21. 0  src/clibs/{affyio-1.8 → affyio}/src/Makevars.win
  22. 0  src/clibs/{affyio-1.8 → affyio}/src/biolib_affyio.c
  23. 0  src/clibs/{affyio-1.8 → affyio}/src/biolib_affyio.h
  24. 0  src/clibs/{affyio-1.8 → affyio}/src/fread_functions.c
  25. 0  src/clibs/{affyio-1.8 → affyio}/src/fread_functions.h
  26. 0  src/clibs/{affyio-1.8 → affyio}/src/read_abatch.c
  27. 0  src/clibs/{affyio-1.8 → affyio}/src/read_abatch.h
  28. 0  src/clibs/{affyio-1.8 → affyio}/src/read_bpmap.c
  29. 0  src/clibs/{affyio-1.8 → affyio}/src/read_cdf.h
  30. 0  src/clibs/{affyio-1.8 → affyio}/src/read_cdf_xda.c
  31. 0  src/clibs/{affyio-1.8 → affyio}/src/read_cdffile2.c
  32. 0  src/clibs/{affyio-1.8 → affyio}/src/read_celfile_generic.c
  33. 0  src/clibs/{affyio-1.8 → affyio}/src/read_celfile_generic.h
  34. 0  src/clibs/{affyio-1.8 → affyio}/src/read_clf.c
  35. 0  src/clibs/{affyio-1.8 → affyio}/src/read_generic.c
  36. 0  src/clibs/{affyio-1.8 → affyio}/src/read_generic.h
  37. 0  src/clibs/{affyio-1.8 → affyio}/src/read_pgf.c
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0  src/clibs/affyio-1.8/DESCRIPTION → src/clibs/affyio/DESCRIPTION
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0  src/clibs/affyio-1.8/HISTORY → src/clibs/affyio/HISTORY
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0  src/clibs/affyio-1.8/LICENSE → src/clibs/affyio/LICENSE
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0  src/clibs/affyio-1.8/NAMESPACE → src/clibs/affyio/NAMESPACE
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0  src/clibs/affyio-1.8/R/check.cdf.type.R → src/clibs/affyio/R/check.cdf.type.R
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0  src/clibs/affyio-1.8/R/read.cdffile.list.R → src/clibs/affyio/R/read.cdffile.list.R
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0  src/clibs/affyio-1.8/R/read.celfile.R → src/clibs/affyio/R/read.celfile.R
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0  src/clibs/affyio-1.8/R/read.celfile.header.R → src/clibs/affyio/R/read.celfile.header.R
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0  src/clibs/affyio-1.8/R/read.probematrices.R → src/clibs/affyio/R/read.probematrices.R
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0  src/clibs/affyio-1.8/README_BIOLIB → src/clibs/affyio/README_BIOLIB
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0  src/clibs/affyio-1.8/aclocal.m4 → src/clibs/affyio/aclocal.m4
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1,810 src/clibs/affyio-1.8/configure → src/clibs/affyio/configure
1,035 additions, 775 deletions not shown
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30 src/clibs/affyio-1.8/configure.in → src/clibs/affyio/configure.in
@@ -16,24 +16,36 @@ dnl Are things (still) the same ?
dnl (taken from the 'writing R extensions manual')
-dnl
-dnl tests the zlib.h
-dnl (the test is found in 'acinclude.m4')
-dnl
-
R_ZLIB
+
AC_CHECK_LIB(pthread, pthread_create)
AC_TRY_LINK_FUNC(pthread_create, [use_pthreads=yes], [use_pthreads=no])
AC_MSG_CHECKING([if we can use pthreads])
+AC_MSG_RESULT($use_pthreads)
+
+AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])
+AC_COMPILE_IFELSE([
+ #include <pthread.h>
+ #include <limits.h>
+
+ int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
+}
+ ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
+AC_MSG_RESULT($use_pthread_stack_min)
+
if test "x$use_pthreads" = "xyes"
then
- LIBS="$LIBS -lpthread"
- AC_DEFINE(USE_PTHREADS, 1)
+if test "x$use_pthread_stack_min" = "xyes"
+ then
+ LIBS="$LIBS -lpthread"
+ AC_DEFINE(USE_PTHREADS, 1)
+ fi
fi
-AC_MSG_RESULT($use_pthreads)
-AC_OUTPUT(src/Makevars)
+
+
+AC_OUTPUT(src/Makevars)
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0  src/clibs/affyio-1.8/man/check.cdf.type.Rd → src/clibs/affyio/man/check.cdf.type.Rd
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0  ...clibs/affyio-1.8/man/read.cdffile.list.Rd → src/clibs/affyio/man/read.cdffile.list.Rd
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0  src/clibs/affyio-1.8/man/read.celfile.Rd → src/clibs/affyio/man/read.celfile.Rd
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0  ...ibs/affyio-1.8/man/read.celfile.header.Rd → src/clibs/affyio/man/read.celfile.header.Rd
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0  ...n/read.celfile.probeintensity.matrices.Rd → ...n/read.celfile.probeintensity.matrices.Rd
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0  src/clibs/affyio-1.8/src/CMakeLists.txt → src/clibs/affyio/src/CMakeLists.txt
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0  src/clibs/affyio-1.8/src/Makevars.in → src/clibs/affyio/src/Makevars.in
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0  src/clibs/affyio-1.8/src/Makevars.win → src/clibs/affyio/src/Makevars.win
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0  src/clibs/affyio-1.8/src/biolib_affyio.c → src/clibs/affyio/src/biolib_affyio.c
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0  src/clibs/affyio-1.8/src/biolib_affyio.h → src/clibs/affyio/src/biolib_affyio.h
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0  src/clibs/affyio-1.8/src/fread_functions.c → src/clibs/affyio/src/fread_functions.c
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0  src/clibs/affyio-1.8/src/fread_functions.h → src/clibs/affyio/src/fread_functions.h
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0  src/clibs/affyio-1.8/src/read_abatch.c → src/clibs/affyio/src/read_abatch.c
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0  src/clibs/affyio-1.8/src/read_abatch.h → src/clibs/affyio/src/read_abatch.h
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0  src/clibs/affyio-1.8/src/read_bpmap.c → src/clibs/affyio/src/read_bpmap.c
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0  src/clibs/affyio-1.8/src/read_cdf.h → src/clibs/affyio/src/read_cdf.h
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0  src/clibs/affyio-1.8/src/read_cdf_xda.c → src/clibs/affyio/src/read_cdf_xda.c
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0  src/clibs/affyio-1.8/src/read_cdffile2.c → src/clibs/affyio/src/read_cdffile2.c
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0  ...ibs/affyio-1.8/src/read_celfile_generic.c → src/clibs/affyio/src/read_celfile_generic.c
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0  ...ibs/affyio-1.8/src/read_celfile_generic.h → src/clibs/affyio/src/read_celfile_generic.h
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0  src/clibs/affyio-1.8/src/read_clf.c → src/clibs/affyio/src/read_clf.c
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0  src/clibs/affyio-1.8/src/read_generic.c → src/clibs/affyio/src/read_generic.c
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0  src/clibs/affyio-1.8/src/read_generic.h → src/clibs/affyio/src/read_generic.h
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0  src/clibs/affyio-1.8/src/read_pgf.c → src/clibs/affyio/src/read_pgf.c
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