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BioC 2.14: INSTALL report for affyio on petty

This page was generated on 2014-10-08 08:56:51 -0700 (Wed, 08 Oct 2014).

Package 21/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyio 1.32.0
Benjamin Milo Bolstad
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/affyio
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: affyio
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyio
StartedAt: 2014-10-07 18:04:31 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:04:45 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 13.9 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyio
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘affyio’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: ‘swap_uint_32’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c init_package.c -o init_package.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_abatch.c -o read_abatch.o
read_abatch.c: In function ‘readfile_group’:
read_abatch.c:4369: warning: unused variable ‘Current_intensity’
read_abatch.c:4378: warning: no return statement in function returning non-void
read_abatch.c: In function ‘checkFileCDF_group’:
read_abatch.c:4387: warning: no return statement in function returning non-void
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function ‘ReadBPMAPHeader’:
read_bpmap.c:78: warning: unused variable ‘version_number_int’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_cdf_xda.c -o read_cdf_xda.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364: warning: ‘token_ends_with’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function ‘read_genericcel_file_intensities’:
read_celfile_generic.c:711: warning: unused variable ‘fread_err’
read_celfile_generic.c:709: warning: unused variable ‘cur_index’
read_celfile_generic.c:708: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘read_genericcel_file_stddev’:
read_celfile_generic.c:761: warning: unused variable ‘fread_err’
read_celfile_generic.c:759: warning: unused variable ‘cur_index’
read_celfile_generic.c:758: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘read_genericcel_file_npixels’:
read_celfile_generic.c:815: warning: unused variable ‘fread_err’
read_celfile_generic.c:813: warning: unused variable ‘cur_index’
read_celfile_generic.c:812: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘generic_get_masks_outliers’:
read_celfile_generic.c:877: warning: unused variable ‘fread_err’
read_celfile_generic.c:875: warning: unused variable ‘cur_index’
read_celfile_generic.c:874: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘generic_apply_masks’:
read_celfile_generic.c:969: warning: unused variable ‘fread_err’
read_celfile_generic.c:963: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘gzread_genericcel_file_intensities’:
read_celfile_generic.c:1715: warning: unused variable ‘fread_err’
read_celfile_generic.c:1713: warning: unused variable ‘cur_index’
read_celfile_generic.c:1712: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘gzread_genericcel_file_stddev’:
read_celfile_generic.c:1766: warning: unused variable ‘fread_err’
read_celfile_generic.c:1764: warning: unused variable ‘cur_index’
read_celfile_generic.c:1763: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘gzread_genericcel_file_npixels’:
read_celfile_generic.c:1820: warning: unused variable ‘fread_err’
read_celfile_generic.c:1818: warning: unused variable ‘cur_index’
read_celfile_generic.c:1817: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers’:
read_celfile_generic.c:1885: warning: unused variable ‘fread_err’
read_celfile_generic.c:1883: warning: unused variable ‘cur_index’
read_celfile_generic.c:1882: warning: unused variable ‘j’
read_celfile_generic.c: In function ‘gzgeneric_apply_masks’:
read_celfile_generic.c:1977: warning: unused variable ‘fread_err’
read_celfile_generic.c:1971: warning: unused variable ‘j’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_clf.c -o read_clf.o
read_clf.c: In function ‘read_clf_header’:
read_clf.c:557: warning: unused variable ‘i’
read_clf.c: At top level:
read_clf.c:292: warning: ‘token_ends_with’ defined but not used
read_clf.c:389: warning: ‘IsCommentLine’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_generic.c -o read_generic.o
read_generic.c: In function ‘decode_nvt_triplet’:
read_generic.c:1683: warning: control reaches end of non-void function
read_generic.c: In function ‘determine_MIMETYPE’:
read_generic.c:458: warning: control reaches end of non-void function
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function ‘multichannel_determine_number_channels’:
read_multichannel_celfile_generic.c:109: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:106: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:105: warning: unused variable ‘k’
read_multichannel_celfile_generic.c:105: warning: unused variable ‘i’
read_multichannel_celfile_generic.c: In function ‘multichannel_determine_channel_name’:
read_multichannel_celfile_generic.c:173: warning: unused variable ‘my_data_set’
read_multichannel_celfile_generic.c:165: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:162: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:161: warning: unused variable ‘j’
read_multichannel_celfile_generic.c:161: warning: unused variable ‘i’
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_intensities_multichannel’:
read_multichannel_celfile_generic.c:223: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:221: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:220: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_stddev_multichannel’:
read_multichannel_celfile_generic.c:280: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:278: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:277: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_npixels_multichannel’:
read_multichannel_celfile_generic.c:344: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:342: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:341: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘generic_get_masks_outliers_multichannel’:
read_multichannel_celfile_generic.c:418: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:416: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:415: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘generic_apply_masks_multichannel’:
read_multichannel_celfile_generic.c:522: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:516: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_number_channels’:
read_multichannel_celfile_generic.c:664: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:661: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:660: warning: unused variable ‘k’
read_multichannel_celfile_generic.c:660: warning: unused variable ‘i’
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_channel_name’:
read_multichannel_celfile_generic.c:725: warning: unused variable ‘my_data_set’
read_multichannel_celfile_generic.c:717: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:714: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:713: warning: unused variable ‘j’
read_multichannel_celfile_generic.c:713: warning: unused variable ‘i’
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_intensities_multichannel’:
read_multichannel_celfile_generic.c:766: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:764: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:763: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_stddev_multichannel’:
read_multichannel_celfile_generic.c:822: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:820: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:819: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_npixels_multichannel’:
read_multichannel_celfile_generic.c:884: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:882: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:881: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers_multichannel’:
read_multichannel_celfile_generic.c:953: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:951: warning: unused variable ‘cur_index’
read_multichannel_celfile_generic.c:950: warning: unused variable ‘j’
read_multichannel_celfile_generic.c: In function ‘gzgeneric_apply_masks_multichannel’:
read_multichannel_celfile_generic.c:1055: warning: unused variable ‘fread_err’
read_multichannel_celfile_generic.c:1049: warning: unused variable ‘j’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_pgf.c -o read_pgf.o
read_pgf.c: In function ‘read_pgf_header’:
read_pgf.c:901: warning: unused variable ‘i’
read_pgf.c: In function ‘insert_level0’:
read_pgf.c:1167: warning: unused variable ‘temp_ptr’
read_pgf.c: In function ‘pgf_count_probeset_types’:
read_pgf.c:1265: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363: warning: ‘token_ends_with’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)