Sean Davis <sdavis2 at="" ...=""> writes: I've tried to install the packages again. Please find below error messages for GEOquery and ArrayExpress. I've tried to download the XML package source but it failed. In fact I'm able to download empty archive. Hi, Maciej. > > I believe the XML package is available. I tried the link in your > error message and it appeared to work just fine now. Perhaps try > again? If trying again does not work, paste the code you are using > to > do the installation and the error message (so we can see what code > results in the error). > > Sean > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("GEOquery") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'GEOquery' also installing the dependency ?XML? pr?bowanie adresu URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : nie mo?na otworzy? adresu URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' Dodatkowo: Komunikat ostrzegawczy: In download.file(url, destfile, method, mode = "wb", ...) : nie mo?na otworzy?: uzyskany status HTTP to '500 Internal Server Error' Ostrze?enie w download.packages(pkgs, destdir = tmpd, available = available, : download of package ?XML? failed pr?bowanie adresu URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GEOquery_2.24. 1.tar.gz' Content type 'application/x-gzip' length 13651847 bytes (13.0 Mb) otwarty adres URL ================================================== downloaded 13.0 Mb ERROR: dependency ?XML? is not available for package ?GEOquery? * removing ?/home/zea/R/x86_64-suse-linux-gnu-library/2.15/GEOquery? The downloaded source packages are in ?/tmp/RtmpT6lJ7b/downloaded_packages? Komunikaty ostrzegawcze: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?GEOquery? had non-zero exit status 2: installed directory not writable, cannot update packages 'cluster', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'nnet', 'rpart', 'survival' And error from "ArrayExpress" > biocLite("ArrayExpress") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'ArrayExpress' also installing the dependencies ?preprocessCore?, ?XML?, ?affy? pr?bowanie adresu URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/preprocessCore _1.20.0.tar.gz' Content type 'application/x-gzip' length 128095 bytes (125 Kb) otwarty adres URL ================================================== downloaded 125 Kb pr?bowanie adresu URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : nie mo?na otworzy? adresu URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' Dodatkowo: Komunikat ostrzegawczy: In download.file(url, destfile, method, mode = "wb", ...) : nie mo?na otworzy?: uzyskany status HTTP to '500 Internal Server Error' Ostrze?enie w download.packages(pkgs, destdir = tmpd, available = available, : download of package ?XML? failed pr?bowanie adresu URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/affy_1.36.1.ta r.gz' Content type 'application/x-gzip' length 1321511 bytes (1.3 Mb) otwarty adres URL ================================================== downloaded 1.3 Mb pr?bowanie adresu URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/ArrayExpress_1 .18.0.tar.gz' Content type 'application/x-gzip' length 194233 bytes (189 Kb) otwarty adres URL ================================================== downloaded 189 Kb * installing *source* package ?preprocessCore? ... configure: loading site script /usr/share/site/x86_64-unknown-linux- gnu checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for library containing pthread_create... -lpthread 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 stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_colSummarize.c -o R_colSummarize.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_rlm_interfaces.c -o R_rlm_interfaces.o R_rlm_interfaces.c: In function ?R_rlm_rma_default_model?: R_rlm_interfaces.c:80:10: warning: unused variable ?scale? [-Wunused-variable] R_rlm_interfaces.c: In function ?R_wrlm_rma_default_model?: R_rlm_interfaces.c:190:10: warning: unused variable ?scale? [-Wunused-variable] R_rlm_interfaces.c: In function ?R_medianpolish_rma_default_model?: R_rlm_interfaces.c:307:11: warning: unused variable ?se? [-Wunused-variable] R_rlm_interfaces.c:306:11: warning: unused variable ?weights? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c: In function ?subColSummarize_avg_log_group?: R_subColSummarize.c:84:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_avg_log?: R_subColSummarize.c:105:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:103:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:99:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:97:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_log_avg_group?: R_subColSummarize.c:255:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_log_avg?: R_subColSummarize.c:273:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:271:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:267:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:265:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_avg_group?: R_subColSummarize.c:426:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_avg?: R_subColSummarize.c:444:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:442:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:438:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:436:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_biweight_log_group?: R_subColSummarize.c:596:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_biweight_log?: R_subColSummarize.c:616:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:614:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:610:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:608:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_biweight_group?: R_subColSummarize.c:768:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_biweight?: R_subColSummarize.c:787:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:785:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:781:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:779:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_median_log_group?: R_subColSummarize.c:939:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_median_log?: R_subColSummarize.c:959:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:957:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:953:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:951:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_log_median_group?: R_subColSummarize.c:1110:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_log_median?: R_subColSummarize.c:1129:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:1127:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:1123:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:1121:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_median_group?: R_subColSummarize.c:1280:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_median?: R_subColSummarize.c:1298:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:1296:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:1292:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:1290:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: In function ?subColSummarize_medianpolish_log_group?: R_subColSummarize.c:1452:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_medianpolish_log?: R_subColSummarize.c:1471:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:1469:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:1465:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:1463:30: warning: variable ?buffer2? set but not used [-Wunused-but-set-variable] R_subColSummarize.c:1463:21: warning: variable ?buffer? set but not used [-Wunused-but-set-variable] R_subColSummarize.c: In function ?subColSummarize_medianpolish_group?: R_subColSummarize.c:1626:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subColSummarize.c: In function ?R_subColSummarize_medianpolish?: R_subColSummarize.c:1645:9: warning: unused variable ?j? [-Wunused-variable] R_subColSummarize.c:1643:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subColSummarize.c:1639:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subColSummarize.c:1637:30: warning: unused variable ?buffer2? [-Wunused-variable] R_subColSummarize.c:1637:21: warning: unused variable ?buffer? [-Wunused-variable] R_subColSummarize.c: At top level: R_subColSummarize.c:1602:14: warning: ?subColSummarize_medianpolish_group? defined but not used [-Wunused-function] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c: In function ?sub_rcModelSummarize_medianpolish_group?: R_subrcModel_interfaces.c:80:11: warning: unused variable ?se? [-Wunused-variable] R_subrcModel_interfaces.c:79:11: warning: unused variable ?weights? [-Wunused-variable] R_subrcModel_interfaces.c:64:20: warning: unused variable ?buffer2? [-Wunused-variable] R_subrcModel_interfaces.c:64:11: warning: unused variable ?buffer? [-Wunused-variable] R_subrcModel_interfaces.c:141:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subrcModel_interfaces.c: In function ?R_sub_rcModelSummarize_medianpolish?: R_subrcModel_interfaces.c:161:9: warning: unused variable ?j? [-Wunused-variable] R_subrcModel_interfaces.c:159:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subrcModel_interfaces.c:155:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subrcModel_interfaces.c:153:30: warning: unused variable ?buffer2? [-Wunused-variable] R_subrcModel_interfaces.c:153:21: warning: unused variable ?buffer? [-Wunused-variable] R_subrcModel_interfaces.c:153:11: warning: unused variable ?results? [-Wunused-variable] R_subrcModel_interfaces.c: In function ?sub_rcModelSummarize_plm_group?: R_subrcModel_interfaces.c:381:10: warning: unused variable ?scale? [-Wunused-variable] R_subrcModel_interfaces.c:360:20: warning: unused variable ?buffer2? [-Wunused-variable] R_subrcModel_interfaces.c:360:11: warning: unused variable ?buffer? [-Wunused-variable] R_subrcModel_interfaces.c:454:1: warning: no return statement in function returning non-void [-Wreturn-type] R_subrcModel_interfaces.c: In function ?R_sub_rcModelSummarize_plm?: R_subrcModel_interfaces.c:475:9: warning: unused variable ?j? [-Wunused-variable] R_subrcModel_interfaces.c:473:7: warning: unused variable ?ncur_rows? [-Wunused-variable] R_subrcModel_interfaces.c:469:8: warning: unused variable ?cur_rows? [-Wunused-variable] R_subrcModel_interfaces.c:467:30: warning: unused variable ?buffer2? [-Wunused-variable] R_subrcModel_interfaces.c:467:21: warning: unused variable ?buffer? [-Wunused-variable] R_subrcModel_interfaces.c:467:11: warning: unused variable ?results? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c avg.c -o avg.o avg.c: In function ?colaverage_no_copy?: avg.c:90:7: warning: unused variable ?i? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c avg_log.c -o avg_log.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c biweight.c -o biweight.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c init_package.c -o init_package.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c lm.c -o lm.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c log_avg.c -o log_avg.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c log_median.c -o log_median.o log_median.c: In function ?logmedian_no_copy?: log_median.c:138:7: warning: unused variable ?i? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c matrix_functions.c -o matrix_functions.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c median.c -o median.o median.c: In function ?colmedian_no_copy?: median.c:146:7: warning: unused variable ?i? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c median_log.c -o median_log.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c medianpolish.c -o medianpolish.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c plmd.c -o plmd.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c plmr.c -o plmr.o plmr.c:82:13: warning: ?XTWY_R? defined but not used [-Wunused-function] plmr.c:152:13: warning: ?XTWX_R? defined but not used [-Wunused-function] plmr.c:279:13: warning: ?XTWX_R_inv? defined but not used [-Wunused-function] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c psi_fns.c -o psi_fns.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c qnorm.c -o qnorm.o qnorm.c: In function ?qnorm_c_determine_target?: qnorm.c:1824:7: warning: unused variable ?non_na? [-Wunused-variable] qnorm.c:1819:9: warning: unused variable ?j? [-Wunused-variable] qnorm.c: In function ?qnorm_c_determine_target_via_subset?: qnorm.c:2411:7: warning: unused variable ?non_na? [-Wunused-variable] qnorm.c:2406:9: warning: unused variable ?j? [-Wunused-variable] qnorm.c: In function ?using_target_via_subset_part1?: qnorm.c:2618:11: warning: variable ?ind? set but not used [-Wunused-but-set-variable] qnorm.c: In function ?using_target_via_subset_part2?: qnorm.c:2717:11: warning: unused variable ?datvec? [-Wunused-variable] qnorm.c:2716:11: warning: unused variable ?sample_percentiles? [-Wunused-variable] qnorm.c: In function ?using_target_via_subset?: qnorm.c:2866:11: warning: unused variable ?datvec? [-Wunused-variable] qnorm.c:2865:11: warning: unused variable ?sample_percentiles? [-Wunused-variable] qnorm.c:2861:7: warning: unused variable ?non_na? [-Wunused-variable] qnorm.c:2860:7: warning: unused variable ?targetnon_na? [-Wunused-variable] qnorm.c:2858:28: warning: unused variable ?target_ind_double_floor? [-Wunused-variable] qnorm.c:2858:10: warning: unused variable ?target_ind_double? [-Wunused-variable] qnorm.c:2857:10: warning: unused variable ?samplepercentile? [-Wunused-variable] qnorm.c:2856:11: warning: unused variable ?ranks? [-Wunused-variable] qnorm.c:2854:11: warning: unused variable ?row_mean? [-Wunused-variable] qnorm.c:2852:14: warning: unused variable ?dimat? [-Wunused-variable] qnorm.c:2850:15: warning: unused variable ?target_ind? [-Wunused-variable] qnorm.c:2850:11: warning: unused variable ?ind? [-Wunused-variable] qnorm.c:2850:9: warning: unused variable ?j? [-Wunused-variable] qnorm.c: In function ?using_target_group_via_subset?: qnorm.c:2896:1: warning: control reaches end of non-void function [-Wreturn-type] qnorm.c: In function ?determine_target_group_via_subset?: qnorm.c:2396:1: warning: control reaches end of non-void function [-Wreturn-type] qnorm.c: In function ?determine_target_group?: qnorm.c:1810:1: warning: control reaches end of non-void function [-Wreturn-type] qnorm.c: In function ?using_target_group?: qnorm.c:1527:1: warning: control reaches end of non-void function [-Wreturn-type] qnorm.c: In function ?distribute_group?: qnorm.c:461:1: warning: control reaches end of non-void function [-Wreturn-type] qnorm.c: In function ?normalize_group?: qnorm.c:456:1: warning: control reaches end of non-void function [-Wreturn-type] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c rlm.c -o rlm.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c rlm_anova.c -o rlm_anova.o rlm_anova.c: In function ?rlm_fit_anova_given_probe_effects_engine?: rlm_anova.c:1235:10: warning: unused variable ?endprobe? [-Wunused-variable] rlm_anova.c: In function ?rlm_compute_se_anova_given_probe_effects?: rlm_anova.c:1426:19: warning: unused variable ?varderivpsi? [-Wunused-variable] rlm_anova.c:1426:17: warning: unused variable ?m? [-Wunused-variable] rlm_anova.c:1426:10: warning: unused variable ?vs? [-Wunused-variable] rlm_anova.c:1419:10: warning: unused variable ?scale? [-Wunused-variable] rlm_anova.c:1418:10: warning: unused variable ?Kappa? [-Wunused-variable] rlm_anova.c:1417:10: warning: unused variable ?sumderivpsi? [-Wunused-variable] rlm_anova.c:1415:10: warning: unused variable ?sumpsi2? [-Wunused-variable] rlm_anova.c:1414:10: warning: unused variable ?k1? [-Wunused-variable] rlm_anova.c: In function ?rlm_wfit_anova_given_probe_effects_engine?: rlm_anova.c:1505:10: warning: unused variable ?endprobe? [-Wunused-variable] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c rlm_se.c -o rlm_se.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c rma_background4.c -o rma_background4.o rma_background4.c: In function ?rma_bg_correct?: rma_background4.c:341:10: warning: unused variable ?param? [-Wunused-variable] rma_background4.c:340:7: warning: unused variable ?j? [-Wunused-variable] rma_background4.c: In function ?R_rma_bg_correct?: rma_background4.c:464:7: warning: unused variable ?j? [-Wunused-variable] rma_background4.c: In function ?rma_bg_correct_group?: rma_background4.c:322:1: warning: control reaches end of non-void function [-Wreturn-type] rma_background4.c: In function ?R_rma_bg_correct?: rma_background4.c:463:13: warning: ?PMcopy? may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c rma_common.c -o rma_common.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c weightedkerneldensity.c -o weightedkerneldensity.o weightedkerneldensity.c: In function ?IQR?: weightedkerneldensity.c:746:14: warning: variable ?high_i? set but not used [-Wunused-but-set-variable] weightedkerneldensity.c:746:7: warning: variable ?low_i? set but not used [-Wunused-but-set-variable] weightedkerneldensity.c: In function ?bandwidth?: weightedkerneldensity.c:551:1: warning: control reaches end of non- void function [-Wreturn-type] gcc -std=gnu99 -shared -L/usr/local/lib64 -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse- linux/bin/ld: cannot find -lgfortran /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse- linux/bin/ld: cannot find -lquadmath collect2: error: ld returned 1 exit status make: *** [preprocessCore.so] B??d 1 ERROR: compilation failed for package ?preprocessCore? * removing ?/home/zea/R/x86_64-suse-linux-gnu-library/2.15/preprocessCore? ERROR: dependency ?preprocessCore? is not available for package ?affy? * removing ?/home/zea/R/x86_64-suse-linux-gnu-library/2.15/affy? ERROR: dependencies ?XML?, ?affy? are not available for package ?ArrayExpress? * removing ?/home/zea/R/x86_64-suse-linux-gnu-library/2.15/ArrayExpress? The downloaded source packages are in ?/tmp/RtmpT6lJ7b/downloaded_packages? Komunikaty ostrzegawcze: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?preprocessCore? had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?affy? had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?ArrayExpress? had non-zero exit status 4: installed directory not writable, cannot update packages 'cluster', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'nnet', 'rpart', 'survival'

It seem that my problem is caused by my faculty network settings. Sorry I solicited you. Best Wishes, thanks for your time