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Question: XML package - 500 internal server error
0
gravatar for Maciej Jończyk
5.8 years ago by
Maciej Jończyk720 wrote:
Hi all, are XML package available? I've tried to install it from varius mirrors and it still fails, giving error '500 Internal Server Error'. I need it to install GEOquery and ArrayExpress. Installation of these packages failed because of XML package instalation failure. In fact I'm not able to download XML_3.96-1.1.tar.gz or any other version from cran. I've downgraded R from version 3 because in that version installator printed error - XML isn't available for that version of R. I'm working on openSUSE 12.3 Here is my sessioninfo. > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-suse-linux-gnu (64-bit) locale: [1] LC_CTYPE=pl_PL.UTF-8 LC_NUMERIC=C [3] LC_TIME=pl_PL.utf8 LC_COLLATE=pl_PL.utf8 [5] LC_MONETARY=pl_PL.utf8 LC_MESSAGES=pl_PL.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=pl_PL.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] Heatplus_2.4.0 Error itself Instalowanie pakiet?w w ?/home/zea/R/x86_64-suse-linux-gnu-library/2.15? (poniewa? ?lib? nie jest okre?lony) pr?bowanie adresu URL 'http://r.meteo.uni.wroc.pl/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://r.meteo.uni.wroc.pl/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, : pobieranie pakietu ?XML? nie powiod?o si? Best Wishes, -- Dr Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
geoquery arrayexpress • 816 views
ADD COMMENTlink modified 5.8 years ago by Sean Davis21k • written 5.8 years ago by Maciej Jończyk720
Answer: XML package - 500 internal server error
0
gravatar for Sean Davis
5.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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 On Mon, May 6, 2013 at 7:13 AM, Maciej Jo?czyk <mjonczyk at="" biol.uw.edu.pl=""> wrote: > Hi all, > > are XML package available? > > I've tried to install it from varius mirrors and it still fails, > giving error '500 Internal Server Error'. > > I need it to install GEOquery and ArrayExpress. Installation of these > packages failed because of XML package instalation failure. > > In fact I'm not able to download XML_3.96-1.1.tar.gz or any other version > from cran. > > I've downgraded R from version 3 because > in that version installator printed error - XML isn't available for that > version of R. > > I'm working on openSUSE 12.3 > > Here is my sessioninfo. >> >> sessionInfo() > > R version 2.15.2 (2012-10-26) > Platform: x86_64-suse-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=pl_PL.UTF-8 LC_NUMERIC=C > [3] LC_TIME=pl_PL.utf8 LC_COLLATE=pl_PL.utf8 > [5] LC_MONETARY=pl_PL.utf8 LC_MESSAGES=pl_PL.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=pl_PL.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] Heatplus_2.4.0 > > Error itself > > Instalowanie pakiet?w w ?/home/zea/R/x86_64-suse-linux-gnu- library/2.15? > (poniewa? ?lib? nie jest okre?lony) > pr?bowanie adresu URL > 'http://r.meteo.uni.wroc.pl/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://r.meteo.uni.wroc.pl/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, > : > pobieranie pakietu ?XML? nie powiod?o si? > > Best Wishes, > > -- > Dr Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Faculty of Biology, University of Warsaw > 02-096 Warsaw, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.8 years ago by Sean Davis21k
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'
ADD REPLYlink written 5.8 years ago by Maciej Jończyk720
It seem that my problem is caused by my faculty network settings. Sorry I solicited you. Best Wishes, thanks for your time
ADD REPLYlink written 5.8 years ago by Maciej Jończyk720
Hi guys, I tried a sample with Variant Annotation's eadVcf. I ran the code successfully in Linux (OK I had some warnings regarding " unpackVcf field '..': NAs introduced by coercion"). But when I tried the same code in R3.0.0 in windows 7, I got the error message: > for(i in 1:length(vcflist1)){ indexTabix(vcflist1[i], format="vcf") vcf <- readVcf(TabixFile(vcflist1[i]), "hg19", params) outputfile=paste(sub(".vcf.gz","",vcflist1[i]),"_test.vcf",sep="") writeVcf(vcf,outputfile) bgzip(outputfile, overwrite=TRUE) indexTabix(paste(outputfile,".gz",sep=""), format="vcf") rm(vcf) rm(outputfile) } Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘readVcf’ for signature ‘"TabixFile", "character", "standardGeneric"’ What did I do wrong? Thanks a lot for the help! Ying > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit)locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.6.5 Rsamtools_1.12.2 Biostrings_2.28.0 GenomicRanges_1.12.2 [5] IRanges_1.18.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-6 [9] AnnotationDbi_1.22.5 Biobase_2.20.0 BiocGenerics_0.6.0 BiocInstaller_1.10.1 loaded via a namespace (and not attached): [1] biomaRt_2.16.0 bitops_1.0-5 BSgenome_1.28.0 GenomicFeatures_1.12.1 RCurl_1.95-4.1 [6] rtracklayer_1.20.2 stats4_3.0.0 tools_3.0.0 XML_3.96-1.1 zlibbioc_1.6.0 > [[alternative HTML version deleted]]
ADD REPLYlink written 5.8 years ago by ying chen340
Hello, The error indicates a problem with the arguments supplied to readVcf(). You can discover available methods with showMethods(), > showMethods("readVcf") Function: readVcf (package VariantAnnotation) file="character", genome="character", param="missing" file="character", genome="character", param="ScanVcfParam" file="character", genome="missing", param="missing" file="TabixFile", genome="character", param="GRanges" file="TabixFile", genome="character", param="GRangesList" file="TabixFile", genome="character", param="missing" file="TabixFile", genome="character", param="RangedData" file="TabixFile", genome="character", param="RangesList" file="TabixFile", genome="character", param="ScanVcfParam" What does your 'param' object look like? From above you can see it must be a 'GRanges', 'GrangesList', 'missing', etc. ... Valerie On 05/06/2013 07:47 AM, ying chen wrote: > Hi guys, I tried a sample with Variant Annotation's eadVcf. I ran the code successfully in Linux (OK I had some warnings regarding " unpackVcf field '..': NAs introduced by coercion"). But when I tried the same code in R3.0.0 in windows 7, I got the error message: > for(i in 1:length(vcflist1)){ > indexTabix(vcflist1[i], format="vcf") > vcf <- readVcf(TabixFile(vcflist1[i]), "hg19", params) > outputfile=paste(sub(".vcf.gz","",vcflist1[i]),"_test.vcf",sep="") > writeVcf(vcf,outputfile) > bgzip(outputfile, overwrite=TRUE) > indexTabix(paste(outputfile,".gz",sep=""), format="vcf") > rm(vcf) > rm(outputfile) > } > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?readVcf? for signature ?"TabixFile", "character", "standardGeneric"? What did I do wrong? Thanks a lot for the help! Ying >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-w64-mingw32/x64 (64-bit)locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base other attached packages: > [1] VariantAnnotation_1.6.5 Rsamtools_1.12.2 Biostrings_2.28.0 GenomicRanges_1.12.2 > [5] IRanges_1.18.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-6 > [9] AnnotationDbi_1.22.5 Biobase_2.20.0 BiocGenerics_0.6.0 BiocInstaller_1.10.1 loaded via a namespace (and not attached): > [1] biomaRt_2.16.0 bitops_1.0-5 BSgenome_1.28.0 GenomicFeatures_1.12.1 RCurl_1.95-4.1 > [6] rtracklayer_1.20.2 stats4_3.0.0 tools_3.0.0 XML_3.96-1.1 zlibbioc_1.6.0 >> > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 5.8 years ago by Valerie Obenchain6.7k
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