[BioC] XML package - 500 internal server error
Maciej Jończyk
mjonczyk at biol.uw.edu.pl
Mon May 6 13:34:55 CEST 2013
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’
próbowanie 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 można otworzyć 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 można otworzyć: uzyskany status HTTP to '500 Internal Server
Error'
Ostrzeżenie w download.packages(pkgs, destdir = tmpd, available =
available, :
download of package ‘XML’ failed
próbowanie 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’
próbowanie 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
próbowanie 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 można otworzyć 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 można otworzyć: uzyskany status HTTP to '500 Internal Server
Error'
Ostrzeżenie w download.packages(pkgs, destdir = tmpd, available =
available, :
download of package ‘XML’ failed
próbowanie adresu URL
'http://bioconductor.org/packages/2.11/bioc/src/contrib/affy_1.36.1.tar.gz'
Content type 'application/x-gzip' length 1321511 bytes (1.3 Mb)
otwarty adres URL
==================================================
downloaded 1.3 Mb
próbowanie 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] Błąd 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'
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