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BioC 2.14: INSTALL report for preprocessCore on zin2

This page was generated on 2014-10-08 08:47:31 -0700 (Wed, 08 Oct 2014).

Package 601/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.26.1
Benjamin Milo Bolstad
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/preprocessCore
Last Changed Rev: 90171 / Revision: 95116
Last Changed Date: 2014-05-09 13:32:05 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64 [ OK ] OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: preprocessCore
Version: 1.26.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD INSTALL preprocessCore
StartedAt: 2014-10-07 18:02:14 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:02:24 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 10.0 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-2.14-bioc/R/library’
* installing *source* package ‘preprocessCore’ ...
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... /bin/grep
checking for egrep... /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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c biweight.c -o biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c init_package.c -o init_package.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c lm.c -o lm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c median_log.c -o median_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c plmd.c -o plmd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c qnorm.c -o qnorm.o
qnorm.c: In function ‘qnorm_c_determine_target_l’:
qnorm.c:1883:7: warning: unused variable ‘non_na’ [-Wunused-variable]
qnorm.c:1878:12: warning: unused variable ‘j’ [-Wunused-variable]
qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’:
qnorm.c:2476:7: warning: unused variable ‘non_na’ [-Wunused-variable]
qnorm.c:2471:12: warning: unused variable ‘j’ [-Wunused-variable]
qnorm.c: In function ‘using_target_via_subset_part1’:
qnorm.c:2687:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
qnorm.c: In function ‘using_target_via_subset_part2’:
qnorm.c:2786:11: warning: unused variable ‘datvec’ [-Wunused-variable]
qnorm.c:2785:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
qnorm.c: In function ‘using_target_via_subset’:
qnorm.c:2935:11: warning: unused variable ‘datvec’ [-Wunused-variable]
qnorm.c:2934:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
qnorm.c:2930:7: warning: unused variable ‘non_na’ [-Wunused-variable]
qnorm.c:2929:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable]
qnorm.c:2927:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable]
qnorm.c:2927:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable]
qnorm.c:2926:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable]
qnorm.c:2925:11: warning: unused variable ‘ranks’ [-Wunused-variable]
qnorm.c:2923:11: warning: unused variable ‘row_mean’ [-Wunused-variable]
qnorm.c:2921:14: warning: unused variable ‘dimat’ [-Wunused-variable]
qnorm.c:2919:18: warning: unused variable ‘target_ind’ [-Wunused-variable]
qnorm.c:2919:14: warning: unused variable ‘ind’ [-Wunused-variable]
qnorm.c:2919:12: warning: unused variable ‘j’ [-Wunused-variable]
qnorm.c: In function ‘using_target_group_via_subset’:
qnorm.c:2965:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘determine_target_group_via_subset’:
qnorm.c:2461:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘determine_target_group’:
qnorm.c:1869:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘using_target_group’:
qnorm.c:1551:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘distribute_group’:
qnorm.c:463:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘normalize_group’:
qnorm.c:458:1: warning: control reaches end of non-void function [-Wreturn-type]
qnorm.c: In function ‘R_qnorm_using_target’:
qnorm.c:2083:25: warning: ‘target_rows’ may be used uninitialized in this function [-Wuninitialized]
qnorm.c: In function ‘R_qnorm_using_target_via_subset’:
qnorm.c:3199:36: warning: ‘target_rows’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c rlm.c -o rlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c rma_background4.c -o rma_background4.o
rma_background4.c: In function ‘max_density’:
rma_background4.c:122:3: warning: passing argument 2 of ‘KernelDensity_lowmem’ from incompatible pointer type [enabled by default]
weightedkerneldensity.h:5:6: note: expected ‘int *’ but argument is of type ‘size_t *’
rma_background4.c: In function ‘rma_bg_correct’:
rma_background4.c:342:10: warning: unused variable ‘param’ [-Wunused-variable]
rma_background4.c:341:10: warning: unused variable ‘j’ [-Wunused-variable]
rma_background4.c: In function ‘rma_bg_correct_group’:
rma_background4.c:323:1: warning: control reaches end of non-void function [-Wreturn-type]
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:464:13: warning: ‘PMcopy’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall  -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  -g -O2  -Wall -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/lib -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/home/biocbuild/bbs-2.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/R/library/preprocessCore/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (preprocessCore)