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Package 24/658HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.35.0
Ben Bolstad
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: affyPLM
Version: 1.35.0
Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.35.0.tar.gz >affyPLM-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=affyPLM.buildbin-libdir --install="check:affyPLM-install.out" --force-multiarch --no-vignettes --timings affyPLM_1.35.0.tar.gz && mv affyPLM.buildbin-libdir/* affyPLM.Rcheck/ && rmdir affyPLM.buildbin-libdir
StartedAt: 2013-03-25 00:50:39 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:57:35 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 415.8 seconds
RetCode: 0
Status:  OK  
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/affyPLM.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.35.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
show,PLMset: warning in ls(env = cdf.env): partial argument match of
  'env' to 'envir'
* checking Rd files ... NOTE
prepare_Rd: MAplot.Rd:11-13: Dropping empty section \usage
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.12-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/i386/affyPLM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64/affyPLM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [79s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
threestep      31.68   0.10   31.90
fitPLM         17.57   0.22   17.78
PLMset2exprSet 10.40   0.11   10.61
** running examples for arch 'x64' ... [79s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
threestep       27.44   0.11   27.58
fitPLM          16.32   0.25   17.41
PLMset2exprSet  11.88   0.09   11.98
bg.correct.LESN  5.56   0.13    5.68
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'C_code_tests.R' [3s]
  Running 'PLM_tests.R' [0s]
  Running 'preprocess_tests.R' [35s]
  Running 'threestepPLM_tests.R' [0s]
 [39s] OK
** running tests for arch 'x64'
  Running 'C_code_tests.R' [3s]
  Running 'PLM_tests.R' [0s]
  Running 'preprocess_tests.R' [35s]
  Running 'threestepPLM_tests.R' [0s]
 [39s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/affyPLM.Rcheck/00check.log'
for details.

affyPLM.Rcheck/00install.out:


install for i386

* installing *source* package 'affyPLM' ...
** libs
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function 'do_PLM_rlm':
do_PLMrlm.c:620:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function 'do_PLMrma':
do_PLMrma.c:209:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function 'do_PLMthreestep':
do_PLMthreestep.c:118:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function 'IdealMM_correct_single':
idealmismatch.c:71:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
idealmismatch.c: In function 'SpecificBiweightCorrect_single':
idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
preprocess.c: In function 'pp_background':
preprocess.c:158:7: warning: variable 'which_lesn' set but not used [-Wunused-but-set-variable]
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:110:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function 'R_rlm_PLMset_c':
rlm_PLM.c:1481:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
threestep.c: In function 'threestep_summary':
threestep.c:82:15: warning: variable 'MM' set but not used [-Wunused-but-set-variable]
threestep.c: In function 'R_threestep_c':
threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function 'do_3summary':
threestep_summary.c:73:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transfns.c -o transfns.o
gcc -m32 -shared -s -static-libgcc -o affyPLM.dll tmp.def LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'affyPLM'
** help
*** installing help indices
** building package indices
** installing vignettes
   'AffyExtensions.Rnw' 
   'MAplots.Rnw' 
   'QualityAssess.Rnw' 
   'ThreeStep.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'affyPLM' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function 'do_PLM_rlm':
do_PLMrlm.c:620:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function 'do_PLMrma':
do_PLMrma.c:209:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function 'do_PLMthreestep':
do_PLMthreestep.c:118:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function 'IdealMM_correct_single':
idealmismatch.c:71:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
idealmismatch.c: In function 'SpecificBiweightCorrect_single':
idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
preprocess.c: In function 'pp_background':
preprocess.c:158:7: warning: variable 'which_lesn' set but not used [-Wunused-but-set-variable]
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:110:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function 'R_rlm_PLMset_c':
rlm_PLM.c:1481:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
threestep.c: In function 'threestep_summary':
threestep.c:82:15: warning: variable 'MM' set but not used [-Wunused-but-set-variable]
threestep.c: In function 'R_threestep_c':
threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function 'do_3summary':
threestep_summary.c:73:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.12-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transfns.c -o transfns.o
gcc -m64 -shared -s -static-libgcc -o affyPLM.dll tmp.def LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lRlapack -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.35.0.zip
* DONE (affyPLM)