affyPLM 1.46.0
Ben Bolstad
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affyPLM | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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###
### Running command:
###
### rm -rf affyPLM.buildbin-libdir affyPLM.Rcheck && mkdir affyPLM.buildbin-libdir affyPLM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.46.0.tar.gz >affyPLM.Rcheck\00install.out 2>&1 && cp affyPLM.Rcheck\00install.out affyPLM-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=affyPLM.buildbin-libdir --install="check:affyPLM-install.out" --force-multiarch --no-vignettes --timings affyPLM_1.46.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/affyPLM.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.46.0'
* 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics'
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'stats' which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
image,PLMset : .local: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... 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 'D:/biocbld/bbs-3.2-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/i386/affyPLM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-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, nor the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
threestep 33.45 0.23 33.68
fitPLM 18.91 0.29 21.03
PLMset2exprSet 9.15 0.03 9.19
** running examples for arch 'x64' ... [70s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
threestep 25.54 0.21 25.74
fitPLM 18.47 0.29 20.28
PLMset2exprSet 9.50 0.08 9.58
* 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' [29s]
Running 'threestepPLM_tests.R' [0s]
[35s] OK
** running tests for arch 'x64' ...
Running 'C_code_tests.R' [3s]
Running 'PLM_tests.R' [5s]
Running 'preprocess_tests.R' [28s]
Running 'threestepPLM_tests.R' [1s]
[37s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/affyPLM.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'affyPLM' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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 -LD:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lRblas -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-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
** testing if installed package can be loaded
install for x64
* installing *source* package 'affyPLM' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"D:/biocbld/bbs-3.2-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local323/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 -LD:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lRblas -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.46.0.zip
* DONE (affyPLM)