preprocessCore 1.2.1
Benjamin Milo Bolstad
| Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/preprocessCore | | Last Changed Rev: 32850 / Revision: 34573 | | Last Changed Date: 2008-07-22 07:01:44 -0700 (Tue, 22 Jul 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/preprocessCore.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.2.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'preprocessCore' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* creating preprocessCore-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/e/biocbld/bbs-2.2-bioc/meat/preprocessCore.Rcheck/tests'
Running 'PLMdtest.R'
make[1]: Leaving directory `/cygdrive/e/biocbld/bbs-2.2-bioc/meat/preprocessCore.Rcheck/tests'
OK
* creating preprocessCore-manual.tex ... OK
* checking preprocessCore-manual.tex using pdflatex ... OK
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/preprocessCore.Rcheck
---------- Making package preprocessCore ------------
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
adding build stamp to DESCRIPTION
making DLL ...
making R_colSummarize.d from R_colSummarize.c
making R_plmd_interfaces.d from R_plmd_interfaces.c
making R_plmr_interfaces.d from R_plmr_interfaces.c
making R_rlm_interfaces.d from R_rlm_interfaces.c
making R_subColSummarize.d from R_subColSummarize.c
making avg.d from avg.c
making avg_log.d from avg_log.c
making biweight.d from biweight.c
making init_package.d from init_package.c
making lm.d from lm.c
making log_avg.d from log_avg.c
making log_median.d from log_median.c
making matrix_functions.d from matrix_functions.c
making median.d from median.c
making median_log.d from median_log.c
making medianpolish.d from medianpolish.c
making plmd.d from plmd.c
making plmr.d from plmr.c
making psi_fns.d from psi_fns.c
making qnorm.d from qnorm.c
making rlm.d from rlm.c
making rlm_anova.d from rlm_anova.c
making rlm_se.d from rlm_se.c
making rma_background4.d from rma_background4.c
making rma_common.d from rma_common.c
making weightedkerneldensity.d from weightedkerneldensity.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function 'R_medianpolish_rma_default_model':
R_rlm_interfaces.c:274: warning: unused variable 'se'
R_rlm_interfaces.c:273: warning: unused variable 'weights'
R_rlm_interfaces.c: In function 'R_rlm_rma_given_probe_effects':
R_rlm_interfaces.c:392: warning: unused variable 'i'
R_rlm_interfaces.c: In function 'R_wrlm_rma_given_probe_effects':
R_rlm_interfaces.c:476: warning: unused variable 'i'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_subColSummarize.c -o R_subColSummarize.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c avg.c -o avg.o
avg.c: In function 'colaverage_no_copy':
avg.c:90: warning: unused variable 'i'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c avg_log.c -o avg_log.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c biweight.c -o biweight.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c init_package.c -o init_package.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c lm.c -o lm.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c log_median.c -o log_median.o
log_median.c: In function 'logmedian_no_copy':
log_median.c:138: warning: unused variable 'i'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c median.c -o median.o
median.c: In function 'colmedian_no_copy':
median.c:146: warning: unused variable 'i'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c median_log.c -o median_log.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c plmd.c -o plmd.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c plmr.c -o plmr.o
plmr.c:82: warning: 'XTWY_R' defined but not used
plmr.c:152: warning: 'XTWX_R' defined but not used
plmr.c:279: warning: 'XTWX_R_inv' defined but not used
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target':
qnorm.c:1801: warning: unused variable 'non_na'
qnorm.c:1796: warning: unused variable 'j'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c rlm.c -o rlm.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c rlm_anova.c -o rlm_anova.o
rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects':
rlm_anova.c:1198: warning: unused variable 'endprobe'
rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects':
rlm_anova.c:1371: warning: unused variable 'varderivpsi'
rlm_anova.c:1371: warning: unused variable 'm'
rlm_anova.c:1371: warning: unused variable 'vs'
rlm_anova.c:1364: warning: unused variable 'scale'
rlm_anova.c:1363: warning: unused variable 'Kappa'
rlm_anova.c:1362: warning: unused variable 'sumderivpsi'
rlm_anova.c:1360: warning: unused variable 'sumpsi2'
rlm_anova.c:1359: warning: unused variable 'k1'
rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects':
rlm_anova.c:1450: warning: unused variable 'endprobe'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:456: warning: unused variable 'j'
rma_background4.c:455: warning: 'PMcopy' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i preprocessCore_res.rc -o preprocessCore_res.o
gcc -std=gnu99 -shared -s -o preprocessCore.dll preprocessCore.def R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.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 preprocessCore_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lgfortran -Le:/biocbld/bbs-2.2-bioc/R/bin -lRlapack -Le:/biocbld/bbs-2.2-bioc/R/bin -lRblas -lR
... DLL made
installing DLL
installing R files
installing inst files
preparing package preprocessCore for lazy loading
installing man source files
installing indices
installing help
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
>>> Building/Updating help pages for package 'preprocessCore'
Formats: text html latex example chm
colSummarize text html latex example chm
normalize.quantiles text html latex chm
normalize.quantiles.in.blocks text html latex example chm
normalize.quantiles.robust text html latex chm
normalize.quantiles.target text html latex chm
rcModelPLMd text html latex example chm
rcModelPLMr text html latex example chm
rcModels text html latex example chm
rma.background.correct text html latex chm
subColSummarize text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\preprocessCore.Rcheck\00_pkg_src\preprocessCore\chm\preprocessCore.chm
Compile time: 0 minutes, 0 seconds
11 Topics
50 Local links
6 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\preprocessCore.Rcheck\00_pkg_src\preprocessCore\chm\preprocessCore.chm, 31,371 bytes
Compression decreased file by 23,600 bytes.
adding MD5 sums
* DONE (preprocessCore)