preprocessCore 1.6.0
Benjamin Milo Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/preprocessCore | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | 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 |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/preprocessCore.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.6.0'
* checking package name space information ... OK
* 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 whether the name space 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 files against version 2 parser ... 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
* checking examples ... OK
* checking tests ...
Running 'PLMdtest.R'
OK
* checking PDF version of manual ... OK
* Installing *source* package 'preprocessCore' ...
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WARNING: this package has a configure script
It probably needs manual configuration
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** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c R_colSummarize.c -o R_colSummarize.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -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:273: warning: unused variable 'se'
R_rlm_interfaces.c:272: warning: unused variable 'weights'
R_rlm_interfaces.c: In function 'R_rlm_rma_given_probe_effects':
R_rlm_interfaces.c:391: warning: unused variable 'i'
R_rlm_interfaces.c: In function 'R_wrlm_rma_given_probe_effects':
R_rlm_interfaces.c:475: warning: unused variable 'i'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c R_subColSummarize.c -o R_subColSummarize.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c avg.c -o avg.o
avg.c: In function 'colaverage_no_copy':
avg.c:90: warning: unused variable 'i'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c avg_log.c -o avg_log.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c biweight.c -o biweight.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c init_package.c -o init_package.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c lm.c -o lm.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c log_avg.c -o log_avg.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c median.c -o median.o
median.c: In function 'colmedian_no_copy':
median.c:146: warning: unused variable 'i'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c median_log.c -o median_log.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c medianpolish.c -o medianpolish.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c plmd.c -o plmd.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target':
qnorm.c:1813: warning: unused variable 'non_na'
qnorm.c:1808: warning: unused variable 'j'
qnorm.c: In function 'qnorm_c_determine_target_via_subset':
qnorm.c:2396: warning: unused variable 'non_na'
qnorm.c:2391: warning: unused variable 'j'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c rlm.c -o rlm.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c rlm_anova.c -o rlm_anova.o
rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects':
rlm_anova.c:1205: warning: unused variable 'endprobe'
rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects':
rlm_anova.c:1378: warning: unused variable 'varderivpsi'
rlm_anova.c:1378: warning: unused variable 'm'
rlm_anova.c:1378: warning: unused variable 'vs'
rlm_anova.c:1371: warning: unused variable 'scale'
rlm_anova.c:1370: warning: unused variable 'Kappa'
rlm_anova.c:1369: warning: unused variable 'sumderivpsi'
rlm_anova.c:1367: warning: unused variable 'sumpsi2'
rlm_anova.c:1366: warning: unused variable 'k1'
rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects':
rlm_anova.c:1457: warning: unused variable 'endprobe'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c rlm_se.c -o rlm_se.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:457: warning: unused variable 'j'
rma_background4.c:456: warning: 'PMcopy' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -s -o preprocessCore.dll tmp.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 -lgfortran -Le:/biocbld/bbs-2.4-bioc/R/bin -lRlapack -Le:/biocbld/bbs-2.4-bioc/R/bin -lRblas -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> 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
Note: removing empty section \seealso in file 'rcModelPLMd.Rd'
Note: removing empty section \seealso in file 'rcModelPLMd.Rd'
rcModelPLMd text html latex example chm
Note: removing empty section \seealso in file 'rcModelPLMr.Rd'
Note: removing empty section \seealso in file 'rcModelPLMr.Rd'
rcModelPLMr text html latex example chm
Note: removing empty section \seealso in file 'rcModels.Rd'
Note: removing empty section \seealso in file 'rcModels.Rd'
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-2~1.4-B\meat\PREPRO~1.RCH\00_PKG~1\PREPRO~1\chm\preprocessCore.chm
Compile time: 0 minutes, 0 seconds
11 Topics
50 Local links
6 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\PREPRO~1.RCH\00_PKG~1\PREPRO~1\chm\preprocessCore.chm, 31,471 bytes
Compression decreased file by 23,695 bytes.
** building package indices ...
** MD5 sums
* DONE (preprocessCore)