preprocessCore 1.15.0
Benjamin Milo Bolstad
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/preprocessCore | | Last Changed Rev: 54802 / Revision: 56603 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/preprocessCore.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.15.0'
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: rcModelPLMd.Rd:35-36: Dropping empty section \seealso
prepare_Rd: rcModelPLMr.Rd:53-54: Dropping empty section \seealso
prepare_Rd: rcModels.Rd:46-47: Dropping empty section \seealso
* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'PLMdtest.R'
OK
* checking PDF version of manual ... OK
* installing *source* package 'preprocessCore' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c R_colSummarize.c -o R_colSummarize.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -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'
R_rlm_interfaces.c: In function 'R_wrlm_rma_default_model':
R_rlm_interfaces.c:190:10: warning: unused variable 'scale'
R_rlm_interfaces.c: In function 'R_medianpolish_rma_default_model':
R_rlm_interfaces.c:307:11: warning: unused variable 'se'
R_rlm_interfaces.c:306:11: warning: unused variable 'weights'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c R_subColSummarize.c -o R_subColSummarize.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c avg.c -o avg.o
avg.c: In function 'colaverage_no_copy':
avg.c:90:7: warning: unused variable 'i'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c avg_log.c -o avg_log.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c biweight.c -o biweight.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c init_package.c -o init_package.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c lm.c -o lm.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c log_avg.c -o log_avg.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/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:138:7: warning: unused variable 'i'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c median.c -o median.o
median.c: In function 'colmedian_no_copy':
median.c:146:7: warning: unused variable 'i'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c median_log.c -o median_log.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c medianpolish.c -o medianpolish.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c plmd.c -o plmd.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c plmr.c -o plmr.o
plmr.c:82:13: warning: 'XTWY_R' defined but not used
plmr.c:152:13: warning: 'XTWX_R' defined but not used
plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target':
qnorm.c:1824:7: warning: unused variable 'non_na'
qnorm.c:1819:9: warning: unused variable 'j'
qnorm.c: In function 'qnorm_c_determine_target_via_subset':
qnorm.c:2411:7: warning: unused variable 'non_na'
qnorm.c:2406:9: warning: unused variable 'j'
qnorm.c: In function 'using_target_via_subset_part2':
qnorm.c:2717:11: warning: unused variable 'datvec'
qnorm.c:2716:11: warning: unused variable 'sample_percentiles'
qnorm.c: In function 'using_target_via_subset':
qnorm.c:2866:11: warning: unused variable 'datvec'
qnorm.c:2865:11: warning: unused variable 'sample_percentiles'
qnorm.c:2861:7: warning: unused variable 'non_na'
qnorm.c:2860:7: warning: unused variable 'targetnon_na'
qnorm.c:2858:28: warning: unused variable 'target_ind_double_floor'
qnorm.c:2858:10: warning: unused variable 'target_ind_double'
qnorm.c:2857:10: warning: unused variable 'samplepercentile'
qnorm.c:2856:11: warning: unused variable 'ranks'
qnorm.c:2854:11: warning: unused variable 'row_mean'
qnorm.c:2852:14: warning: unused variable 'dimat'
qnorm.c:2850:15: warning: unused variable 'target_ind'
qnorm.c:2850:11: warning: unused variable 'ind'
qnorm.c:2850:9: warning: unused variable 'j'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c rlm.c -o rlm.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/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_engine':
rlm_anova.c:1235:10: warning: unused variable 'endprobe'
rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects':
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi'
rlm_anova.c:1426:17: warning: unused variable 'm'
rlm_anova.c:1426:10: warning: unused variable 'vs'
rlm_anova.c:1419:10: warning: unused variable 'scale'
rlm_anova.c:1418:10: warning: unused variable 'Kappa'
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi'
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2'
rlm_anova.c:1414:10: warning: unused variable 'k1'
rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects_engine':
rlm_anova.c:1505:10: warning: unused variable 'endprobe'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c rlm_se.c -o rlm_se.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/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:464:7: warning: unused variable 'j'
rma_background4.c:463:13: warning: 'PMcopy' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -s -static-libgcc -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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRblas -lgfortran -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/preprocessCore.Rcheck/preprocessCore/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (preprocessCore)