affyPLM 1.38.0
Ben Bolstad
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/affyPLM | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPLM/DESCRIPTION’ ... OK
* this is package ‘affyPLM’ version ‘1.38.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘affyPLM’ can be installed ... [14s/15s] 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
* 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... WARNING
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck/00_pkg_src/affyPLM/man/normalize.exprSet.Rd’:
‘[affy]{normalize}’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck/00_pkg_src/affyPLM/man/normalize.quantiles.probeset.Rd’:
‘[affy]{normalize}’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck/00_pkg_src/affyPLM/man/normalize.scaling.Rd’:
‘[affy]{normalize}’
See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘AffyExtensions.Rnw’, ‘MAplots.Rnw’, ‘QualityAssess.Rnw’,
‘ThreeStep.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [60s/60s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
threestep 21.493 0.280 21.819
fitPLM 11.784 0.276 12.116
PLMset2exprSet 9.748 0.152 9.918
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘C_code_tests.R’ [4s/4s]
Running ‘PLM_tests.R’ [0s/0s]
Running ‘preprocess_tests.R’ [32s/32s]
Running ‘threestepPLM_tests.R’ [71s/71s]
[107s/107s] 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
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck/00check.log’
for details.
* installing *source* package ‘affyPLM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/usr/local/lib -o affyPLM.so 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 -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.13-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/affyPLM.Rcheck/affyPLM/libs
** 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
* DONE (affyPLM)