| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:39 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the preprocessCore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1530/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preprocessCore 1.63.1 (landing page) Ben Bolstad
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: preprocessCore |
| Version: 1.63.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings preprocessCore_1.63.1.tar.gz |
| StartedAt: 2023-06-06 04:23:06 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 04:23:22 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 16.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings preprocessCore_1.63.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/preprocessCore.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.63.1’
* 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 ‘preprocessCore’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* 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 ... 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 ... WARNING
checkRd: (7) normalize.quantiles.Rd:47: Invalid email address: bmbolstad.com
checkRd: (7) rma.background.correct.Rd:35: Invalid email address: bmbolstad.com
* 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘PLMdtest.R’
Running ‘qnormtest.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.
preprocessCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL preprocessCore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘preprocessCore’ ... ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for library containing pthread_create... none required checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled configure: Enabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_colSummarize.c -o R_colSummarize.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c avg.c -o avg.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c avg_log.c -o avg_log.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c biweight.c -o biweight.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c init_package.c -o init_package.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c lm.c -o lm.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c log_avg.c -o log_avg.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c log_median.c -o log_median.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c matrix_functions.c -o matrix_functions.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c median.c -o median.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c median_log.c -o median_log.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c medianpolish.c -o medianpolish.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c plmd.c -o plmd.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c plmr.c -o plmr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c psi_fns.c -o psi_fns.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c rlm.c -o rlm.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c rlm_anova.c -o rlm_anova.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c rlm_se.c -o rlm_se.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c rma_background4.c -o rma_background4.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.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 -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-preprocessCore/00new/preprocessCore/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (preprocessCore)
preprocessCore.Rcheck/tests/PLMdtest.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'q()' to quit R.
>
>
> library(preprocessCore)
>
>
> values <- rnorm(100)
> group.labels <- sample(0:4,replace=TRUE, 100)
>
> results <- double(10000)
> ngroups <- 2
>
>
> for (i in 1:10000){
+ values <- rnorm(100,sd=1)
+ values <- values/sd(values)
+ group.labels <- sample(0:(ngroups-1),replace=TRUE, 100)
+ blah <- .C("R_split_test",as.double(values), as.integer(100), as.integer(ngroups), as.integer(group.labels),double(1))
+ results[i] <- blah[[5]]
+ }
>
> plot(sort(results),qchisq(0:9999/10000,ngroups-1))
> lm(qchisq(0:9999/10000,ngroups-1) ~ sort(results))
Call:
lm(formula = qchisq(0:9999/10000, ngroups - 1) ~ sort(results))
Coefficients:
(Intercept) sort(results)
0.03487 0.92566
>
>
>
> boxplot(values ~ group.labels,ylim=c(-2,2))
>
>
>
> sc <- median(abs(resid(lm(values ~ 1))))/0.6745
> sum((resid(lm(values ~ 1))/sc)^2)/2
[1] 44.76882
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 44.76418
>
>
> values <- rnorm(100)
> group.labels <- sample(0:4,replace=TRUE, 100)
> values[group.labels == 1] <- values[group.labels == 1] + 0.4
>
>
> blah <- .C("R_split_test",as.double(values), as.integer(100), as.integer(5), as.integer(group.labels),double(1))
>
> boxplot(values ~ group.labels,ylim=c(-2,2))
>
>
>
> library(preprocessCore)
>
> .C("R_test_get_design_matrix",as.integer(4),as.integer(5))
1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00
0.00 1.00 0.00 0.00 0.00 1.00 0.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00
0.00 0.00 1.00 0.00 0.00 -1.00 -1.00 -1.00
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00
0.00 0.00 0.00 1.00 0.00 -1.00 -1.00 -1.00
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00
0.00 0.00 0.00 0.00 1.00 -1.00 -1.00 -1.00
1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00
0.00 0.00 1.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00
0.00 0.00 0.00 1.00 0.00 -1.00 -1.00 -1.00 -1.00
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00
0.00 0.00 0.00 0.00 1.00 -1.00 -1.00 -1.00 -1.00
1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 -1.00
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 -1.00
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00
[[1]]
[1] 4
[[2]]
[1] 5
>
>
>
> chips <- as.factor(rep(c(1,2,3,4,5,6),c(5,5,5,5,5,5)))
> probes <- rep(c(1,3,4,5,6),6)
>
> probes[c(1,6,11)] <- 2
> ##probes[24 + c(8,16,24)] <- 10
> probes <- as.factor(probes)
>
>
> model.matrix(~ -1 + probes)%*%contr.sum(6)
[,1] [,2] [,3] [,4] [,5]
1 0 1 0 0 0
2 0 0 1 0 0
3 0 0 0 1 0
4 0 0 0 0 1
5 -1 -1 -1 -1 -1
6 0 1 0 0 0
7 0 0 1 0 0
8 0 0 0 1 0
9 0 0 0 0 1
10 -1 -1 -1 -1 -1
11 0 1 0 0 0
12 0 0 1 0 0
13 0 0 0 1 0
14 0 0 0 0 1
15 -1 -1 -1 -1 -1
16 1 0 0 0 0
17 0 0 1 0 0
18 0 0 0 1 0
19 0 0 0 0 1
20 -1 -1 -1 -1 -1
21 1 0 0 0 0
22 0 0 1 0 0
23 0 0 0 1 0
24 0 0 0 0 1
25 -1 -1 -1 -1 -1
26 1 0 0 0 0
27 0 0 1 0 0
28 0 0 0 1 0
29 0 0 0 0 1
30 -1 -1 -1 -1 -1
>
>
> probes <- rep(c(1,3,4,5,6),6)
>
> probes[c(1,6,11)] <- 2
> probes[c(20,25,30)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(7)
[,1] [,2] [,3] [,4] [,5] [,6]
1 0 1 0 0 0 0
2 0 0 1 0 0 0
3 0 0 0 1 0 0
4 0 0 0 0 1 0
5 0 0 0 0 0 1
6 0 1 0 0 0 0
7 0 0 1 0 0 0
8 0 0 0 1 0 0
9 0 0 0 0 1 0
10 0 0 0 0 0 1
11 0 1 0 0 0 0
12 0 0 1 0 0 0
13 0 0 0 1 0 0
14 0 0 0 0 1 0
15 0 0 0 0 0 1
16 1 0 0 0 0 0
17 0 0 1 0 0 0
18 0 0 0 1 0 0
19 0 0 0 0 1 0
20 -1 -1 -1 -1 -1 -1
21 1 0 0 0 0 0
22 0 0 1 0 0 0
23 0 0 0 1 0 0
24 0 0 0 0 1 0
25 -1 -1 -1 -1 -1 -1
26 1 0 0 0 0 0
27 0 0 1 0 0 0
28 0 0 0 1 0 0
29 0 0 0 0 1 0
30 -1 -1 -1 -1 -1 -1
>
>
>
>
> probes <- rep(c(1,3,4,5,6),6)
>
> probes[c(1,6,11)] <- 2
> probes[c(5,10,15)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(7)
[,1] [,2] [,3] [,4] [,5] [,6]
1 0 1 0 0 0 0
2 0 0 1 0 0 0
3 0 0 0 1 0 0
4 0 0 0 0 1 0
5 -1 -1 -1 -1 -1 -1
6 0 1 0 0 0 0
7 0 0 1 0 0 0
8 0 0 0 1 0 0
9 0 0 0 0 1 0
10 -1 -1 -1 -1 -1 -1
11 0 1 0 0 0 0
12 0 0 1 0 0 0
13 0 0 0 1 0 0
14 0 0 0 0 1 0
15 -1 -1 -1 -1 -1 -1
16 1 0 0 0 0 0
17 0 0 1 0 0 0
18 0 0 0 1 0 0
19 0 0 0 0 1 0
20 0 0 0 0 0 1
21 1 0 0 0 0 0
22 0 0 1 0 0 0
23 0 0 0 1 0 0
24 0 0 0 0 1 0
25 0 0 0 0 0 1
26 1 0 0 0 0 0
27 0 0 1 0 0 0
28 0 0 0 1 0 0
29 0 0 0 0 1 0
30 0 0 0 0 0 1
>
>
>
> probes <- rep(c(1,3,4,5,6),6)
>
> probes[c(1,6,11)] <- 2
> probes[1+c(1,6,11)] <- 8
> probes[2+c(1,6,11)] <- 9
> probes[3+c(1,6,11)] <- 10
> probes[c(5,10,15)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(10)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
1 0 1 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 1 0
3 0 0 0 0 0 0 0 0 1
4 -1 -1 -1 -1 -1 -1 -1 -1 -1
5 0 0 0 0 0 0 1 0 0
6 0 1 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 1 0
8 0 0 0 0 0 0 0 0 1
9 -1 -1 -1 -1 -1 -1 -1 -1 -1
10 0 0 0 0 0 0 1 0 0
11 0 1 0 0 0 0 0 0 0
12 0 0 0 0 0 0 0 1 0
13 0 0 0 0 0 0 0 0 1
14 -1 -1 -1 -1 -1 -1 -1 -1 -1
15 0 0 0 0 0 0 1 0 0
16 1 0 0 0 0 0 0 0 0
17 0 0 1 0 0 0 0 0 0
18 0 0 0 1 0 0 0 0 0
19 0 0 0 0 1 0 0 0 0
20 0 0 0 0 0 1 0 0 0
21 1 0 0 0 0 0 0 0 0
22 0 0 1 0 0 0 0 0 0
23 0 0 0 1 0 0 0 0 0
24 0 0 0 0 1 0 0 0 0
25 0 0 0 0 0 1 0 0 0
26 1 0 0 0 0 0 0 0 0
27 0 0 1 0 0 0 0 0 0
28 0 0 0 1 0 0 0 0 0
29 0 0 0 0 1 0 0 0 0
30 0 0 0 0 0 1 0 0 0
>
>
>
>
>
>
>
>
>
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
>
> true.chips <- c(8,9,10,11,12,13)
>
>
> y <- outer(true.probes,true.chips,"+")
>
>
>
> estimate.coefficients <- function(y){
+
+
+ colmean <- apply(y,2,mean)
+
+ y <- sweep(y,2,FUN="-",colmean)
+
+ rowmean <- apply(y,1,mean)
+ y <- sweep(y,1,FUN="-",rowmean)
+
+
+ list(y,colmean,rowmean)
+ }
> estimate.coefficients(y)
[[1]]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[[2]]
[1] 8 9 10 11 12 13
[[3]]
[1] 4 3 2 1 -1 -2 -3 -4
>
>
>
> y <- outer(true.probes,true.chips,"+")
>
>
> estimate.coefficients(y)
[[1]]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[[2]]
[1] 8 9 10 11 12 13
[[3]]
[1] 4 3 2 1 -1 -2 -3 -4
>
>
>
>
> y2 <- sweep(y,2,FUN="-",apply(y,2,mean))
>
>
>
> c(3.875, 2.875, 1.875, 0.875,
+ -1.125, -2.125, -3.125, -4, -2.25)
[1] 3.875 2.875 1.875 0.875 -1.125 -2.125 -3.125 -4.000 -2.250
>
>
>
>
> cp <- rep(c(1,2,3,4,5,6),rep(8,6))
> pr <- rep(c(1,2,3,4,5,6,7,8),6)
>
>
> pr[c(32,40,48)] <- 9
>
>
>
>
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
>
> true.chips <- c(8,9,10,11,12,10)
>
>
> y <- outer(true.probes,true.chips,"+") + rnorm(48,0,0.1)
>
> y[8,4:6] <- c(11,12,10)+2 + rnorm(3,0,0.1)
>
>
> lm(as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr),"contr.sum"))
Call:
lm(formula = as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr),
"contr.sum"))
Coefficients:
as.factor(cp)1 as.factor(cp)2
8.2175 9.2538
as.factor(cp)3 as.factor(cp)4
10.2131 11.2104
as.factor(cp)5 as.factor(cp)6
12.2300 10.2008
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.8168 2.7482
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7779 0.7859
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.2107 -2.2717
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.3146 -4.2489
>
>
> matplot(y,type="l")
> matplot(matrix(fitted( lm(as.vector(y) ~ -1 + as.factor(cp) +
+ C(as.factor(pr),"contr.sum"))),ncol=6),type="l")
>
>
> library(preprocessCore)
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
>
> true.chips <- c(8,9,10,11,12,10)
>
> y <- outer(true.probes,true.chips,"+") + rnorm(48,0,0.25)
>
> y[8,4:6] <- c(11,12,10)+ 2.5 + rnorm(3,0,0.25)
> y[5,4:6] <- c(11,12,10)+-2.5 + rnorm(3,0,0.25)
>
>
>
> ###.C("plmd_fit_R", as.double(y), as.integer(8), as.integer(6),
> ### as.integer(2), as.integer(c(1,1,1,2,2,2) - 1),
> ### double(6 +2*8),
> ### double(48),
> ### double(48))
>
> ###matplot(matrix(.C("plmd_fit_R", as.double(y), as.integer(8), as.integer(6),
> ### as.integer(2), as.integer(c(1,1,1,2,2,2) - 1),
> ### double(6 +2*8),
> ### double(48),
> ### double(48))[[7]],ncol=6))
> ###
>
>
> ##.Call("R_plmd_model",y,0,1.3345,as.integer(c(1,1,1,2,2,2) - 1),as.integer(2))
> rcModelPLM(y)
$Estimates
[1] 8.2010672 9.4732745 10.4652076 11.3183523 12.1343962 10.5264781
[7] 3.6574175 2.5774612 1.8180471 0.5940025 -2.1417423 -2.3146898
[13] -3.2877988 -0.9026974
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 1.0000000 1.0000000 0.8010136 1.0000000 1.0000000
[2,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 0.9310802 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 0.4122198 1.0000000 1.0000000 0.4257133 1.0000000 0.3515521
[6,] 1.0000000 1.0000000 1.0000000 0.9266360 0.8132244 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 0.1216357 0.1086931 0.1129385 0.1093306 0.1103536 0.1239778
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.24948128 -0.07056097 -0.29962736 -0.45533472 0.266190180 0.21924619
[2,] -0.17845011 0.08420685 -0.05936224 0.08872093 -0.094947960 0.15983253
[3,] 0.17323444 -0.39177041 0.33765400 -0.18739496 -0.101444688 0.14272088
[4,] -0.22581124 0.31984689 0.02242054 0.17135234 0.068038638 -0.35584716
[5,] 0.88480969 0.21653971 0.27696521 -0.85690398 -0.128622599 -1.03774925
[6,] 0.02345641 0.10152101 -0.01571439 0.39382245 -0.448415345 -0.10953079
[7,] -0.04185892 0.07799935 0.10244882 -0.07287242 -0.009339061 -0.05637776
[8,] -2.99902008 -3.35608255 -3.22994000 3.33656763 3.305626249 2.94229462
$StdErrors
[1] 0.2178342 0.2104590 0.2093894 0.2222080 0.2119804 0.2188360 0.2181266
[8] 0.2153765 0.2163382 0.2153765 0.2497384 0.2190783 0.2153765 0.5606374
$Scale
[1] 0.2711972
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 7.9250266 9.1001230 10.1067854 10.9928420 11.8304279 10.1218201
[7] 4.0317926 2.9177530 2.1523646 0.9231413 -1.3980346 -2.5928250
[13] -1.9616890 -2.9475069 -3.7618402 2.6368443
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 1.0000000 0.8313179 0.5202841 1.0000000 1.0000000
[2,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 0.7432145 0.7250259 1.0000000 1.0000000 1.0000000
[4,] 0.9404095 0.7208812 1.0000000 1.0000000 1.0000000 0.9357121
[5,] 0.6288898 1.0000000 1.0000000 1.0000000 0.4187540 1.0000000
[6,] 1.0000000 1.0000000 1.0000000 0.7160018 0.5272824 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.15114677 -0.0717846 -0.31558026 -0.50419951 0.19578331 0.249529046
[2,] -0.24270132 0.1170665 -0.04123183 0.07393945 -0.13127153 0.224198697
[3,] 0.11495758 -0.3529364 0.36175875 -0.19620210 -0.13179391 0.213061399
[4,] -0.27890946 0.3638596 0.05170394 0.16772385 0.04286807 -0.280327993
[5,] 0.41714261 -0.1540165 -0.10832025 -0.08031090 0.62642840 -0.182008517
[6,] -0.05350382 0.1216717 -0.01029300 0.36633194 -0.49744794 -0.057873647
[7,] -0.10611013 0.1108590 0.12057923 -0.08765391 -0.04566263 0.007988403
[8,] 0.13616329 -0.1237883 -0.01237501 0.12253627 0.07005281 -0.192589081
$StdErrors
[1] 0.10834448 0.10974895 0.10909734 0.10953836 0.10856182 0.09931450
[7] 0.12288066 0.09998332 0.12363683 0.14159250 0.17590517 0.17369925
[13] 0.12313439 0.09998332 0.14405715 0.00000000
$WasSplit
[1] 0 0 0 0 1 0 0 1
>
> ###R_plmd_model(SEXP Y, SEXP PsiCode, SEXP PsiK, SEXP Groups, SEXP Ngroups)
>
>
>
>
>
> pr[seq(3,48,8)][1:3] <- 10
>
> y[seq(3,48,8)][1:3] <- c(8,9,10) -3 + rnorm(3,0,0.1)
> lm(as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr),"contr.sum"))
Call:
lm(formula = as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr),
"contr.sum"))
Coefficients:
as.factor(cp)1 as.factor(cp)2
7.932 9.119
as.factor(cp)3 as.factor(cp)4
10.041 10.765
as.factor(cp)5 as.factor(cp)6
11.636 9.909
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
4.095 3.030
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
2.326 1.047
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.796 -1.871
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-2.835 -3.748
C(as.factor(pr), "contr.sum")9
2.849
>
>
> proc.time()
user system elapsed
2.219 0.071 2.281
preprocessCore.Rcheck/tests/qnormtest.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(preprocessCore)
>
> err.tol <- 10^-8
>
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> x
[,1] [,2] [,3]
[1,] 100 110.0 120
[2,] 15 16.5 18
[3,] 200 220.0 240
[4,] 250 275.0 300
> normalize.quantiles(x)
[,1] [,2] [,3]
[1,] 110.0 110.0 110.0
[2,] 16.5 16.5 16.5
[3,] 220.0 220.0 220.0
[4,] 275.0 275.0 275.0
>
> x.norm.truth <- matrix(rep(c(110.0,16.5,220,275.0),3),ncol=3)
>
> if (all(abs(x.norm.truth - normalize.quantiles(x)) < err.tol) != TRUE){
+ stop("Disagreement in normalize.quantiles(x)")
+ }
>
> normalize.quantiles.determine.target(x)
[1] 16.5 110.0 220.0 275.0
>
> x.norm.target.truth <- c(16.5,110.0,220.0,275.0)
>
> if (all(abs(x.norm.target.truth - normalize.quantiles.determine.target(x)) < err.tol) != TRUE){
+ stop("Disagreement in normalize.quantiles.determine.target(x)")
+ }
>
>
> y <- x
> y[2,2] <- NA
> y
[,1] [,2] [,3]
[1,] 100 110 120
[2,] 15 NA 18
[3,] 200 220 240
[4,] 250 275 300
> normalize.quantiles(y)
[,1] [,2] [,3]
[1,] 134.44444 47.66667 134.44444
[2,] 47.66667 NA 47.66667
[3,] 226.11111 180.27778 226.11111
[4,] 275.00000 275.00000 275.00000
>
> y.norm.target.truth <- c(47.6666666666667,134.4444444444444,226.1111111111111,275.0000000000000)
>
> y.norm.truth <- matrix(c(134.4444444444444, 47.6666666666667, 134.4444444444444,
+ 47.6666666666667, NA, 47.6666666666667,
+ 226.1111111111111, 180.2777777777778, 226.1111111111111,
+ 275.0000000000000, 275.0000000000000, 275.0000000000000),byrow=TRUE,ncol=3)
>
>
> if (all(abs(y.norm.truth - normalize.quantiles(y)) < err.tol,na.rm=TRUE) != TRUE){
+ stop("Disagreement in normalize.quantiles(y)")
+ }
>
>
>
> if (all(abs(y.norm.target.truth - normalize.quantiles.determine.target(y)) < err.tol) != TRUE){
+ stop("Disagreement in normalize.quantiles.determine.target(y)")
+ }
>
>
>
> if (all(abs(normalize.quantiles.use.target(y,y.norm.target.truth) - y.norm.truth) < err.tol,na.rm=TRUE) != TRUE){
+ stop("Disagreement in normalize.quantiles.use.target(y)")
+ }
>
>
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> rownames(x) <- letters[1:4]
> colnames(x) <- LETTERS[1:3]
> y <- normalize.quantiles(x, keep.names = TRUE)
> if(!all(colnames(x)==colnames(y))){
+ stop("Disagreement between initial and final column names despite keep.names=TRUE")
+ }
> if(!all(rownames(x)==rownames(y))){
+ stop("Disagreement between initial and final row names despite keep.names=TRUE")
+ }
>
> proc.time()
user system elapsed
0.197 0.028 0.211
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.002 | 0.000 | 0.002 | |
| normalize.quantiles.in.blocks | 0.044 | 0.000 | 0.045 | |
| rcModelPLMd | 0.018 | 0.000 | 0.018 | |
| rcModelPLMr | 0.037 | 0.004 | 0.041 | |
| rcModels | 0.007 | 0.000 | 0.007 | |
| subColSummarize | 0.003 | 0.002 | 0.005 | |
| subrcModels | 0.004 | 0.006 | 0.010 | |