Ben Bolstad
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/affyPLM |
| git_branch: RELEASE_3_17 |
| git_last_commit: d20fa58 |
| git_last_commit_date: 2023-05-01 20:07:56 -0400 (Mon, 01 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:10 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 29/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyPLM 1.76.1 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the affyPLM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyPLM.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: affyPLM |
| Version: 1.76.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:affyPLM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings affyPLM_1.76.1.tar.gz |
| StartedAt: 2023-10-15 19:05:52 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 19:11:24 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 332.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: affyPLM.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:affyPLM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings affyPLM_1.76.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/affyPLM.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘affyPLM/DESCRIPTION’ ... OK
* this is package ‘affyPLM’ version ‘1.76.1’
* 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 ‘affyPLM’ can be installed ... WARNING
Found the following significant warnings:
rlm_PLM.c:868:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/affyPLM.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘affyPLM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PLMset2exprSet
> ### Title: Convert a PLMset to an ExpressionSet
> ### Aliases: PLMset2exprSet pset2eset
> ### Keywords: manip
>
> ### ** Examples
>
> if (require(affydata)) {
+ data(Dilution)
+ Pset <- fitPLM(Dilution)
+ eset <- pset2eset(Pset)
+ }
Loading required package: affydata
Package LibPath Item
[1,] "affydata" "/home/biocbuild/bbs-3.17-bioc/R/site-library" "Dilution"
Title
[1,] "AffyBatch instance Dilution"
also installing the dependencies ‘sys’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘bit’, ‘rlang’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘httr’, ‘png’, ‘DBI’, ‘RSQLite’, ‘KEGGREST’, ‘AnnotationDbi’
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* installing *source* package ‘sys’ ...
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exec.c -o exec.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-sys/00new/sys/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 (sys)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c ansi.c -o ansi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c cleancall.c -o cleancall.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c diff.c -o diff.o
diff.c: In function ‘clic_diff_chr’:
diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized]
104 | SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c errors.c -o errors.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c inst.c -o inst.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-unix.c -o keypress-unix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress-win.c -o keypress-win.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c keypress.c -o keypress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c md5.c -o md5.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress-altrep.c -o progress-altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c progress.c -o progress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha1.c -o sha1.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c sha256.c -o sha256.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c thread.c -o thread.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c tty.c -o tty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utf8.c -o utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vt.c -o vt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse.c -o vtparse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c vtparse_table.c -o vtparse_table.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c win-utf8.c -o win-utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -Wall -c winfiles.c -o winfiles.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-cli/00new/cli/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (cli)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (glue)
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -Wall -c fastmap.cpp -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/ -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-fastmap/00new/fastmap/libs
** R
** 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 (fastmap)
* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit.so attrutil.o bit.o chunkutil.o clone.o init.o integerutil.o merge.o rle.o sort.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-bit/00new/bit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (bit)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c capture.c -o capture.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c internal.c -o internal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (rlang)
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callbacks.c -o callbacks.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c download.c -o download.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape.c -o escape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fetch.c -o fetch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c form.c -o form.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c getdate.c -o getdate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c handle.c -o handle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ieproxy.c -o ieproxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interrupt.c -o interrupt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c multi.c -o multi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c nslookup.c -o nslookup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c options.c -o options.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c reflist.c -o reflist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typechecking.c -o typechecking.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c winidn.c -o winidn.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c writer.c -o writer.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (curl)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_array.c -o collapse_array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_object.c -o collapse_object.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c escape_chars.c -o escape_chars.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_datelist.c -o is_datelist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_recordlist.c -o is_recordlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c null_to_na.c -o null_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c num_to_char.c -o num_to_char.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c parse.c -o parse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c prettify.c -o prettify.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c push_parser.c -o push_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c r-base64.c -o r-base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c row_collapse.c -o row_collapse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c transpose_list.c -o transpose_list.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c validate.c -o validate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-mime/00new/mime/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 (mime)
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R6)
* installing *source* package ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgconfig)
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c dummy.c -o dummy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c read.c -o read.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -c write.c -o write.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-png/00new/png/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 (png)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DBI)
* installing *source* package ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘askpass’ ...
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-askpass/00new/askpass/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 (askpass)
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-cachem/00new/cachem/libs
** R
** 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 (cachem)
* installing *source* package ‘bit64’ ...
** package ‘bit64’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c integer64.c -o integer64.o
integer64.c: In function ‘runif_integer64’:
integer64.c:998:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
998 | while( (*((long long *) &ii)) == NA_INTEGER64){
| ~^~~~~~~~~~~~~~~~~~
integer64.c:1006:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
1006 | ret[i] = min + ( (long long)(*((unsigned long long *)(&ii))) % d);
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit64.so bsearch.o cache.o hash64.o init.o integer64.o sort64.o sortuse64.o -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-bit64/00new/bit64/libs
** R
** data
** exec
** 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 (bit64)
* installing *source* package ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-lazy-character.c -o altrep-lazy-character.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep-rle.c -o altrep-rle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c altrep.c -o altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg-counter.c -o arg-counter.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c arg.c -o arg.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c assert.c -o assert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c-unchop.c -o c-unchop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c c.c -o c.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c callables.c -o callables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-bare.c -o cast-bare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast-dispatch.c -o cast-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c cast.c -o cast.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c compare.c -o compare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c complete.c -o complete.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c conditions.c -o conditions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dictionary.c -o dictionary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c dim.c -o dim.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c empty.c -o empty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c equal.c -o equal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c expand.c -o expand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fields.c -o fields.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c fill.c -o fill.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c globals.c -o globals.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c group.c -o group.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c growable.c -o growable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c interval.c -o interval.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match-joint.c -o match-joint.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c match.c -o match.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c missing.c -o missing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c names.c -o names.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-collate.c -o order-collate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-groups.c -o order-groups.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-sortedness.c -o order-sortedness.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order-truelength.c -o order-truelength.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c order.c -o order.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c poly-op.c -o poly-op.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy-restore.c -o proxy-restore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c proxy.c -o proxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype-common.c -o ptype-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype.c -o ptype.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c ptype2.c -o ptype2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rank.c -o rank.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rep.c -o rep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang-dev.c -o rlang-dev.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c runs.c -o runs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c set.c -o set.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c shape.c -o shape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size-common.c -o size-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c size.c -o size.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-array.c -o slice-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign-array.c -o slice-assign-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-assign.c -o slice-assign.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-chop.c -o slice-chop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice-interleave.c -o slice-interleave.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c slice.c -o slice.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript-loc.c -o subscript-loc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c subscript.c -o subscript.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c translate.c -o translate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-data-frame.c -o type-data-frame.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-date-time.c -o type-date-time.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-factor.c -o type-factor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-info.c -o type-info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-integer64.c -o type-integer64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c type-tibble.c -o type-tibble.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2-s3.c -o typeof2-s3.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c typeof2.c -o typeof2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c unspecified.c -o unspecified.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils-dispatch.c -o utils-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c vctrs-core.c -o vctrs-core.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-vctrs/00new/vctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (vctrs)
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c aes.c -o aes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bignum.c -o bignum.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c cert.c -o cert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c compatibility.c -o compatibility.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c diffie.c -o diffie.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c envelope.c -o envelope.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c error.c -o error.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c info.c -o info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c keygen.c -o keygen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c keys.c -o keys.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c onload.c -o onload.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c openssh.c -o openssh.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c password.c -o password.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pbkdf.c -o pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pem.c -o pem.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pkcs12.c -o pkcs12.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c pkcs7.c -o pkcs7.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c rand.c -o rand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c rsa.c -o rsa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c signing.c -o signing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c stream.c -o stream.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c write.c -o write.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c x25519.c -o x25519.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -Wall -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (openssl)
* installing *source* package ‘memoise’ ...
** package ‘memoise’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (memoise)
* installing *source* package ‘blob’ ...
** package ‘blob’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (blob)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr)
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘RSQLite’ had non-zero exit status
* installing *source* package ‘KEGGREST’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGGREST)
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu95av2cdf’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpx5VFUS/downloaded_packages’
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Calls: fitPLM -> geneNames -> geneNames -> getCdfInfo
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘C_code_tests.R’
Running ‘PLM_tests.R’
Running ‘preprocess_tests.R’
ERROR
Running the tests in ‘tests/preprocess_tests.R’ failed.
Last 13 lines of output:
'/tmp/RtmpLdbMTi/downloaded_packages'
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Calls: threestep ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
In addition: Warning messages:
1: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'RSQLite' had non-zero exit status
2: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'AnnotationDbi' had non-zero exit status
3: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'hgu95av2cdf' had non-zero exit status
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘AffyExtensions.Rnw’... failed
‘MAplots.Rnw’... failed
‘QualityAssess.Rnw’... failed
‘ThreeStep.Rnw’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘AffyExtensions.Rnw’
...
The downloaded source packages are in
‘/tmp/RtmpnUxo2W/downloaded_packages’
When sourcing ‘AffyExtensions.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted
when running code in ‘MAplots.Rnw’
...
The downloaded source packages are in
‘/tmp/Rtmpil3wTB/downloaded_packages’
When sourcing ‘MAplots.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted
when running code in ‘QualityAssess.Rnw’
...
The downloaded source packages are in
‘/tmp/RtmpsqaV26/downloaded_packages’
When sourcing ‘QualityAssess.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘AffyExtensions.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: affydata
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’
trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu95av2cdf’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp15t9Gm/downloaded_packages’
Error: processing vignette 'AffyExtensions.Rnw' failed with diagnostics:
chunk 2 (label = defaultModel)
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
--- failed re-building ‘AffyExtensions.Rnw’
--- re-building ‘MAplots.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: affydata
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’
trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu95av2cdf’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpVqvODV/downloaded_packages’
Error: processing vignette 'MAplots.Rnw' failed with diagnostics:
chunk 2 (label = makeExpressionSet)
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
--- failed re-building ‘MAplots.Rnw’
--- re-building ‘QualityAssess.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: affydata
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’
trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu95av2cdf’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpUyB2Hi/downloaded_packages’
Error: processing vignette 'QualityAssess.Rnw' failed with diagnostics:
chunk 2 (label = loadData)
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
--- failed re-building ‘QualityAssess.Rnw’
--- re-building ‘ThreeStep.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
--- finished re-building ‘ThreeStep.Rnw’
SUMMARY: processing the following files failed:
‘AffyExtensions.Rnw’ ‘MAplots.Rnw’ ‘QualityAssess.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/affyPLM.Rcheck/00check.log’
for details.
affyPLM.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL affyPLM
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘affyPLM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
620 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
209 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
118 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
71 | int first_ind;
| ^~~~~~~~~
idealmismatch.c: In function ‘SpecificBiweightCorrect_single’:
idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
183 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
158 | int which_lesn;
| ^~~~~~~~~~
preprocess.c: In function ‘pp_bothstages’:
preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
677 | int rows,cols;
| ^~~~
preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
677 | int rows,cols;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
110 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
1481 | int rows,cols;
| ^~~~
rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
1481 | int rows,cols;
| ^~~~
rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’:
rlm_PLM.c:868:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
868 | snprintf(tmp_str2,9,"%d",j+2);
| ^~
rlm_PLM.c:868:31: note: directive argument in the range [2, 2147483647]
868 | snprintf(tmp_str2,9,"%d",j+2);
| ^~~~
In file included from /usr/include/stdio.h:894,
from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:44,
from preprocess.h:4,
from rlm_PLM.c:71:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
60 | int i;
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
82 | double *PM,*MM;
| ^~
threestep.c: In function ‘R_threestep_c’:
threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
193 | int rows,cols;
| ^~~~
threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
193 | int rows,cols;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/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]
73 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c transfns.c -o transfns.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -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 -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-affyPLM/00new/affyPLM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (affyPLM)
affyPLM.Rcheck/tests/C_code_tests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> ####
> #### This code is messy, possibly incomplete and only for
> #### the use of developers.
> ####
> ####
>
> test.c.code <- FALSE
> test.PLM.modelmatrix <- FALSE
> test.rlm <- FALSE
>
> if (test.c.code){
+
+ library(affyPLM)
+ narrays <- 10
+ nprobes <- 11
+ nprobetypes <- 2
+ ncols <- 10
+
+ MMs <- rnorm(narrays*nprobes*nprobetypes)
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+
+ #test making intercept column
+ matrix(.C("R_PLM_matrix_intercept",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),0)[[1]],ncol=10)
+
+ #test making an MM covariate column
+ matrix(.C("R_PLM_matrix_MM",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.double(MMs))[[1]],ncol=10)
+
+ # sample effect aka chip effect, aka expression values
+ matrix(.C("R_PLM_matrix_sample_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0))[[1]],ncol=10)
+ matrix(.C("R_PLM_matrix_sample_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1))[[1]],ncol=10)
+ matrix(.C("R_PLM_matrix_sample_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1))[[1]],ncol=10)
+
+
+
+ #probe-type parameter overall
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(0),integer(narrays),as.integer(1))[[1]],ncol=10)
+
+ #probe-type parameter within sample
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(1),integer(narrays),as.integer(1))[[1]],ncol=10)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(1),integer(narrays),as.integer(1))[[1]],ncol=10)
+ ncols <- 20
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(1),integer(narrays),as.integer(0))[[1]],ncol=20)
+
+
+ #probe-type-parameter within a chip-level factor (eg treatment, or genotype variable)
+ trt.cov <- rep(0:1,5)
+ ncols <- 10
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=10)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=10)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=10)
+
+ trt.cov <- rep(0:4,2)
+ matrix(.C("R_PLM_matrix_probe_type_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(2),as.integer(trt.cov),as.integer(4))[[1]],ncol=10)
+
+
+
+
+ #probe effects - overall
+ ncols <- 11
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+
+
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(0),as.integer(trt.cov),as.integer(4))[[1]],ncol=11)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(0),as.integer(trt.cov),as.integer(4))[[1]],ncol=11)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(0),as.integer(trt.cov),as.integer(4))[[1]],ncol=11)
+
+
+
+ #probe effects within treatment or genotype factor
+ trt.cov <- rep(0:1,5)
+ ncols <- 22
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(2),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+
+
+ #probe effects within probetype
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(3),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(3),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(3),as.integer(trt.cov),as.integer(1))[[1]],ncol=22)
+
+
+ #probe effects within probetype within treatment or genotype factor variable
+ trt.cov <- rep(0:1,5)
+ ncols <- 44
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+
+ nprobetypes <- 1
+ trt.cov <- rep(0:1,5)
+ ncols <- 44
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+ matrix(.C("R_PLM_matrix_probe_effect",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(-1),as.integer(4),as.integer(trt.cov),as.integer(1))[[1]],ncol=44)
+
+
+ # copy across chip level variables into model matrix
+ nprobetypes <- 1
+ trt.cov <- rep(0:1,5)
+ ncols <- 10
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ trt.variables <- rnorm(10)
+
+ matrix(.C("R_PLM_matrix_chiplevel",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.double(trt.variables),as.integer(1))[[1]],ncol=10)
+
+
+ ###
+ ### Build a few design matrices and compare with R model.matrix
+ ###
+
+
+ for (nprobetypes in 1:2){
+ for (narrays in 2:15){
+ for (nprobes in 2:20){
+ for (constraint.type in c("contr.sum","contr.treatment")){
+ if (constraint.type == "contr.sum"){
+ ct.type <- -1
+ } else {
+ ct.type <- 1
+ }
+
+
+ ncols <- nprobes -1 + narrays
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(1),as.integer(0),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ probe.effect <- factor(rep(1:nprobes,narrays*nprobetypes))
+ sample.effect <- factor(rep(rep(c(1:narrays),rep(nprobes,narrays)),nprobetypes))
+ if (nprobetypes == 2){
+ probe.type.effect <- factor(rep(1:2,c(narrays*nprobes,narrays*nprobes)))
+ } else {
+ probe.type.effect <- factor(rep(1,narrays*nprobes))
+ }
+
+ if (any(X!=model.matrix(~ C(sample.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes, " ", nprobetypes)
+ }
+
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(0),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ -1 + C(sample.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- nprobes
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(0),as.integer(0),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+
+ ncols <- nprobes
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(0),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~-1+ C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ }
+ }
+ }
+ }
+
+ ###
+ ### Build a few more design matrices and compare with R model.matrix
+ ###
+
+
+ for (narrays in 2:15){
+ for (nprobes in 2:20){
+ for (constraint.type in c("contr.sum","contr.treatment")){
+ probe.effect <- factor(rep(1:nprobes,narrays*nprobetypes))
+ sample.effect <- factor(rep(rep(c(1:narrays),rep(nprobes,narrays)),nprobetypes))
+ if (constraint.type == "contr.sum"){
+ ct.type <- -1
+ } else {
+ ct.type <- 1
+ }
+
+
+ if (nprobetypes == 2){
+ probe.type.effect <- factor(rep(1:2,c(narrays*nprobes,narrays*nprobes)))
+ } else {
+ probe.type.effect <- factor(rep(1,narrays*nprobes))
+ }
+ ncols <- nprobetypes + nprobes -1
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(1),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~-1+ C(probe.type.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- nprobetypes + nprobes -1
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(0),as.integer(1),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ C(probe.type.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- narrays + nprobetypes + nprobes -2
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(1),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ -1 + C(sample.effect,constraint.type) + C(probe.type.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- narrays + nprobetypes + nprobes -2
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(1),as.integer(1),as.integer(1),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ + C(sample.effect,constraint.type) + C(probe.type.effect,constraint.type) + C(probe.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- narrays + nprobetypes -1
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(1),as.integer(1),as.integer(0),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ C(sample.effect,constraint.type) + C(probe.type.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- narrays + nprobetypes -1
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(1),as.integer(1),as.integer(0),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ -1 + C(sample.effect,constraint.type) + C(probe.type.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- nprobetypes
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(1),as.integer(0),as.integer(1),as.integer(0),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~ C(probe.type.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ ncols <- nprobetypes
+ X <- matrix(0,narrays*nprobes*nprobetypes,ncols)
+ X <- matrix(.C("R_PLM_Matrix_constructtest",as.double(as.vector(X)), as.integer(narrays),as.integer(nprobes),as.integer(nprobetypes),as.integer(0),as.integer(0),as.integer(1),as.integer(0),as.integer(ct.type))[[1]],ncol=ncols)
+
+ if (any(X!=model.matrix(~-1 + C(probe.type.effect,constraint.type)))){
+ stop("Model matrix function problem ",narrays," ", nprobes," ", nprobetypes)
+ }
+
+ }
+
+
+ }
+ }
+
+
+ narrays <- 2
+ nprobes <- 7
+ nprobetypes <- 2
+
+ probe.effect <- factor(rep(1:nprobes,narrays*nprobetypes))
+ sample.effect <- factor(rep(rep(c(1:narrays),rep(nprobes,narrays)),nprobetypes))
+ if (constraint.type == "contr.sum"){
+ ct.type <- -1
+ } else {
+ ct.type <- 1
+ }
+
+
+ if (nprobetypes == 2){
+ probe.type.effect <- factor(rep(1:2,c(narrays*nprobes,narrays*nprobes)))
+ } else {
+ probe.type.effect <- factor(rep(1,narrays*nprobes))
+ }
+
+
+ model.matrix(~-1 +probe.effect/probe.type.effect)
+
+
+ library(affyPLM)
+ output <- verify.output.param(list(weights = FALSE, residuals = FALSE, varcov = "none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ library(affydata)
+ data(Dilution)
+
+ # fit a PM ~ samples model
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0), probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ sample.effect <- rep(1:4,c(16,16,16,16))
+ probe.effect <- rep(1:16,4)
+
+ library(MASS)
+ fit <- rlm(as.vector(log2(pm(Dilution)[1:16,])) ~ -1 + factor(sample.effect))
+
+ if (any(Fitresults[[1]][1,] != coef(fit))){
+ stop("Problem in model fitting procedure")
+ }
+
+ sample.effect <- rep(1:4,c(20,20,20,20))
+ probe.effect <- rep(1:20,4)
+ fit <- rlm(as.vector(log2(pm(Dilution)[201781:201800,])) ~ -1 + factor(sample.effect))
+ if (any(Fitresults[[1]][12625,] != coef(fit))){
+ stop("Problem in model fitting procedure")
+ }
+
+
+ # fit a samples + probes model
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0), probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+ sample.effect <- rep(1:4,c(16,16,16,16))
+ probe.effect <- rep(1:16,4)
+
+ fit <- rlm(as.vector(log2(pm(Dilution)[1:16,])) ~ -1 + factor(sample.effect)+C(factor(probe.effect),"contr.sum"))
+
+ if (any(abs(Fitresults[[1]][1,] -coef(fit)[1:4]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[2]][[1]]) - coef(fit)[5:19]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+
+
+ sample.effect <- rep(1:4,c(20,20,20,20))
+ probe.effect <- rep(1:20,4)
+ fit <- rlm(as.vector(log2(pm(Dilution)[201781:201800,])) ~ -1 + factor(sample.effect)+C(factor(probe.effect),"contr.sum"))
+
+ if (any(abs(Fitresults[[1]][12625,] -coef(fit)[1:4])> 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[2]][[12625]])- coef(fit)[5:23])>1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ # fit an MM ~ samples model
+ R.model <- list(mmorpm.covariate=0,response.variable=-1,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0), probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ sample.effect <- rep(1:4,c(16,16,16,16))
+ probe.effect <- rep(1:16,4)
+
+ library(MASS)
+ fit <- rlm(as.vector(log2(mm(Dilution)[1:16,])) ~ -1 + factor(sample.effect))
+
+ if (any(abs(Fitresults[[1]][1,] - coef(fit)) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ sample.effect <- rep(1:4,c(20,20,20,20))
+ probe.effect <- rep(1:20,4)
+ fit <- rlm(as.vector(log2(mm(Dilution)[201781:201800,])) ~ -1 + factor(sample.effect))
+ if (any(abs(Fitresults[[1]][12625,] - coef(fit))>1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ # fit a MM ~ samples + probes model
+ R.model <- list(mmorpm.covariate=0,response.variable=-1,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0), probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+ sample.effect <- rep(1:4,c(16,16,16,16))
+ probe.effect <- rep(1:16,4)
+
+ fit <- rlm(as.vector(log2(mm(Dilution)[1:16,])) ~ -1 + factor(sample.effect)+C(factor(probe.effect),"contr.sum"))
+
+ if (any(abs(Fitresults[[1]][1,]-coef(fit)[1:4]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[2]][[1]])- coef(fit)[5:19])>1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+
+
+ sample.effect <- rep(1:4,c(20,20,20,20))
+ probe.effect <- rep(1:20,4)
+ fit <- rlm(as.vector(log2(mm(Dilution)[201781:201800,])) ~ -1 + factor(sample.effect)+C(factor(probe.effect),"contr.sum"))
+
+ if (any(abs(Fitresults[[1]][12625,]- coef(fit)[1:4])>1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[2]][[12625]])-coef(fit)[5:23])>1e14)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+ # a treatment model
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- model.matrix(~ -1 + as.factor(treatment.effect))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=-1,which.parameter.types=as.integer(c(0,1,0,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =covariates, probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ treatment.effect <- rep(c(1,1,2,2),c(16,16,16,16))
+ fit <- rlm(as.vector(log2(mm(Dilution)[1:16,])) ~ -1 + factor(treatment.effect))
+
+ if (any(abs(Fitresults[[1]][1,]-coef(fit)[1:2]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ output <- verify.output.param(list(weights = FALSE, residuals = FALSE, varcov = "none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+
+ # a treatment + probes model with contr.treatment constraint
+ R.model <- list(mmorpm.covariate=0,response.variable=-1,which.parameter.types=as.integer(c(0,1,0,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =covariates, probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ treatment.effect <- rep(c(1,1,2,2),c(20,20,20,20))
+ probe.effect <- rep(1:20,4)
+ fit <- rlm(as.vector(log2(mm(Dilution)[201761:201780,])) ~ -1 + factor(treatment.effect)+C(factor(probe.effect),"contr.treatment"))
+
+ if (any(abs(Fitresults[[1]][12624,]-coef(fit)[1:2]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[2]][[12624]])-coef(fit)[3:21])>1e14)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+
+
+ # MM + samples + probes
+ R.model <- list(mmorpm.covariate=1,response.variable=1,which.parameter.types=as.integer(c(0,0,0,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0), probe.type.levels=list(),probe.trt.levels=list())
+
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ sample.effect <- rep(1:4,c(16,16,16,16))
+ probe.effect <- rep(1:16,4)
+
+ fit <- rlm(as.vector(log2(pm(Dilution)[1:16,])) ~ -1 + as.vector(log2(mm(Dilution)[1:16,])))
+
+
+ if (any(abs(as.vector(Fitresults[[6]][[1]]) - coef(fit)) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ R.model <- list(mmorpm.covariate=1,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ fit <- rlm(as.vector(log2(pm(Dilution)[1:16,])) ~ -1 + as.vector(log2(mm(Dilution)[1:16,]))+ as.factor(sample.effect))
+ if (any(abs(as.vector(Fitresults[[6]][[1]]) - coef(fit)[1]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[1]][1,]) - coef(fit)[2:5]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ R.model <- list(mmorpm.covariate=1,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ fit <- rlm(as.vector(log2(pm(Dilution)[1:16,])) ~ -1 + as.vector(log2(mm(Dilution)[1:16,]))+ as.factor(sample.effect) + C(as.factor(probe.effect),"contr.sum"))
+ if (any(abs(as.vector(Fitresults[[6]][[1]]) - coef(fit)[1]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[1]][1,]) - coef(fit)[2:5]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+ ## PM and MM are response
+
+
+ sample.effect <- rep(1:4,c(32,32,32,32))
+ probe.effect <- rep(1:16,8)
+
+
+
+ # PMMM ~ -1 + samples
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ fit <- rlm(as.vector(rbind(log2(pm(Dilution)[1:16,]),log2(mm(Dilution)[1:16,]))) ~ -1 + as.factor(sample.effect))
+ if (any(abs(as.vector(Fitresults[[1]][1,]) - coef(fit)) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ # PMMM ~ -1 + samples +PROBES
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ fit <- rlm(as.vector(rbind(log2(pm(Dilution)[1:16,]),log2(mm(Dilution)[1:16,]))) ~ -1 + as.factor(sample.effect)+C(as.factor(probe.effect),"contr.sum") )
+ if (any(abs(as.vector(Fitresults[[1]][1,]) - coef(fit)[1:4]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ # a probe.type effect
+ probe.type.effect <- rep(rep(1:2,c(16,16)),4)
+
+ # PMMM ~ -1 + samples + probe.type + PROBES
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,1,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,-1,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ fit <- rlm(as.vector(rbind(log2(pm(Dilution)[1:16,]),log2(mm(Dilution)[1:16,]))) ~ -1 + as.factor(sample.effect)+ C(as.factor(probe.type.effect),"contr.sum")+ C(as.factor(probe.effect),"contr.sum") )
+
+ if (any(abs(as.vector(Fitresults[[1]][1,]) - coef(fit)[1:4]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+ if (any(abs(as.vector(Fitresults[[6]][1,]) - coef(fit)[5]) > 1e-13)){
+ stop("Problem in model fitting procedure")
+ }
+
+
+
+ #### store weights PM ~ -1 + samples
+
+ output <- verify.output.param(list(weights = TRUE, residuals = TRUE, varcov = "none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ #### store weights PMMM ~ -1 + samples
+
+ output <- verify.output.param(list(weights = TRUE, residuals = TRUE, varcov = "none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ #### store weights PMMM ~ -1 + samples + probe.type + probes
+
+ output <- verify.output.param(list(weights = TRUE, residuals = TRUE, varcov ="none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,1,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,1,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PM ~ -1 + treatment + probes in treatment
+ output <- verify.output.param(list(weights = TRUE, residuals = TRUE, varcov = "none", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- model.matrix(~ -1 + as.factor(treatment.effect))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,1,0,0,1)),strata=as.integer(c(0,0,0,0,2)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =covariates,probe.type.levels=list(),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1 + treatment + probes in treatment
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- model.matrix(~ -1 + as.factor(treatment.effect))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,1,0,0,1)),strata=as.integer(c(0,0,0,0,2)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =covariates,probe.type.levels=list(),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1 + treatment + probe.effect in treatment
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- model.matrix(~ -1 + as.factor(treatment.effect))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,1,0,1,0)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,-1,0)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =covariates,probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,0)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes.type + probes
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=NULL,max.probe.type.trt.factor=0,probe.trt.factor=NULL,max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list(),probe.trt.levels=list())
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes.type + probes with both within treatment factor
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,1)),strata=as.integer(c(0,0,0,2,2)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ ## PMMM ~ -1+ probes.type + probes with both within treatment factor and probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,1)),strata=as.integer(c(0,0,0,2,4)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ ## PMMM ~ -1+ probes.type + probes probe.types within treatment factor and probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,1)),strata=as.integer(c(0,0,0,2,3)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes.type + probes probe.types within samples and probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,1,1)),strata=as.integer(c(0,0,0,1,3)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ ## PMMM ~ intercept + probes.type + probes probe.types within samples and probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,0,0,1,1)),strata=as.integer(c(0,0,0,1,3)),constraints=as.integer(c(0,0,0,-1,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ intercept + probes probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,0,0,0,1)),strata=as.integer(c(0,0,0,0,3)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## PMMM ~ -1+ probes probes also within probe.type
+ output <- list(weights = TRUE, residuals = TRUE, varcov = c("none","chiplevel", "all"), resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,0,0,1)),strata=as.integer(c(0,0,0,0,3)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ # now play with varcov output
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ # now play with varcov output and treatment
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- model.matrix(~ -1 + as.factor(treatment.effect))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,1,0,0,0)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =covariates,probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ # now play with varcov output and an intercept
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,0,1,0,1)),strata=as.integer(c(0,0,0,0,0)),constraints=as.integer(c(0,0,-1,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=1,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ # now play with varcov output and treatment and intercept
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- matrix(model.matrix(~ as.factor(treatment.effect))[,2])
+ colnames(covariates) <- "trt_2"
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,1,0,0,0)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =covariates,probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ # now play with varcov all option output and treatment and intercept
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ treatment.effect <- c(1,1,2,2)
+
+ covariates <- matrix(model.matrix(~ as.factor(treatment.effect))[,2])
+ colnames(covariates) <- "trt_2"
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,1,0,0,0)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,0)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =covariates,probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ # now play with varcov all option output and samples and intercept
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(1,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,-1,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ # now play with varcov all option output and samples and intercept, MM covarite
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=1,response.variable=1,which.parameter.types=as.integer(c(1,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,-1,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+
+
+
+
+ ## now play with varcov all option output and samples and intercept, MM covariate and input chip weights
+ output <- verify.output.param(list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE))
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=c(1,1,0.5,0.5),weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ## now play with varcov all option output and samples and intercept, MM covariate and input chip weights
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=runif(201800))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=1,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=c(rep(c(1,0.5),c(201800,201800))))
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="cuberoot", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log10", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+
+ R.model <- list(mmorpm.covariate=0,response.variable=0,which.parameter.types=as.integer(c(0,0,1,0,1)),strata=as.integer(c(0,0,0,2,0)),constraints=as.integer(c(0,0,0,0,-1)),probe.type.trt.factor=as.integer(c(0,0,1,1)),max.probe.type.trt.factor=1,probe.trt.factor=as.integer(c(0,0,1,1)),max.probe.trt.factor=0,chipcovariates =matrix(0,0,0),probe.type.levels=list("blah"=c("A","B")),probe.trt.levels=list("blah"=c("A","B")))
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ }
>
>
>
> if (test.PLM.modelmatrix){
+
+ library(affyPLM);data(Dilution)
+
+ #PLM.designmatrix3(Dilution)
+
+ #PLM.designmatrix3(Dilution,model=MM ~ PM -1 + samples +probe.type:probes)
+
+ #PLM.designmatrix3(Dilution,model=MM ~ PM -1 + samples:probe.type + liver:probe.type:probes + liver:samples)
+ #PLM.designmatrix3(Dilution,model=MM ~ PM + samples:probe.type + liver:probe.type:probes + liver + samples)
+
+
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ #blah <- c(1,5,5,1)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ probes + blah,constraint.type=c(probes="contr.sum"))
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 + blah:probe.type)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 +probes:probe.type)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 +probes:blah)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 +probes:probe.type:blah)
+ #output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ # R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ samples,constraint.type=c(samples="contr.sum"))
+ # R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ blah)
+ # R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 + samples)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ probes + blah)
+ #R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ probes + blah)
+ #Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ library(affyPLM);data(Dilution)
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ probe.type + probe.type:probes + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ library(affyPLM);data(Dilution)
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ samples:probe.type + probe.type:probes + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="chiplevel", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ blah <- c(1,2,2)
+ R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ blah:probe.type + probe.type:probes + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ blah <- c(1,2,2)
+ R.model <- PLM.designmatrix3(Dilution,model=PM ~ -1 + probes + MM + blah)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+ output <- list(weights = TRUE, residuals = TRUE, varcov ="all", resid.SE = TRUE)
+ modelparam <- list(trans.fn="log2", se.type = 4, psi.type = 0, psi.k =1.345,max.its = 20, init.method = "ls",weights.chip=NULL,weights.probe=NULL)
+ blah <- c(1,2,2)
+ R.model <- PLM.designmatrix3(Dilution,model=PM ~ -1 + probes + MM + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+
+
+ #test some of the verification functions
+
+
+ output <- verify.output.param()
+ modelparam <- verify.model.param(Dilution,PM ~ -1 + probes + MM + samples)
+ R.model <- PLM.designmatrix3(Dilution,model=PM ~ -1 + probes + MM + samples)
+
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+ ##verify.model.param(Dilution,PM ~ -1 + probes + MM + samples,model.param=list(weights.probe=rep(1,10)))
+
+ modelparam <- verify.model.param(Dilution,PMMM ~ -1 + probes + samples,model.param=list(weights.chip=c(1,2,3),weights.probe=rep(1,2400*2)))
+ R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 + probes + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ modelparam <- verify.model.param(Dilution,PM ~ -1 + probes + samples,model.param=list())
+ R.model <- PLM.designmatrix3(Dilution,model=PM ~ -1 + probes + samples)
+ Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+ ## probes <- rep(1:16,3)
+ ## chips <- rep(1:3,c(16,16,16))
+
+ ## library(MASS)
+
+ ##fit <- rlm(log2(as.vector(pm(Dilution,"HG2188-HT2258_at"))) ~ -1 + as.factor(chips) + C(as.factor(probes),"contr.sum"))
+
+
+ #test creating a PLMset based on the output from rlm_PLMset
+
+ ### x <- new("PLMset")
+ ### x@chip.coefs=Fitresults[[1]]
+ ### x@probe.coefs= Fitresults[[2]]
+ ### x@weights=Fitresults[[3]]
+ ### x@se.chip.coefs=Fitresults[[4]]
+ ### x@se.probe.coefs=Fitresults[[5]]
+ ### x@exprs=Fitresults[[6]]
+ ### x@se.exprs=Fitresults[[7]]
+ ### x@residuals=Fitresults[[8]]
+ ### x@residualSE=Fitresults[[9]]
+ ### x@varcov = Fitresults[[10]]
+ ### x@cdfName = Dilution@cdfName
+ ### x@phenoData = Dilution@phenoData
+ ### x@annotation = Dilution@annotation
+ ### x@description = Dilution@description
+ ### x@notes = Dilution@notes
+ ### x@nrow= Dilution@nrow
+ ### x@ncol= Dilution@ncol
+ ### x@model.description = c(x@model.description, list(R.model=R.model))
+ ### image(x)
+
+
+
+
+ ### data(Dilution)
+ ### output <- verify.output.param()
+ ### modelparam <- verify.model.param(Dilution,PMMM ~ -1 + probe.type:probes + samples + samples:probe.type,model.param=list())
+ ### R.model <- PLM.designmatrix3(Dilution,model=PMMM ~ -1 + probe.type:probes + samples+ samples:probe.type)
+ ### Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+ ### output <- verify.output.param()
+ ### modelparam <- verify.model.param(Dilution,MM ~ -1 + probes + samples,model.param=list())
+ ### R.model <- PLM.designmatrix3(Dilution,model=MM ~ -1 + probes + samples)
+ ### Fitresults <- .Call("rlm_PLMset",pm(Dilution),mm(Dilution),probeNames(Dilution),length(geneNames(Dilution)),R.model,output,modelparam)
+
+
+
+ ### x <- new("PLMset")
+ ### x@chip.coefs=Fitresults[[1]]
+ ### x@probe.coefs= Fitresults[[2]]
+ ### x@weights=Fitresults[[3]]
+ ### x@se.chip.coefs=Fitresults[[4]]
+ ### x@se.probe.coefs=Fitresults[[5]]
+ ### x@exprs=Fitresults[[6]]
+ ### x@se.exprs=Fitresults[[7]]
+ ### x@residuals=Fitresults[[8]]
+ ### x@residualSE=Fitresults[[9]]
+ ### x@varcov = Fitresults[[10]]
+ ### x@cdfName = Dilution@cdfName
+ ### x@phenoData = Dilution@phenoData
+ ### x@annotation = Dilution@annotation
+ ### x@description = Dilution@description
+ ### x@notes = Dilution@notes
+ ### x@nrow= Dilution@nrow
+ ### x@ncol= Dilution@ncol
+ ### x@model.description = c(x@model.description, list(R.model=R.model))
+ ### image(x)
+ ### image(x,type="pos.resids")
+ ### image(x,type="neg.resids")
+ ### image(x,type="sign.resids")
+
+ ### resid(x,"1091_at")
+
+
+
+ ### weights(x,c("1091_at","1092_at"))
+
+
+ ### image(x,type="resids",standardize=TRUE)
+
+
+
+
+
+
+ }
>
>
>
>
>
> if (test.rlm){
+
+
+ library(affyPLM);data(Dilution)
+
+ y <- as.vector(log2(pm(Dilution)[1:16,]))
+
+ w <- runif(64)
+
+ probes <- rep(1:16,4)
+ samples <- rep(1:4,c(16,16,16,16))
+
+ x <- model.matrix( ~ -1 + as.factor(samples) + C(as.factor(probes),"contr.sum"))
+ x <- as.vector(x)
+
+ cols <- 19
+ rows <- 64
+
+
+ # rlm_wfit_R(double *x, double *y, double *w, int *rows, int *cols, double *out_beta, double *out_resids, double *out_weights)
+
+ fit1 <-.C("rlm_wfit_R",as.double(x),as.double(y),as.double(w),as.integer(rows),as.integer(cols),double(cols),double(rows),double(rows))
+
+
+ library(MASS)
+
+ fit2 <- rlm(y ~ -1 + as.factor(samples) + C(as.factor(probes),"contr.sum"),weights=w,wt.method="case")
+
+ if (any(abs(coef(fit2) - fit1[[6]]) > 10e-14)){
+ stop("Weighted RLM did not work")
+ }
+
+
+
+
+
+ y <- as.vector(log2(pm(Dilution,"1001_at")))
+ x <- as.vector(log2(mm(Dilution,"1001_at")))
+
+ rlm(y ~ -1 + x + as.factor(samples) + C(as.factor(probes),"contr.sum"))
+
+
+
+
+
+
+
+
+
+
+
+ }
>
>
>
>
> proc.time()
user system elapsed
1.186 0.040 1.214
affyPLM.Rcheck/tests/PLM_tests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> do.all.tests <- FALSE
> if (do.all.tests){
+
+ # this file tests fitPLM and the PLMset object
+
+ library(affyPLM)
+
+ library(affydata)
+ data(Dilution)
+
+
+ Pset <- fitPLM(Dilution)
+
+ #check accessors for parameters and se
+
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+ coefs.probe(Pset)[1:5]
+ se.probe(Pset)[1:5]
+ coefs.const(Pset)
+ se.const(Pset)
+
+ #accessors for weights and residuals
+
+ weights(Pset)[[1]][1:5,]
+ resid(Pset)[[1]][1:5,]
+
+
+ #test varcov
+
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,output.param=list(varcov="chiplevel"))
+ varcov(Pset)[1:3]
+
+
+ #test each of the possible weight functions
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Huber"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="fair"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Cauchy"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Geman-McClure"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Welsch"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Tukey"))
+ Pset <- fitPLM(Dilution,background=FALSE,normalize=FALSE,model.param=list(psi.type="Andrews"))
+
+ # a larger example to do some testing of the graphical functions
+
+ data(Dilution)
+
+ Pset <- fitPLM(Dilution)
+
+ #testing the image capabilities
+
+ image(Pset,which=2)
+ image(Pset,which=2,type="resids")
+ image(Pset,which=2,type="pos.resids")
+ image(Pset,which=2,type="neg.resids")
+ image(Pset,which=2,type="resids",use.log=FALSE,add.legend=TRUE)
+
+ boxplot(Pset)
+ Mbox(Pset)
+
+
+ #test some non-default models functions
+ # no preprocessing for speed
+
+ Pset <- fitPLM(Dilution, PM ~ -1 + probes + liver,background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+
+
+ Pset <- fitPLM(Dilution, PM ~ -1 + probes + liver + scanner,background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+
+ #checking the constraints
+ Pset <- fitPLM(Dilution, PM ~ -1 + probes + liver + scanner,constraint.type=c(default="contr.sum"),background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+
+ Pset <- fitPLM(Dilution, PM ~ -1 + liver + scanner,constraint.type=c(default="contr.sum"),background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+ coefs.probe(Pset) # should be empty
+
+ Pset <- fitPLM(Dilution, PM ~ -1 + liver + scanner,constraint.type=c(probes="contr.treatment"),background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+ coefs.probe(Pset) # should be empty
+
+
+ Pset <- fitPLM(Dilution, PM ~ -1 + probes + liver + scanner,constraint.type=c(probes="contr.treatment"),background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+ coefs.probe(Pset)[1:16]
+
+
+ scanner2 <- c(1,2,1,2)
+ Pset <- fitPLM(Dilution, PM ~ -1 + probes + liver + scanner2,constraint.type=c(probes="contr.sum"),background=FALSE,normalize=FALSE)
+ coefs(Pset)[1:5,]
+ se(Pset)[1:5,]
+ coefs.probe(Pset)[1:16]
+
+ #
+ #Pset <- fitPLM(Dilution,model=PM~-1+probes+scanner,normalize=FALSE,background=FALSE,model.param=list(se.type=3))
+ #se(Pset)[1:10,]
+
+ #check that fitPLM rlm agrees with threestep rlm and threestepPLM rlm
+
+
+ Pset <- fitPLM(Dilution)
+ eset <- threestep(Dilution,summary.method="rlm")
+ Pset2 <- threestepPLM(Dilution,summary.method="rlm")
+
+ if (any(abs(coefs(Pset) - exprs(eset)) > 1e-14)){
+ stop("no agreement between fitPLM and threestep")
+ }
+
+ if (any(abs(coefs(Pset) - coefs(Pset2)) > 1e-14)){
+ stop("no agreement between fitPLM and threestep")
+ }
+ }
>
> proc.time()
user system elapsed
0.173 0.021 0.183
affyPLM.Rcheck/tests/preprocess_tests.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> #test the preprocessing functionality
>
> library(affyPLM)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
> library(affydata)
Package LibPath Item
[1,] "affydata" "/home/biocbuild/bbs-3.17-bioc/R/site-library" "Dilution"
Title
[1,] "AffyBatch instance Dilution"
> data(Dilution)
>
>
> ### NO LONGER SUPPORTED eset <- threestep(Dilution,background.method="RMA.1")
> eset <- threestep(Dilution,background.method="RMA.2")
also installing the dependencies 'RSQLite', 'AnnotationDbi'
trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
ERROR: dependencies 'plogr', 'cpp11' are not available for package 'RSQLite'
* removing '/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/RSQLite'
ERROR: dependency 'RSQLite' is not available for package 'AnnotationDbi'
* removing '/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/AnnotationDbi'
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu95av2cdf'
* removing '/tmp/RtmpqviUpf/RLIBS_3103fd5f63a438/hgu95av2cdf'
The downloaded source packages are in
'/tmp/RtmpLdbMTi/downloaded_packages'
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Calls: threestep ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
In addition: Warning messages:
1: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'RSQLite' had non-zero exit status
2: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'AnnotationDbi' had non-zero exit status
3: In install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package 'hgu95av2cdf' had non-zero exit status
Execution halted
affyPLM.Rcheck/affyPLM-Ex.timings
| name | user | system | elapsed |