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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyPLM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings affyPLM_1.75.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/affyPLM.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.75.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'affyPLM' can be installed ... WARNING
Found the following significant warnings:
  rlm_PLM.c:870:32: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
  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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/affyPLM.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/affyPLM/libs/x64/affyPLM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* 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: threestep
> ### Title: Three Step expression measures
> ### Aliases: threestep
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+ 
+   # should be equivalent to rma()
+   eset <- threestep(Dilution)
+ 
+   # Using Tukey Biweight summarization
+   eset <- threestep(Dilution, summary.method="tukey.biweight")
+ 
+   # Using Average Log2 summarization
+   eset <- threestep(Dilution, summary.method="average.log")
+ 
+   # Using IdealMismatch background and Tukey Biweight and no normalization.
+   eset <- threestep(Dilution, normalize=FALSE,background.method="IdealMM",
+                     summary.method="tukey.biweight")
+ 
+   # Using average.log summarization and no background or normalization.
+   eset <- threestep(Dilution, background=FALSE, normalize=FALSE,
+                     background.method="IdealMM",summary.method="tukey.biweight")
+ 
+   # Use threestep methodology with the rlm model fit
+   eset <- threestep(Dilution, summary.method="rlm")
+ 
+   # Use threestep methodology with the log of the average
+   eset <- threestep(Dilution, summary.method="log.average")
+ 
+   # Use threestep methodology with log 2nd largest method
+   eset <- threestep(Dilution, summary.method="log.2nd.largest")
+ 
+   eset <- threestep(Dilution, background.method="LESN2")
+ }
Loading required package: affydata
Error in threestep(Dilution, summary.method = "log.average") : 
  'R_Calloc' could not allocate memory (562812514467904 of 8 bytes)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'C_code_tests.R'
  Running 'PLM_tests.R'
  Running 'preprocess_tests.R'
  Running 'threestepPLM_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/affyPLM.Rcheck/00check.log'
for details.