##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multtest.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings multtest_2.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/multtest.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'multtest/DESCRIPTION' ... OK
* this is package 'multtest' version '2.58.0'
* 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 'multtest' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* checking installed package size ... OK
* checking package 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'multtest/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

EBMTP: no visible global function definition for 'makeCluster'
EBMTP: no visible global function definition for 'clusterEvalQ'
EBMTP: no visible global function definition for 'stopCluster'
MTP: no visible global function definition for 'makeCluster'
MTP: no visible global function definition for 'clusterEvalQ'
MTP: no visible global function definition for 'stopCluster'
boot.null: no visible global function definition for 'clusterApply'
boot.null: no visible global function definition for 'clusterApplyLB'
EBupdate,EBMTP: no visible binding for global variable 'y'
update,MTP: no visible binding for global variable 'y'
Undefined global functions or variables:
  clusterApply clusterApplyLB clusterEvalQ makeCluster stopCluster y
* checking Rd files ... NOTE
checkRd: (-1) mt.maxT.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) mt.maxT.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) mt.plot.Rd:37: Escaped LaTeX specials: \#
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'EBMTP,ANY,ANY,ANY'
  generic '[' and siglist 'MTP,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.18-bioc/R/library/multtest/libs/x64/multtest.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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'MTP.pdf' 'MTP.tex' 'MTPALL.pdf' 'golub.R' 'multtest.bib'
  'multtest.pdf'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/multtest.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL multtest
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'multtest' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rpack.c -o Rpack.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c VScount.c -o VScount.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bootloop.c -o bootloop.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mt.c -o mt.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairt_sampling.c -o pairt_sampling.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c random.c -o random.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sampling.c -o sampling.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sampling_fixed.c -o sampling_fixed.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stat_func.c -o stat_func.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stat_order.c -o stat_order.o
gcc -shared -s -static-libgcc -o multtest.dll tmp.def Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-multtest/00new/multtest/libs/x64
** R
** data
** 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 (multtest)