##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multtest_2.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multtest.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.62.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘multtest’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 code 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 whether 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 ... NOTE
Documented arguments not in \usage in Rd file 'boot.null.Rd':
  ‘csnull’

Documented arguments not in \usage in Rd file 'meanX.Rd':
  ‘surv.object’
Objects in \usage without \alias in Rd file 'meanX.Rd':
  ‘corr.Tn’

Assignments in \usage in Rd file 'mt.internal.Rd':
  mt.niceres <- function(res, X, index) mt.legend(x, y = NULL, 
      legend, fill = NULL, col = "black", lty, lwd, pch, angle = 45, 
      density = NULL, bty = "o", bg = par("bg"), pt.bg = NA, cex = 1, 
      pt.cex = cex, pt.lwd = lwd, xjust = 0, yjust = 1, x.intersp = 1, 
      y.intersp = 1, adj = c(0, 0.5), text.width = NULL, text.col = par("col"), 
      merge = do.lines && has.pch, trace = FALSE, plot = TRUE, 
      ncol = 1, horiz = FALSE, ...)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/multtest/libs/multtest.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

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 package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/multtest.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL multtest
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c Rpack.c -o Rpack.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c VScount.c -o VScount.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c bootloop.c -o bootloop.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c mt.c -o mt.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c pairt_sampling.c -o pairt_sampling.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c sampling_fixed.c -o sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c stat_func.c -o stat_func.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -Wall -c stat_order.c -o stat_order.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o multtest.so 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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-multtest/00new/multtest/libs
** 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
** 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 (multtest)