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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maanova.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings maanova_1.65.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/maanova.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maanova/DESCRIPTION' ... OK
* this is package 'maanova' version '1.65.0'
* 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 'maanova' can be installed ... OK
* 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 ... NOTE
'library' or 'require' calls in package code:
  'qvalue' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.consensus.hc plot.consensus.kmean print.madata
  print.summary.madata print.summary.mamodel subset.madata
  summary.madata summary.mamodel transform.madata transform.rawdata
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fdr: no visible global function definition for 'qvalue'
matest: no visible global function definition for 'makeMPIcluster'
matest: no visible global function definition for 'clusterApply'
matest: no visible global function definition for 'clusterEvalQ'
matest: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApply clusterEvalQ makeMPIcluster qvalue stopCluster
* 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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/maanova/libs/x64/maanova.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. 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' ... OK
* checking examples ... 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/maanova.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL maanova
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'maanova' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c makeratio.c -o makeratio.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
  /* work on a copy of x */
   
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
 /*#ifndef IEEE_754
  
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
     /* work on a copy of x */
      
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
   int i, j, k;
             ^
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c util.c -o util.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maanova.dll tmp.def makeratio.o masvd.o shift.o util.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-maanova/00new/maanova/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maanova'
    finding HTML links ... done
    PairContrast                            html  
    Rmaanova.version                        html  
    abf1                                    html  
    adjPval                                 html  
    arrayview                               html  
    consensus                               html  
    dyeswapfilter                           html  
    fill.missing                            html  
    fitmaanova                              html  
    fom                                     html  
    geneprofile                             html  
    gridcheck                               html  
    kidney                                  html  
    maanova-internal                        html  
    macluster                               html  
    matest                                  html  
    read.madata                             html  
    resiplot                                html  
    riplot                                  html  
    subset.madata                           html  
    summarytable                            html  
    transform.madata                        html  
    varplot                                 html  
    volcano                                 html  
    write.madata                            html  
** 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 (maanova)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'maigesPack' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'metabomxtr' is missing or broken
 done