##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ADaCGH2.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ADaCGH2_2.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ADaCGH2.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '2.38.0'
* 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 'ADaCGH2' 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 ... 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 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/ADaCGH2/libs/x64/ADaCGH2.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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
pChromPlot         27.03   0.06   27.13
pSegment           23.34   0.02   23.36
outputToCGHregions 13.17   0.03   13.25
inputToADaCGH       6.42   0.05    6.49
* 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 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ADaCGH2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'ADaCGH2' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
   65 |     double totalNorm;
      |            ^~~~~~~~~
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
  152 |       }/* for j */
      |         
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
  176 |       }/* for j */
      |         
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
  128 |   int k,j;
      |         ^
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
   97 |             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |             lowWeightSum += weight[k-1] - weight[lowEnd];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:99:27: warning: 'highWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
   99 |             highWeightSum += weight[highEnd] - weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
   96 |             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-ADaCGH2/00new/ADaCGH2/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 (ADaCGH2)