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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPseqR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChIPseqR_1.61.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ChIPseqR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.61.0'
* 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 'ChIPseqR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 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 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 ... NOTE
.fixCounts: no visible global function definition for 'runLength'
.fixCounts: no visible global function definition for 'runValue'
getBindLen: no visible global function definition for 'window'
pickPeak: no visible global function definition for 'start'
pickPeak: no visible global function definition for 'runLength'
pickPeak : <anonymous>: no visible global function definition for
  'window'
[[,BindScore-ANY-numeric: no visible global function definition for
  'window'
decompress,Rle: no visible global function definition for 'runValue'
decompress,RleList : <anonymous>: no visible global function definition
  for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'Rle'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue<-'
plot,RLEReadCounts-missing : <anonymous>: no visible global function
  definition for 'window'
Undefined global functions or variables:
  Rle runLength runValue runValue<- start window
Consider adding
  importFrom("stats", "start", "window")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RLEBindScore-class.Rd: Rle-class
  RLEReadCounts-class.Rd: RleList-class
  compress-BindScore.Rd: Rle-class, RleList-class
  compress-ReadCounts.Rd: Rle-class, RleList-class
  exportBindSequence.Rd: XStringSet-class, XStringViews-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/ChIPseqR/libs/x64/ChIPseqR.dll':
  Found '_exit', possibly from '_exit' (C)
  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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
alignFeature       9.34   1.81   11.15
BindScore          7.25   0.09    7.36
RLEBindScore-class 6.01   0.17    6.18
simpleNucCall      5.77   0.24    6.00
callBindingSites   5.14   0.14    5.28
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ChIPseqR
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:22: warning: unused variable 'tmp_stat' [-Wunused-variable]
   66 |         double stat, tmp_stat;
      |                      ^~~~~~~~
gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs/x64
** R
** 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 (ChIPseqR)