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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ACME.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ACME_2.60.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ACME.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.60.0'
* 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 'ACME' can be installed ... WARNING
Found the following significant warnings:
  windowChisq.c:58:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  windowChisq.c:63:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  windowChisq.c:86:20: warning: initialization of 'void * (*)(void)' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
See 'F:/biocbuild/bbs-3.19-bioc/meat/ACME.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 30.8Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata  27.3Mb
* 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
.plotACMECalcSet: no visible global function definition for 'par'
.plotACMECalcSet: no visible global function definition for 'axis'
.plotACMECalcSet: no visible global function definition for 'abline'
.plotACMESet: no visible global function definition for 'par'
do.aGFF.calc: no visible global function definition for 'quantile'
findClosestGene: no visible binding for global variable 'refflat'
findClosestGene: no visible binding for '<<-' assignment to 'refflat'
findRegions : <anonymous>: no visible global function definition for
  'median'
getRefflat: no visible global function definition for 'download.file'
getRefflat: no visible global function definition for 'read.delim'
plotgff: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'par'
plotgffcalc: no visible global function definition for 'axis'
plotgffcalc: no visible global function definition for 'abline'
read.resultsGFF: no visible global function definition for 'read.delim'
windowChisq: no visible global function definition for 'pchisq'
write.bedGraph: no visible global function definition for 'write.table'
write.sgr: no visible global function definition for 'write.table'
plot,ACMECalcSet: no visible global function definition for 'par'
plot,ACMECalcSet: no visible global function definition for 'axis'
plot,ACMECalcSet: no visible global function definition for 'abline'
plot,ACMESet: no visible global function definition for 'par'
plot,aGFF: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'par'
plot,aGFFCalc: no visible global function definition for 'axis'
plot,aGFFCalc: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis download.file median par pchisq quantile read.delim
  refflat write.table
Consider adding
  importFrom("graphics", "abline", "axis", "par")
  importFrom("stats", "median", "pchisq", "quantile")
  importFrom("utils", "download.file", "read.delim", "write.table")
to your NAMESPACE file.
* 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-3.19-bioc/R/library/ACME/libs/x64/ACME.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
read.resultsGFF 4.39   0.34   40.11
* 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: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/ACME.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ACME
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'ACME' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c windowChisq.c -o windowChisq.o
windowChisq.c: In function 'windowChisq':
windowChisq.c:58:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   58 |           firstprobe>0) {
      |           ~~~~~~~~~~^~
windowChisq.c:63:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   63 |           lastprobe<(na-1)) {
      |           ~~~~~~~~~^~~~~~~
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
   21 |   double *xa,*xlocations,*xchivals;
      |           ^~
windowChisq.c: At top level:
windowChisq.c:86:20: warning: initialization of 'void * (*)(void)' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
   86 |     {"windowChisq",&windowChisq,5},
      |                    ^
windowChisq.c:86:20: note: (near initialization for 'callMethods[0].fun')
gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-ACME/00new/ACME/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 (ACME)