##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACME.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ACME_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ACME.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.48.0'
* 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:58:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  windowChisq.c:86:20: warning: initialization of 'void * (*)()' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ACME.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 30.9Mb
  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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ACME/libs/i386/ACME.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ACME/libs/x64/ACME.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
read.resultsGFF 4.22   0.03    5.80
findClosestGene 1.83   0.17    8.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
write.bedGraph 3.51   0.09    6.39
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ACME.Rcheck/00check.log'
for details.