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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASEB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASEB_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ASEB.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASEB/DESCRIPTION’ ... OK
* this is package ‘ASEB’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ASEB’ can be installed ... WARNING
Found the following significant warnings:
  asebC.cpp:422:4: warning: 'random_shuffle<std::__wrap_iter<int *>>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/ASEB.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
SequenceInfo: no visible global function definition for ‘new’
drawEScurve,data.frame: no visible global function definition for ‘pdf’
drawEScurve,data.frame: no visible global function definition for
  ‘jpeg’
drawEScurve,data.frame: no visible global function definition for
  ‘lines’
drawEScurve,data.frame: no visible global function definition for ‘rgb’
drawEScurve,data.frame: no visible global function definition for
  ‘dev.off’
drawStat,data.frame: no visible global function definition for ‘pdf’
drawStat,data.frame: no visible global function definition for ‘jpeg’
drawStat,data.frame: no visible global function definition for ‘lines’
drawStat,data.frame: no visible global function definition for
  ‘dev.off’
ids,SequenceInfo: no visible global function definition for ‘slot’
ids<-,SequenceInfo-character: no visible global function definition for
  ‘slot<-’
sequences,SequenceInfo: no visible global function definition for
  ‘slot’
sequences<-,SequenceInfo-character: no visible global function
  definition for ‘slot<-’
show,SequenceInfo: no visible global function definition for ‘show’
Undefined global functions or variables:
  dev.off jpeg lines new pdf rgb show slot slot<-
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "rgb")
  importFrom("graphics", "lines")
  importFrom("methods", "new", "show", "slot", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ASEB/libs/ASEB.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

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 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/ASEB.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ASEB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ASEB’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c asebC.cpp -o asebC.o
asebC.cpp:422:4: warning: 'random_shuffle<std::__wrap_iter<int *>>' is deprecated [-Wdeprecated-declarations]
   random_shuffle(indexes.begin(), indexes.end());  // 2022/01/27
   ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<int *>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ASEB.so asebC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-ASEB/00new/ASEB/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ASEB)