##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings seqbias_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.50.0’
* 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 ‘seqbias’ can be installed ... WARNING
Found the following significant warnings:
  ./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:29:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:33:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:34:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:24:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:59:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:60:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:84:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:51:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:71:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/iterator.cpp:11:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:54:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:148:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:150:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:166:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:168:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/nodeownership.cpp:18:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/singledocparser.h:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:237:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:284:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
* 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
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for ‘is’
count.reads : <anonymous>: no visible global function definition for
  ‘seqnames’
count.reads : <anonymous>: no visible global function definition for
  ‘start’
count.reads : <anonymous>: no visible global function definition for
  ‘end’
count.reads : <anonymous>: no visible global function definition for
  ‘strand’
random.intervals: no visible global function definition for ‘is’
random.intervals : uniform_ints : <anonymous>: no visible global
  function definition for ‘runif’
random.intervals: no visible global function definition for ‘GRanges’
random.intervals: no visible global function definition for ‘IRanges’
seqbias.fit: no visible global function definition for ‘new’
seqbias.load: no visible global function definition for ‘new’
seqbias.predict: no visible global function definition for ‘is’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘seqnames’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘start’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘end’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘strand’
Undefined global functions or variables:
  GRanges IRanges end is new runif seqnames start strand
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "runif", "start")
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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/seqbias/libs/seqbias.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 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 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: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck/00check.log’
for details.