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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rdisop_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Rdisop.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 ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.58.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rdisop’ can be installed ... WARNING
Found the following significant warnings:
  ./imslib/src/ims/composedelement.h:204:58: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: 'auto_ptr<ims::IntegerMassDecomposer<>>' is deprecated [-Wdeprecated-declarations]
  disop.cpp:325:6: warning: 'bind2nd<std::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:26:7: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:28:17: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:30:17: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:116:73: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:33:21: warning: 'bind2nd<std::equal_to<std::string>, std::string>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:34:8: warning: 'mem_fun_ref<const std::string &, ims::Element>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:74:11: warning: 'mem_fun_ref<const std::string &, ims::Element>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:75:11: warning: 'mem_fun_ref<const std::string &, ims::Element>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/matchmatrix.h:61:7: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/matchmatrix.h:65:7: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: 'auto_ptr<std::map<int, int>>' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/decomp/realmassdecomposer.cpp:21:20: warning: 'auto_ptr<ims::IntegerMassDecomposer<>>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/Rdisop.Rcheck/00install.out’ for details.
* 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 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 ... OK
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rdisop/libs/Rdisop.so’:
  Found ‘_rand’, possibly from ‘rand’ (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 ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/Rdisop.Rcheck/00check.log’
for details.