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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhisat2_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Rhisat2.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhisat2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhisat2’ version ‘1.18.0’
* package encoding: UTF-8
* 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 ‘Rhisat2’ can be installed ... WARNING
Found the following significant warnings:
  ./gfm.h:1185:3: warning: 'auto_ptr<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
  ./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
  ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
  hisat2.cpp:1823:2: warning: 'auto_ptr<Presets>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3167:2: warning: 'auto_ptr<PatternSourcePerThreadFactory>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3168:2: warning: 'auto_ptr<PatternSourcePerThread>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3189:2: warning: 'auto_ptr<Mapq>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:4035:9: warning: 'auto_ptr<BitPairReference>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/Rhisat2.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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Rhisat2.Rcheck/00check.log’
for details.