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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:muscle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings muscle_3.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘muscle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscle’ version ‘3.48.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘muscle’ can be installed ... WARNING
Found the following significant warnings:
  alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
  clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
  msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
  objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
  objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
  params.cpp:445:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
  profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/muscle/libs/muscle.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_vsprintf’, possibly from ‘vsprintf’ (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 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 ... 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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/muscle.Rcheck/00check.log’
for details.