CRAN Package Check Results for Maintainer ‘Simon Penel <simon.penel at univ-lyon1.fr>’

Last updated on 2015-02-05 23:51:05.

Package ERROR WARN NOTE OK
ade4 1 14
seqinr 6 9

Package ade4

Current CRAN status: WARN: 1, NOTE: 14

Version: 1.6-2
Check: installed package size
Result: NOTE
     installed size is 5.4Mb
     sub-directories of 1Mb or more:
     data 1.5Mb
     pictures 2.1Mb
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.6-2
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘MASS’ ‘pixmap’ ‘spdep’ ‘splancs’ ‘waveslim’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 1.6-2
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     kplot.sepan.coa
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 1.6-2
Check: R code for possible problems
Result: NOTE
    prep.mdpcoa : fun1: no visible global function definition for
     ‘dist.dna’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.6-2
Check: compiled code
Result: NOTE
    File ‘ade4/libs/ade4.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘adesub.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘adesub.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 1.6-2
Check: compiled code
Result: NOTE
    File ‘ade4/libs/ade4.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Object: ‘adesub.o’
     Found ‘_srand’, possibly from ‘srand’ (C)
     Object: ‘adesub.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks

Version: 1.6-2
Check: compiled code
Result: NOTE
    File 'ade4/libs/i386/ade4.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'adesub.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'adesub.o'
    File 'ade4/libs/x64/ade4.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'adesub.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'adesub.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64

Version: 1.6-2
Check: compiled code
Result: NOTE
    File ‘ade4/libs/ade4.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘adesub.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘adesub.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-linux-x86_64

Version: 1.6-2
Check: examples
Result: WARN
    checking a package with encoding 'UTF-8' in an ASCII locale
    
     OK
Flavor: r-release-osx-x86_64-snowleopard

Version: 1.6-2
Check: compiled code
Result: NOTE
    File 'ade4/libs/i386/ade4.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'adesub.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'adesub.o'
    File 'ade4/libs/x64/ade4.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'adesub.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'adesub.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-release-windows-ix86+x86_64

Package seqinr

Current CRAN status: NOTE: 6, OK: 9

Version: 3.1-3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘segmented’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 3.1-3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.matrix.alignment getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA
     getAnnot.SeqFastadna getAnnot.default getAnnot.list getAnnot.logical
     getAnnot.qaw getFrag.SeqAcnucWeb getFrag.SeqFastaAA
     getFrag.SeqFastadna getFrag.SeqFrag getFrag.character getFrag.default
     getFrag.list getFrag.logical getFrag.qaw getKeyword.SeqAcnucWeb
     getKeyword.default getKeyword.list getKeyword.logical getKeyword.qaw
     getLength.SeqAcnucWeb getLength.SeqFastaAA getLength.SeqFastadna
     getLength.SeqFrag getLength.character getLength.default
     getLength.list getLength.logical getLength.qaw
     getLocation.SeqAcnucWeb getLocation.default getLocation.list
     getLocation.logical getLocation.qaw getName.SeqAcnucWeb
     getName.SeqFastaAA getName.SeqFastadna getName.SeqFrag
     getName.default getName.list getName.logical getName.qaw
     getSequence.SeqAcnucWeb getSequence.SeqFastaAA
     getSequence.SeqFastadna getSequence.SeqFrag getSequence.character
     getSequence.default getSequence.list getSequence.logical
     getSequence.qaw getTrans.SeqAcnucWeb getTrans.SeqFastadna
     getTrans.SeqFrag getTrans.character getTrans.default getTrans.list
     getTrans.logical getTrans.qaw plot.SeqAcnucWeb print.SeqAcnucWeb
     print.qaw summary.SeqFastaAA summary.SeqFastadna
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 3.1-3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA getAnnot.SeqFastadna
     getAnnot.default getAnnot.list getAnnot.logical getAnnot.qaw
     getFrag.SeqAcnucWeb getFrag.SeqFastaAA getFrag.SeqFastadna
     getFrag.SeqFrag getFrag.character getFrag.default getFrag.list
     getFrag.logical getFrag.qaw getKeyword.SeqAcnucWeb getKeyword.default
     getKeyword.list getKeyword.logical getKeyword.qaw
     getLength.SeqAcnucWeb getLength.SeqFastaAA getLength.SeqFastadna
     getLength.SeqFrag getLength.character getLength.default
     getLength.list getLength.logical getLength.qaw
     getLocation.SeqAcnucWeb getLocation.default getLocation.list
     getLocation.logical getLocation.qaw getName.SeqAcnucWeb
     getName.SeqFastaAA getName.SeqFastadna getName.SeqFrag
     getName.default getName.list getName.logical getName.qaw
     getSequence.SeqAcnucWeb getSequence.SeqFastaAA
     getSequence.SeqFastadna getSequence.SeqFrag getSequence.character
     getSequence.default getSequence.list getSequence.logical
     getSequence.qaw getTrans.SeqAcnucWeb getTrans.SeqFastadna
     getTrans.SeqFrag getTrans.character getTrans.default getTrans.list
     getTrans.logical getTrans.qaw as.matrix.alignment print.SeqAcnucWeb
     print.qaw summary.SeqFastaAA summary.SeqFastadna plot.SeqAcnucWeb
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-linux-x86_64-debian-gcc