[BioC] DNAcopy installation error
Martin Morgan
mtmorgan at fhcrc.org
Fri Feb 26 18:10:00 CET 2010
On 02/26/2010 08:33 AM, seth redmond wrote:
> I'm running into lots of errors when I try to install DNAcopy and the
> errors aren't suggesting anything obvious to me... This is DNAcopy 1.20
> and R v2.10. Any ideas what I might be doing wrong?
>
> (errors below)
>
> -s
>
>
> * install options are ' --no-html'
>
> * installing *source* package 'DNAcopy' ...
> ** libs
> g77 -fPIC -g -c cbsWtstats.f -o cbsWtstats.o
> cbsWtstats.f: In subroutine `wtmaxo':
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
Hi Seth --
I think this is because g77 is an old compiler, and DNAcopy is using
fortran 90 conventions; the easiest solution is likely to update your
compilers (to a gcc that includes gfortran) and then to start from
scratch with R -- recompiling R and reinstalling all packages.
That's my best bet, but since it represents a fair amount of work it
might pay to wait for other insights or to ask (with a subject like 'g77
invalid type-declaration') on the R-devel mailing list.
Martin
> ^
> Invalid type-declaration attribute at (^) -- must be one of:
> DIMENSION(array-spec), EXTERNAL, INTRINSIC, PARAMETER, or SAVE
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Invalid type-declaration attribute at (^) -- must be one of:
> DIMENSION(array-spec), EXTERNAL, INTRINSIC, PARAMETER, or SAVE
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Invalid type-declaration attribute at (^) -- must be one of:
> DIMENSION(array-spec), EXTERNAL, INTRINSIC, PARAMETER, or SAVE
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Invalid type-declaration attribute at (^) -- must be one of:
> DIMENSION(array-spec), EXTERNAL, INTRINSIC, PARAMETER, or SAVE
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> ^
> Expression at (^) has incorrect data type or rank for its context
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bpsmax' at (2) [initially
> seen at (1)]
> cbsWtstats.f:24:
> double precision, allocatable :: bpsmax(:), bpsmin(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bpsmin' at (2) [initially
> seen at (1)]
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bb' at (2) [initially
> seen at (1)]
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `ibmin' at (2) [initially
> seen at (1)]
> cbsWtstats.f:26:
> integer, allocatable :: bb(:), ibmin(:), ibmax(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `ibmax' at (2) [initially
> seen at (1)]
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bssbij' at (2) [initially
> seen at (1)]
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bssijmax' at (2)
> [initially seen at (1)]
> cbsWtstats.f:29:
> double precision, allocatable :: bssbij(:), bssijmax(:), awt(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `awt' at (2) [initially
> seen at (1)]
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `bloci' at (2) [initially
> seen at (1)]
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `blocj' at (2) [initially
> seen at (1)]
> cbsWtstats.f:31:
> integer, allocatable :: bloci(:), blocj(:), loc(:)
> 1
> cbsWtstats.f:34: (continued):
> rn = dfloat(n)
> 2
> Invalid declaration of or reference to symbol `loc' at (2) [initially
> seen at (1)]
> cbsWtstats.f:44:
> allocate(bpsmax(nb), bpsmin(nb))
> ^
> Invalid declaration of or reference to symbol `allocate' at (^)
> [initially seen at (^)]
> cbsWtstats.f:44:
> allocate(bpsmax(nb), bpsmin(nb))
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:45:
> allocate(bb(nb), ibmin(nb), ibmax(nb))
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:46:
> allocate(bssbij(nb2), bssijmax(nb2), awt(nb2))
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:47:
> allocate(bloci(nb2), blocj(nb2), loc(nb2))
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:278:
> deallocate(bpsmax, bpsmin, bb, ibmin, ibmax)
> ^
> Invalid declaration of or reference to symbol `deallocate' at (^)
> [initially seen at (^)]
> cbsWtstats.f:278:
> deallocate(bpsmax, bpsmin, bb, ibmin, ibmax)
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:279:
> deallocate(bssbij, bssijmax, bloci, blocj, loc, awt)
> ^
> Invalid form for assignment statement at (^)
> cbsWtstats.f:93: confused by earlier errors, bailing out
> make: *** [cbsWtstats.o] Error 1
> ERROR: compilation failed for package 'DNAcopy'
> * removing '/home/snr02/work/R/DNAcopy.Rcheck/DNAcopy'
>
>
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
More information about the Bioconductor
mailing list