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(:) ^ 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' -- Seth Redmond Scientific Programmer, VectorBase Kafatos / Christophides Groups Div. Cell and Molecular Biology Imperial College, London seth.redmond at imperial.ac.uk --

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