[GenABEL-dev] Problem when loading filevector files in current DatABEL on CRAN (?)

[L.C. Karssen]

Dear all,

I was trying to load a filevector/DatABEL file in R today using R 3.0.2
and DatABEL 0.9-4 (from CRAN). I tried several files (e.g. the ones
included in the ProbABEL examples directory) and always got the
following error:

library(DatABEL)
DatABEL v.0.9-4 (March 12, 2013) loaded

> databel("./mach1.dose.large")
uninames$unique.names = TRUE
uninames$unique.rownames = TRUE
uninames$unique.colnames = TRUE
backingfilename = ./mach1.dose.large
cachesizeMb = 64
number of columns (variables) =  5000
number of rows (observations) =  1320
usedRowIndex: 1  2  3  4  5  ...
usedColIndex: 1  2  3  4  5  6  7  8  9  10  ...
Upper-left 10 columns and  5 rows:
file contains data of unknown type 5
Error in !.Call("assignDoubleMatrix", from at data, newi, newj, ret,
as.integer(1)) :
  invalid argument type


After I checked out the latest version from SVN, built it (using the
makedistrib_DatABEL.sh script) and installed it (I gave it a fake 0.9-5
version number) I was able to read the file:

> library(DatABEL)
DatABEL v.0.9-5 (March 12, 2013) loaded

Installed DatABEL version (0.9-5) is not the same as stable
version available from CRAN (0.9-4). Unless used intentionally,
consider updating to the latest CRAN version. For that, use
'install.packages("DatABEL")', or ask your system administrator
to update the package.


> databel("./mach1.dose.large")
uninames$unique.names = TRUE
uninames$unique.rownames = TRUE
uninames$unique.colnames = TRUE
backingfilename = ./mach1.dose.large
cachesizeMb = 64
number of columns (variables) =  5000
number of rows (observations) =  1320
usedRowIndex: 1  2  3  4  5  ...
usedColIndex: 1  2  3  4  5  6  7  8  9  10  ...
Upper-left 10 columns and  5 rows:
    rs48146833818 rs60765062039 rs61390741602 rs14182581817 rs72744993535
id1         0.472         1.369         0.001         0.555         1.955
id2         1.983         1.992         1.984         1.985         1.999
id3         1.112         1.897         0.991         1.115         1.981
id4         0.307         1.523         0.001         0.330         1.960
id5         0.519         0.988         0.003         0.533         1.727
    rs61166101522 rs130430004482 rs60542571458 rs60866164126 rs60394033150
id1             2              2         0.064         0.789         0.427
id2             2              2         1.969         1.203         0.545
id3             2              2         1.002         0.868         0.442
id4             2              2         0.048         0.568         0.308
id5             2              2         0.161         1.092         0.939
>


Any reason why this happened? As far as I traced back in SVN I can see
that both Maksim and I made some changes in the DatABEL code in the past
few months, but they don't seem to be in relevant sections of the code.
Maybe this has to do with changes we made in filevector (fvlib)...

Anyway, can somebody else verify this? If so, we should upload a new
version to CRAN ASAP.


Thanks,

Lennart.


P.S. If this is indeed related to changes in fvlib it makes the changes
to the way we use fvlib Maksim, Yurii and I proposed earlier even more
urgent (see
http://lists.r-forge.r-project.org/pipermail/genabel-devel/2014-February/000958.html).
Looking forward to any comments you may have on that proposal as well!


-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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