[GenABEL-dev] GenABEL: Installation/load error on Unix, MAC and Windows...

[Maria G]

On MAC I can see (if installing from R) that it tries to install the version "GenABEL_1.7-0.tgz", but not "GenABEL_1.7-3.tgz":

> install.packages("GenABEL")
Installing package(s) into '/Network/Servers/isd08a58.isd.med.uni-muenchen.de/Volumes/Homefolder/mgonik/Library/R/2.14/library'
(as 'lib' is unspecified)
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.14/GenABEL_1.7-0.tgz'
Content type 'application/x-gzip' length 6901675 bytes (6.6 Mb)
opened URL
==================================================
downloaded 6.6 Mb


The downloaded packages are in
	/var/folders/cb/vz9n6ftn7t19t0xwyz2wydsh000107/T//RtmpBPDzFq/downloaded_packages
> library(GenABEL)
Error in get(Info[i, 1], envir = env) : 
  internal error -3 in R_decompress1
Error: package/namespace load failed for 'GenABEL'



10.01.2013, 19:47, "L.C. Karssen" <lennart at karssen.org>:
> Dear Maria,
>
> On 01/10/2013 04:41 PM, Maria G wrote:
>
>>  Dear Lennart,
>>
>>  I don't see 1.7-3 version for MAC (which I use) here:
>>  http://cran.at.r-project.org/web/packages/GenABEL/index.html
>
> You're right... That's strange.
> Yurii, you have a Mac, do you know why it is lagging on Macs?
>
> Best,
>
> Lennart.
>
>>  best
>>  Maria
>>
>>  10.01.2013, 19:37, "L.C. Karssen" <lennart at karssen.org>:
>>>  Dear both,
>>>
>>>  Yesterday evening Yurii uploaded GenABEL v1.7-3 to CRAN. I installed it
>>>  on our servers this morning but be careful with your choice of download
>>>  mirror. I used the Dutch one at first, but that one still had the older
>>>  version. The US mirror had the latest version.
>>>
>>>  Lennart.
>>>
>>>  On 01/10/2013 04:08 PM, Maria G wrote:
>>>>   Thanks a lot, Nicola!!
>>>>
>>>>   Don't you mind if I copy your answer to the Forum?
>>>>   or may be you would like to publish the answer there from your personal name?
>>>>
>>>>   best
>>>>   Maria
>>>>
>>>>   10.01.2013, 19:06, "Nicola Pirastu" <pirastu at burlo.trieste.it>:
>>>>>   Hi Maria,
>>>>>
>>>>>   the problem was addressed a few days ago and I think it will be fixed permanently in the next release.
>>>>>
>>>>>   Meanwhile it is possible to go around it by adding a few lines in the file /GenABEL/R/checkPackageVersionOnCRAN.R
>>>>>
>>>>>   this is how it looks like now:
>>>>>
>>>>>           stringSplit <- strsplit(targetLine,splitPattern)
>>>>>           cranVersion <- stringSplit[[1]][length(stringSplit[[1]])-1]
>>>>>
>>>>>   and this is the how I personally fixed it:
>>>>>
>>>>>        stringSplit <- strsplit(targetLine,splitPattern)
>>>>>
>>>>>         if(length(stringSplit)>0){
>>>>>
>>>>>           cranVersion <- stringSplit[[1]][length(stringSplit[[1]])-1]
>>>>>
>>>>>           }else{
>>>>>                   cranVersion <- "1.7-2"
>>>>>         }
>>>>>
>>>>>   Basically for some reason it does not catch the version number from CRAN which was not supposed to happen, so I just added a check.
>>>>>
>>>>>   What you have to do is:
>>>>>
>>>>>   1) uncompress the GenABEL tar
>>>>>
>>>>>   2) open the /GenABEL/R/checkPackageVersionOnCRAN.R file
>>>>>
>>>>>   3) add the two lines
>>>>>
>>>>>   4) save and reinstall the GenABEL package.
>>>>>
>>>>>   This worked at least for me. I'm sure someone figured out something more elegant, but this is an easy work around.
>>>>>
>>>>>   Hope it helps.
>>>>>
>>>>>   Nicola
>>>>>
>>>>>   Il giorno 10/gen/2013, alle ore 15:56, Maria G <mgmaria at yandex.ru> ha scritto:
>>>>>>    Dear maintainers,
>>>>>>
>>>>>>    I would like to attract your attention to recently arised problem with loading GenABEL under any version of OS.
>>>>>>
>>>>>>    Please, have a look at the Forum here:
>>>>>>
>>>>>>    http://forum.genabel.org/viewtopic.php?f=6&t=733&p=1332#p1332
>>>>>>
>>>>>>    Hope to get good news from you soon
>>>>>>
>>>>>>    best
>>>>>>
>>>>>>    Maria
>>>>>>
>>>>>>    _______________________________________________
>>>>>>    genabel-devel mailing list
>>>>>>    genabel-devel at lists.r-forge.r-project.org
>>>>>>    https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>  --
>>>  -----------------------------------------------------------------
>>>  L.C. Karssen
>>>  Utrecht
>>>  The Netherlands
>>>
>>>  lennart at karssen.org
>>>  http://blog.karssen.org
>>>
>>>  Stuur mij aub geen Word of Powerpoint bestanden!
>>>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>  ------------------------------------------------------------------
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------