[BioC] Problem while installing \"org.At.tair.db\" and \"ath1121501.db\"

Tue Feb 7 16:37:23 CET 2012

Hi Sean,

Thanks for this. I am facing some difficulties while posting my response. Sometimes it tells my query is greater than 80 chars or avoid top posting. Sorry about this. 

Can I just write it here. 

Hi Sean,

Thanks for your help. I just managed to sort out few things. 
Now the problem is only with the installation of org.At.tair.db.
It gives me the following errors.
It will be helpful if you could give me some clue.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'org.At.tair.db',
 details:
 call: sqliteExecStatement(con, statement, bind.data)
 error: RS-DBI driver: (error in statement: database is locked)
ERROR: loading failed
* removing ‘/home/reetu/R/x86_64-redhat-linux-gnu-library/2.11/
org.At.tair.db’

The downloaded packages are in
	‘/tmp/Rtmpjh4uP8/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'org.At.tair.db' had non-zero exit status

Many thanks for your help.

RT

________________________________________
From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
Sent: Tuesday, February 07, 2012 2:44 PM
To: TUTEJA, REETU
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Problem while installing \"org.At.tair.db\" and \"ath1121501.db\"

On Tue, Feb 7, 2012 at 9:16 AM, TUTEJA, REETU <R.TUTEJA1 at nuigalway.ie> wrote:
> Hi Sean,
>
> Thanks for your response. I have not deleted any file. I thought problem is somewhere with the directory. I tired to change permissions but still not working. Installation of other R packages uses the same directory. I cant figure it out where the problem is.
>
> ERROR: failed to lock directory
>> /home/XXX/R/x86_64-redhat-linux-gnu-library/2.11 for modifying
>> Try removing /home/XXX/R/x86_64-redhat-linux-gnu-library/2.11/00LOCK

Hi, Reetu.  It is a good idea to keep the discussions on the list.

The error message is telling you how to fix the problem.  Please
follow the instructions noted above and then let us know if you have
further problems.

Sean

> Just one more thing, I successfully installed the same package on master node. Can you provide some hint about this.
>
> Thanks,
> Reetu
>
> ________________________________________
> From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
> Sent: Tuesday, February 07, 2012 1:06 PM
> To: Reetu [guest]
> Cc: bioconductor at r-project.org; TUTEJA, REETU
> Subject: Re: [BioC] Problem while installing \"org.At.tair.db\" and \"ath1121501.db\"
>
> On Tue, Feb 7, 2012 at 8:03 AM, Reetu [guest] <guest at bioconductor.org> wrote:
>>
>> Hi All,
>>
>> I am trying to install "org.At.tair.db" and "ath1121501.db" packages on working
>> node of my server and getting the following problems. Except these two packages
>> I successfully installed few other packages from R on the same node. I am not
>> getting where exactly the problem is. Can someone please help.
>>
>> Thanks,
>> RT
>>
>>  -- output of sessionInfo():
>>
>> Session Info:
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.11.0
>>
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>> BioC_mirror = http://www.bioconductor.org
>> Change using chooseBioCmirror().
>>> biocLite("org.At.tair.db")
>> Using R version 2.11.0, biocinstall version 2.6.10.
>> Installing Bioconductor version 2.6 packages:
>> [1] "org.At.tair.db"
>> Please wait...
>>
>> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>>  argument 'lib' is missing: using
>> '/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11'
>> trying URL
>> 'http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/org.At.tair.db_2.4.3.tar.gz'
>> Content type 'application/x-gzip' length 26130925 bytes (24.9 Mb)
>> opened URL
>> ==================================================
>> downloaded 24.9 Mb
>>
>> ERROR: failed to lock directory
>> â€˜/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11â€™ for modifying
>> Try removing â€˜/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11/00LOCKâ€™
>
> Did you remove the file noted above?  I'd do that and then try the
> installation again.
>
> Sean
>
>> The downloaded packages are in
>>    â€˜/tmp/Rtmphd9Etx/downloaded_packagesâ€™
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package 'org.At.tair.db' had non-zero exit status
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>