[BioC] Package "makecdfenv"

Thu May 22 17:39:44 CEST 2014

Hi Romain,

As I mentioned in the last email, I cc'ed the Bioconductor list, so all 
you had to do was look to see what the email address was in my response. 
Or you could go to the bioconductor website, which has a mailing list 
section.

Also, please remember to 'Reply-all' when responding.

On 5/22/2014 11:24 AM, Romain Desert wrote:
> Thank you James for your answser,
>
> unforturnately I had already tested install.packages(<package name 
> goes here>, repos = NULL, type = "source")  and it doesn't work.
>
> Error message is :
>
> 'D:\home\rdesert\mes' n'est pas reconnu en tant que commande interne
> ou externe, un programme ex‚cutable ou un fichier de commandes.
> Warning in install.packages :
>    running command '"D:/home/rdesert/mes documents/R/R-3.1.0/bin/x64/R" CMD INSTALL -l "D:\home\rdesert\mes documents\R\R-3.1.0\library" "rmhu01aa520485cdf"' had status 1
> Warning in install.packages :
>    installation of package ‘rmhu01aa520485cdf’ had non-zero exit status
>
> I hope you have some other idea to help me.
> Otherwise, could you tell me where is the Bioconductor list, to ask my 
> question in an appropriate place?

It would be helpful if you gave the output from sessionInfo(), as well 
as traceback() after you got the error. I have no problems creating and 
installing this package on Windows:

>make.cdf.package("GPL14189_rmhu01aa520485.cdf.gz", "rmhu10aa520485cdf", compress=TRUE, species="Homo_sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 437 dots........................................................................................................................................................................................................................................................................................................................................................................................................................................................
Creating package in C:/Users/bioinf_admin/Desktop/rmhu10aa520485cdf

README PLEASE:
A source package has now been produced in
C:/Users/bioinf_admin/Desktop/rmhu10aa520485cdf.
Before using this package it must be installed via 'R CMD INSTALL'
at a terminal prompt (or DOS command shell).
If you are using Windows, you will need to get set up to install packages.
See the 'R Installation and Administration' manual, specifically
Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset'
for more information.

Alternatively, you could use make.cdf.env(), which will not require you to install a package.
However, this environment will only persist for the current R session
unless you save() it.

>install.packages("rmhu10aa520485cdf/", repos=NULL, type="source")
Installing package into ‘C:/Users/bioinf_admin/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'rmhu10aa520485cdf' ...
** R
** data
** preparing package for lazy loading
Warning: replacing previous import by 'utils::head' when loading 'rmhu10aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading 'rmhu10aa520485cdf'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: replacing previous import by 'utils::head' when loading 'rmhu10aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading 'rmhu10aa520485cdf'
*** arch - x64
Warning: replacing previous import by 'utils::head' when loading 'rmhu10aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading 'rmhu10aa520485cdf'
* DONE (rmhu10aa520485cdf)

>sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] makecdfenv_1.40.0    affyio_1.32.0        BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] affy_1.42.2           Biobase_2.24.0        BiocGenerics_0.10.0   parallel_3.1.0        preprocessCore_1.26.1
[6] tools_3.1.0           zlibbioc_1.10.0

Best,

Jim

>
> Best regards,
> Romain
>
> Le 22/05/2014 16:00, James W. MacDonald a écrit :
>> Hi Romain,
>>
>> I am cc'ing the Bioconductor list, which is the primary place to ask 
>> these sorts of questions.
>>
>>
>> On Thursday, May 22, 2014 8:46:39 AM, Romain Desert wrote:
>>> Dear Mr MacDonald,
>>>
>>> I curantly work on a custom affymetrix data chip from GEO. To process
>>> CEL files with the "affy" package on R, I have to create a custom
>>> package. To this end, I used the "make.cdf.package" function of the
>>> "makecdfenv" package.
>>>
>>> Unfortunately, I am now incapable to install the created package. I
>>> don't work on linux so I can't use 'R CMD INSTALL'.
>>
>> This is something I need to fix. You can install the package on 
>> Windows, regardless, using
>>
>> install.packages(<package name goes here>, repos = NULL, type = 
>> "source")
>>
>> and since there is no compiled code, it will be installed without 
>> problems.
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> make.cdf.env didn't worked either. Maybe I don't know how to use it in
>>> a good way.
>>>
>>> Could you give me some advices?
>>> Thank you in advance.
>>>
>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>
>
> -- 
> Romain Desert - PhD Student
> INSERM UMR 991
> Hopital Pontchaillou
> rue Henri Le Guilloux
> 35033 RENNES CEDEX 9
> FRANCE
> Tél :    33-(0)6 38 43 49 37
>
> romain.desert at inserm.fr
> http://inserm-umr991.univ-rennes1.fr/  

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099