[BioC] Package "makecdfenv"
Romain Desert
romain.desert at univ-rennes1.fr
Fri May 23 12:09:12 CEST 2014
Ok Jim, sorry for the cc'ed I hadn't see and the reply all. And thank
you again for your help.
I see you installed rmhu01aa520485.cdf from the GPL14189 plateform. It
is not exactly the one that I try to install. Mine is rmhu01aa520485cdf
from GPL10687 plateform.
Othewise, my sessionInfo are :
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] makecdfenv_1.40.0 affyio_1.32.0 BiocInstaller_1.14.2
affy_1.42.1
[5] Biobase_2.24.0 BiocGenerics_0.10.0 limma_3.20.2
loaded via a namespace (and not attached):
[1] preprocessCore_1.26.0 tools_3.1.0 zlibbioc_1.10.0
and traceback :
> traceback()
3: stop("directory '", pkgdir, "' exists; use unlink=TRUE ", "to remove
it, or choose another destination directory")
2: createPackage(packagename, destinationDir = path.expand(package.path),
originDir = file.path(home, "Code"), symbolValues = symbols,
unlink = unlink, quiet = !verbose)
1: make.cdf.package("GPL10687_RM-HU01Aa520485_custom_MMPM.cdf",
packagename = pname, cdf.path = getwd(), package.path = getwd(),
compress = F, author = "The Bioconductor Project", maintainer =
"Biocore Package Maintainer <maintainer at bioconductor.org>",
version = packageDescription("makecdfenv", fields = "Version"),
species = "Homo_sapiens", unlink = FALSE, verbose = TRUE)
with pname = "rmhu01aa520485cdf". If you want to upload the cdf file to
try to install it, you will find it in GEO at GSE25097.
Best regards,
Romain
Le 22/05/2014 17:39, James W. MacDonald a écrit :
> 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/
>
--
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/
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