[BioC] Package "makecdfenv"
James W. MacDonald
jmacdon at u.washington.edu
Fri May 23 15:28:03 CEST 2014
Hi Romain,
>
make.cdf.package("Downloads/GPL10687_RM-HU01Aa520485_custom_MMPM.cdf.gz", "rmhu01aa520485cdf",
compress=T, species="Homo_sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 376
dots.........................................................................................................................................................................................................................................................................................................................................................................................................
Creating package in C:/Users/bioinf_admin/rmhu01aa520485cdf
README PLEASE:
A source package has now been produced in
C:/Users/bioinf_admin/rmhu01aa520485cdf.
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("rmhu01aa520485cdf/", repos=NULL, type="source")
Installing package into ‘C:/Users/bioinf_admin/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'rmhu01aa520485cdf' ...
** R
** data
** preparing package for lazy loading
Warning: replacing previous import by 'utils::head' when loading
'rmhu01aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading
'rmhu01aa520485cdf'
** 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
'rmhu01aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading
'rmhu01aa520485cdf'
*** arch - x64
Warning: replacing previous import by 'utils::head' when loading
'rmhu01aa520485cdf'
Warning: replacing previous import by 'utils::tail' when loading
'rmhu01aa520485cdf'
* DONE (rmhu01aa520485cdf)
On 5/23/2014 6:09 AM, Romain Desert wrote:
> 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)
This isn't the traceback after trying to install the package. Instead it
is the traceback after failing to build the package, and the error is
pretty clear - you have already built a package of the same name in that
directory, so if you want to build it again you need to use unlink = TRUE.
Best,
Jim
>
> 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/
>>
>
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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