[BioC] Package "makecdfenv"
Romain Desert
romain.desert at univ-rennes1.fr
Fri May 23 15:50:28 CEST 2014
Hi Jim,
that is true, it was en error message for already having created the
package. In fact I don't have an Error message when I try to install the
package, it just doen't work.
> make.cdf.package("GPL10687_RM-HU01Aa520485_custom_MMPM.cdf",
"rmhu01aa520485cdf", compress=F, species="Homo_sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 376
dots...........................................................................................................................................................................................................................................................................................................................................................................................................
Creating package in d:/home/rdesert/bureau/Documents/Bases puces/META
BASE/Sung/rmhu01aa520485cdf
README PLEASE:
A source package has now been produced in
d:/home/rdesert/bureau/Documents/Bases puces/META
BASE/Sung/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")
'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
> traceback()
4: .Call("CheckCDFXDA", filename, PACKAGE = "affyio")
3: isCDFXDA(file.path(path.expand(cdf.path), filename))
2: make.cdf.env(filename, cdf.path = cdf.path, compress = compress,
return.env.only = FALSE)
1: make.cdf.package("Downloads/GPL10687_RM-HU01Aa520485_custom_MMPM.cdf",
"rmhu01aa520485cdf", compress = F, species = "Homo_sapiens")
Best,
Romain
Le 23/05/2014 15:28, James W. MacDonald a écrit :
> 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/
>>>
>>
>>
>
--
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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