[BioC] Package "makecdfenv"
James W. MacDonald
jmacdon at u.washington.edu
Fri May 23 16:16:37 CEST 2014
Hi Romain,
On 5/23/2014 9:50 AM, Romain Desert wrote:
> 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.
This is probably the problem ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Which I translate as 'D:\home\rdesert\mes isn't an internal or external
command so I will fail now, thanks.'
And I can then further translate this to 'R doesn't like spaces in the
library path, because we are unix people and spaces are for windows n00bs'.
To test this you could do something like this at an R prompt:
dir.create("D:/home/rdesert/R/win-library/3.1")
.libPaths("D:/home/rdesert/R/win-library/3.1")
install.packages(rmhu01aa520485cdf/", repos=NULL, type="source")
which should then install in your new, space-free library. You might
need to add a lib = "D:/home/rdesert/R/win-library/3.1" to the call to
install.packages(), but it shouldn't be necessary.
Another Windows-centric possibility is to do this at the command prompt
D:/home/desert/mesdoc~1/R/R-3.1.0/bin/x64/R CMD INSTALL -l
"D:/home/rdesert/mesdoc~1/R/R-3.1.0/library" rmhu01aa520485cdf
Hope that helps.
Jim
> 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/
>>>>
>>>
>>>
>>
>
>
--
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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