[BioC] Package "makecdfenv"
James W. MacDonald
jmacdon at uw.edu
Fri May 23 16:18:30 CEST 2014
On 5/23/2014 10:16 AM, James W. MacDonald wrote:
> 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
And note that this ^^^^^^^^^^^^^^^ should all be on one line.
Jim
>
> 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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