[Rd] about integration of a library into package creation
hello,
i try to create a package , and i call a library in the namespace file
such as : useDynLib(quadprog)
after checking my directory with the command "rcmd check" (i am on
WindowsXP)
i get an error: package / namespace load failed
the path of the library is: D:\R\library\quadprog
the path of the building files is: D:\RBuild\svcR
and the comand i use to compile is: rcmd check D://RBuild//svcR
i dont understand, it is a path problem about the dll related to the
library ?
thank for help
Nicolas
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution arrete'e
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
__
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Re: [Rd] about integration of a library into package creation
>
>
>You didn't show the results of installing your package. Did that work?
>
>Generally we advise to do a successful install before you try to run
checks.
>
>Duncan Murdoch
D:\RBuild\svcR> rcmd build D://RBuild//svcR --force --docs='all' --binary
hence i obtain the file svcR_1.0.zip
and following messages :
D:\RBuild\svcR>rcmd build D://RBuild//svcR --force --docs='all' --binary
* checking for file 'D://RBuild//svcR/DESCRIPTION' ... OK
* preparing 'D://RBuild//svcR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
tar: svcR/svcR_1.0.tar: file is the archive; not dumped
* excluding invalid files from 'svcR'
Subdirectory 'R' contains invalid file names:
ade4.dll quadprog.dll spdep.dll
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in C:/DOCUME~1/Nicolas/LOCALS~1/Temp/Rinst249298526
Using auto-selected zip options ''
-- Making package svcR
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'svcR'
Formats: text html latex example chm
iris_att texthtmllatex chm
iris_mat texthtmllatex chm
iris_var texthtmllatex chm
svcR texthtmllatex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling
c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm
Compile time: 0 minutes, 1 second
5 Topics
8 Local links
1 Internet link
1 Graphic
Created
c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm, 18,
283 bytes
Compression increased file by 6,096 bytes.
preparing package svcR for lazy loading
adding MD5 sums
packaged installation of package 'svcR' as svcR_1.0.zip
* DONE (svcR)
in R environment (Rgui front-end)
i write:
> install.packages("D:/RBuild/svcR/svcR_1.0.zip", repos=NULL)
package 'svcR' successfully unpacked and MD5 sums checked
updating HTML package descriptions
> library(svcR)
Attachement du package : 'svcR'
The following object(s) are masked _by_ .GlobalEnv :
findModelCluster
>
and finally when i typewrite my function
i obtain :
impossible de trouver la fonction "dudi.coa"
it can not find the function called in the library that i call in the R
source code
by library(ade4)
if i call my function by source(), it works well
thank you for help
-
Nicolas
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Re: [Rd] about integration of a library into package creation
in that sense, it is useless to load the library from R source code
making my package
which is supposed to include it and load it
so if i understand the R philosophy it is not possible to load dll from
outside ;
the user has to load my package and manually has to load the necessary
libraries
each time he has to use my library, right ?
--
Nicolas
Prof Brian Ripley a écrit :
>
> And also to load the package, maybe with
>
> rterm R_DEFAULT_PACKAGES=NULL
>
>> library(svcR)
>
>
> as these messages often indicate missing package dependencies.
>
>>> * checking package subdirectories ... WARNING
>>> Subdirectory 'src' contains no source files.
>>> * checking R files for syntax errors ... OK
>>> * checking R files for library.dynam ... OK
>>> * checking S3 generic/method consistency ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>>call. = FALSE, domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Execution arrete'e
>>> See section 'Generic functions and methods' of the 'Writing R
>>> Extensions'
>>> manual.
>>> * checking replacement functions ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>
>
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Re: [Rd] about integration of a library into package creation
your answer is correct after checking some doc
but examples are rare
when i write in the description file
Depends: R (>= 2.3), quadprog, ade4, spdep
and in the namespcae file
useDynLib(quadprog)
useDynLib(spdep)
useDynLib(ade4)
importFrom("dist.dudi", "ade4")
importFrom("solve.QP", "quadprog")
importFrom("mstree", "ade4")
importFrom("neig2mat", "ade4")
importFrom("dist.dudi", "ade4")
importFrom("dudi.pca", "ade4")
importFrom("dudi.coa", "ade4")
importFrom("knearneigh", "spdep")
i obtain :
Namespace dependencies not required:
dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
if i delete the importFrom lines
i get an error about "loading / namespace not succesful" for svcr
i think the solution is not far but it is disturbing
thank for help
---
Nicolas
Duncan Murdoch a écrit :
> On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
>
>> in that sense, it is useless to load the library from R source code
>> making my package
>> which is supposed to include it and load it
>>
>> so if i understand the R philosophy it is not possible to load dll
>> from outside ;
>> the user has to load my package and manually has to load the
>> necessary libraries
>> each time he has to use my library, right ?
>
>
> Not at all. When set up correctly, the user should just need to say
> library(svcR) and all necessary packages and DLLs will be loaded.
>
> The way to specify other packages is through the "Depends" line in the
> DESCRIPTION file, and/or the import/importFrom lines in your NAMESPACE
> file.
>
> Duncan Murdoch
>
>>
>> --
>> Nicolas
>>
>> Prof Brian Ripley a écrit :
>>
>>>
>>> And also to load the package, maybe with
>>>
>>> rterm R_DEFAULT_PACKAGES=NULL
>>>
>>>> library(svcR)
>>>
>>>
>>>
>>> as these messages often indicate missing package dependencies.
>>>
>>>>> * checking package subdirectories ... WARNING
>>>>> Subdirectory 'src' contains no source files.
>>>>> * checking R files for syntax errors ... OK
>>>>> * checking R files for library.dynam ... OK
>>>>> * checking S3 generic/method consistency ... WARNING
>>>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>>>> 'svcR'
>>>>> Sequence d'appel :
>>>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>>>> libraryPkgName(packag
>>>>> e)),
>>>>>call. = FALSE, domain = NA)
>>>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>> verbose =
>>>>> FALSE)
>>>>> Execution arrete'e
>>>>> See section 'Generic functions and methods' of the 'Writing R
>>>>> Extensions'
>>>>> manual.
>>>>> * checking replacement functions ... WARNING
>>>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>>>> 'svcR'
>>>>> Sequence d'appel :
>>>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>>>> libraryPkgName(packag
>>>>> e)),
>>>>
>>>>
>>>
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
__
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Re: [Rd] about integration of a library into package creation
i follow your recommendation writing this :
in the description file
Depends: R (>= 2.3), quadprog, ade4, spdep
Imports: quadprog, ade4, spdep
in the namespace file
useDynLib(quadprog)
useDynLib(spdep)
useDynLib(ade4)
importFrom("ade4", "dist.dudi")
importFrom("quadprog", "solve.QP")
importFrom("ade4", "mstree")
importFrom("ade4", "neig2mat")
importFrom("ade4", "dist.dudi")
importFrom("ade4", "dudi.pca")
importFrom("ade4", "dudi.coa")
importFrom("spdep", "knearneigh")
and the result of compiling is :
preparing package svcR for lazy loading
Erreur dans loadNamespace(ns, lib.loc) : le package 'quadprog' n'a pas
d'espace de noms
Exécution arrêtée
make: *** [lazyload] Error 1
*** Installation of svcR failed ***
it says that quadprog has not a namespace
perhaps it is due to location of quadprog.dll
i have put it into inst/src directory
thank for help
Nicolas
Uwe Ligges a écrit :
> Nicolas Turenne wrote:
>
>> your answer is correct after checking some doc
>> but examples are rare
>>
>> when i write in the description file
>> Depends: R (>= 2.3), quadprog, ade4, spdep
>> and in the namespcae file
>>
>> useDynLib(quadprog)
>> useDynLib(spdep)
>> useDynLib(ade4)
>> importFrom("dist.dudi", "ade4")
>
>
>
> Please do it the right way (package name first!):
>
> importFrom("ade4", "dist.dudi")
>
> Uwe Ligges
>
>
>
>
>> importFrom("solve.QP", "quadprog")
>> importFrom("mstree", "ade4")
>> importFrom("neig2mat", "ade4")
>> importFrom("dist.dudi", "ade4")
>> importFrom("dudi.pca", "ade4")
>> importFrom("dudi.coa", "ade4")
>> importFrom("knearneigh", "spdep")
>>
>> i obtain :
>> Namespace dependencies not required:
>> dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
>>
>> if i delete the importFrom lines
>> i get an error about "loading / namespace not succesful" for svcr
>>
>> i think the solution is not far but it is disturbing
>>
>> thank for help
>>
>> ---
>> Nicolas
>>
>>
>> Duncan Murdoch a écrit :
>>
>>> On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
>>>
>>>> in that sense, it is useless to load the library from R source code
>>>> making my package
>>>> which is supposed to include it and load it
>>>>
>>>> so if i understand the R philosophy it is not possible to load dll
>>>> from outside ;
>>>> the user has to load my package and manually has to load the
>>>> necessary libraries
>>>> each time he has to use my library, right ?
>>>
>>>
>>> Not at all. When set up correctly, the user should just need to say
>>> library(svcR) and all necessary packages and DLLs will be loaded.
>>>
>>> The way to specify other packages is through the "Depends" line in
>>> the DESCRIPTION file, and/or the import/importFrom lines in your
>>> NAMESPACE file.
>>>
>>> Duncan Murdoch
>>>
>>>> --
>>>> Nicolas
>>>>
>>>> Prof Brian Ripley a écrit :
>>>>
>>>>> And also to load the package, maybe with
>>>>>
>>>>> rterm R_DEFAULT_PACKAGES=NULL
>>>>>
>>>>>> library(svcR)
>>>>>
>>>>>
>>>>>
>>>>> as these messages often indicate missing package dependencies.
>>>>>
>>>>>>> * checking package subdirectories ... WARNING
>>>>>>> Subdirectory 'src' contains no source files.
>>>>>>> * checking R files for syntax errors ... OK
>>>>>>> * checking R files for library.dynam ... OK
>>>>>>> * checking S3 generic/method consistency ... WARNING
>>>>>>> Erreur : le chargement du package / espace de noms a echoue'
>>>>>>> pour 'svcR'
>>>>>>> Sequence d'appel :
>>>>>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>>>>>> libraryPkgName(packag
>>>>>>> e)),
>>>>>>>call. = FALSE, domain = NA)
>>>>>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>>>> verbose =
>>>>>>> FALSE)
>>>>>>> Execution arrete'e
>>>>>>> See section 'Generic functions and methods' of the 'Writing R
>>>>>>> Extensions'
>>>>>>> manual.
>>>>>>> * checking replacement functions ... WARNING
>>>>>>> Erreur : le chargement du package / espace de noms a echoue'
>>>>>>> pour 'svcR'
>>>>>>> Sequence d'appel :
>>>>>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>>>>>> libraryPkgName(packag
>>>>>>> e)),
>>>>>>
>>>>>>
>>>> __
>>>> R-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>>
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
__
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Re: [Rd] about integration of a library into package creation
it looks strange...
if i do only the compiling with the package "spdep"
and i avoid useDynLib, it compiles well,
but with the package "ade4" and "quadprog" it claims that
packages has no namespace
Erreur dans loadNamespace(ns, lib.loc) : le package 'quadprog' n'a pas
d'espace de noms
do you have an explanation ?
thank for help
---
Nicolas
Duncan Murdoch a écrit :
> Nicolas Turenne wrote:
>
>> i follow your recommendation writing this :
>> in the description file
>> Depends: R (>= 2.3), quadprog, ade4, spdep
>> Imports: quadprog, ade4, spdep
>>
>> in the namespace file
>> useDynLib(quadprog)
>> useDynLib(spdep)
>> useDynLib(ade4)
>> importFrom("ade4", "dist.dudi")
>> importFrom("quadprog", "solve.QP")
>> importFrom("ade4", "mstree")
>> importFrom("ade4", "neig2mat")
>> importFrom("ade4", "dist.dudi")
>> importFrom("ade4", "dudi.pca")
>> importFrom("ade4", "dudi.coa")
>> importFrom("spdep", "knearneigh")
>>
>
>
> I think you are doing too much!
> 1. You should not use "useDynLib" for the DLL from another package.
> Let the other package load its own DLL.
>
> 2. If you declare that your package Depends on the other packages,
> then they will be loaded and attached, and the importFrom lines will
> not be needed.
> "Import"ing and "Depend"ing are similar but not identical concepts.
> Routines that are imported are available to your package *before* the
> global environment (i.e. user workspace). Routines that are in
> packages attached by Depends come after the global environment, so
> there's a possibility that the user could create a routine named e.g.
> "mstree", and your code would use that version, rather than the one
> from ade4. So normally "Imports" is better than "Depends".
>
> However, it appears that you can only import packages that have a
> namespace. (I was unaware of this restriction; perhaps it's not
> really true, and the error message means something else.)
>
> So you can probably get rid of the error message by using only
> Depends, but you may want to keep the Imports from packages other than
> quadprog.
>
> Duncan Murdoch
>
>> and the result of compiling is :
>> preparing package svcR for lazy loading
>> Erreur dans loadNamespace(ns, lib.loc) : le package 'quadprog' n'a
>> pas d'espace de noms
>> Exécution arrêtée
>> make: *** [lazyload] Error 1
>> *** Installation of svcR failed ***
>>
>> it says that quadprog has not a namespace
>> perhaps it is due to location of quadprog.dll
>> i have put it into inst/src directory
>>
>> thank for help
>>
>> Nicolas
>>
>> Uwe Ligges a écrit :
>>
>>
>>
>>> Nicolas Turenne wrote:
>>>
>>>
>>>
>>>> your answer is correct after checking some doc
>>>> but examples are rare
>>>>
>>>> when i write in the description file
>>>> Depends: R (>= 2.3), quadprog, ade4, spdep
>>>> and in the namespcae file
>>>>
>>>> useDynLib(quadprog)
>>>> useDynLib(spdep)
>>>> useDynLib(ade4)
>>>> importFrom("dist.dudi", "ade4")
>>>>
>>>
>>>
>>> Please do it the right way (package name first!):
>>>
>>> importFrom("ade4", "dist.dudi")
>>>
>>> Uwe Ligges
>>>
>>>
>>>
>>>
>>>
>>>
>>>> importFrom("solve.QP", "quadprog")
>>>> importFrom("mstree", "ade4")
>>>> importFrom("neig2mat", "ade4")
>>>> importFrom("dist.dudi", "ade4")
>>>> importFrom("dudi.pca", "ade4")
>>>> importFrom("dudi.coa", "ade4")
>>>> importFrom("knearneigh", "spdep")
>>>>
>>>> i obtain :
>>>> Namespace dependencies not required:
>>>> dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
>>>>
>>>> if i delete the importFrom lines
>>>> i get an error about "loading / namespace not succesful" for svcr
>>>>
>>>> i think the solution is not far but it is disturbing
>>>>
&g
Re: [Rd] about integration of a library into package creation
it works fine if i avoid importFrom directive
thank you very much
i have a last question
the R source code cannot admit gloval variable ? because i have global
variables
and i get the following message after loading my package by the command
'library(svcR)':
The following object(s) are masked _by_ .GlobalEnv : findModelCluster
thank for help
--
Nicolas
Duncan Murdoch a écrit :
> Nicolas Turenne wrote:
>
>> i follow your recommendation writing this :
>> in the description file
>> Depends: R (>= 2.3), quadprog, ade4, spdep
>> Imports: quadprog, ade4, spdep
>>
>> in the namespace file
>> useDynLib(quadprog)
>> useDynLib(spdep)
>> useDynLib(ade4)
>> importFrom("ade4", "dist.dudi")
>> importFrom("quadprog", "solve.QP")
>> importFrom("ade4", "mstree")
>> importFrom("ade4", "neig2mat")
>> importFrom("ade4", "dist.dudi")
>> importFrom("ade4", "dudi.pca")
>> importFrom("ade4", "dudi.coa")
>> importFrom("spdep", "knearneigh")
>>
>
>
> I think you are doing too much!
> 1. You should not use "useDynLib" for the DLL from another package.
> Let the other package load its own DLL.
>
> 2. If you declare that your package Depends on the other packages,
> then they will be loaded and attached, and the importFrom lines will
> not be needed.
> "Import"ing and "Depend"ing are similar but not identical concepts.
> Routines that are imported are available to your package *before* the
> global environment (i.e. user workspace). Routines that are in
> packages attached by Depends come after the global environment, so
> there's a possibility that the user could create a routine named e.g.
> "mstree", and your code would use that version, rather than the one
> from ade4. So normally "Imports" is better than "Depends".
>
> However, it appears that you can only import packages that have a
> namespace. (I was unaware of this restriction; perhaps it's not
> really true, and the error message means something else.)
>
> So you can probably get rid of the error message by using only
> Depends, but you may want to keep the Imports from packages other than
> quadprog.
>
> Duncan Murdoch
>
>> and the result of compiling is :
>> preparing package svcR for lazy loading
>> Erreur dans loadNamespace(ns, lib.loc) : le package 'quadprog' n'a
>> pas d'espace de noms
>> Exécution arrêtée
>> make: *** [lazyload] Error 1
>> *** Installation of svcR failed ***
>>
>> it says that quadprog has not a namespace
>> perhaps it is due to location of quadprog.dll
>> i have put it into inst/src directory
>>
>> thank for help
>>
>> Nicolas
>>
>> Uwe Ligges a écrit :
>>
>>
>>
>>> Nicolas Turenne wrote:
>>>
>>>
>>>
>>>> your answer is correct after checking some doc
>>>> but examples are rare
>>>>
>>>> when i write in the description file
>>>> Depends: R (>= 2.3), quadprog, ade4, spdep
>>>> and in the namespcae file
>>>>
>>>> useDynLib(quadprog)
>>>> useDynLib(spdep)
>>>> useDynLib(ade4)
>>>> importFrom("dist.dudi", "ade4")
>>>>
>>>
>>>
>>> Please do it the right way (package name first!):
>>>
>>> importFrom("ade4", "dist.dudi")
>>>
>>> Uwe Ligges
>>>
>>>
>>>
>>>
>>>
>>>
>>>> importFrom("solve.QP", "quadprog")
>>>> importFrom("mstree", "ade4")
>>>> importFrom("neig2mat", "ade4")
>>>> importFrom("dist.dudi", "ade4")
>>>> importFrom("dudi.pca", "ade4")
>>>> importFrom("dudi.coa", "ade4")
>>>> importFrom("knearneigh", "spdep")
>>>>
>>>> i obtain :
>>>> Namespace dependencies not required:
>>>> dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
>>>>
>>>> if i delete the importFrom lines
>>>> i get an error about "loading / namespace not succesful" for svcr
>>>>
>>>> i think the solution is not far but it is disturbing
>>>>
>>>> thank for
Re: [Rd] about integration of a library into package creation
i solve the problem of masked GlobalEnv which is induced from conflicts with objects in memory removing objects before installing the package solves the warning message Nicolas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] about integration of a library into package creation
Hello, I dont understand such error coming from my installed package and dont appearing when i load the code source directly . The problem occur when the function capture the path value (FileIn), and so cannot find the file inside the directory. > findModelCluster(MetOpt, MetLab, Nu, q, K=1, G, Cx, Cy, DName="iris", fileIn="D:\\R\\library\\svcR\\data\\"); Erreur dans findModelCluster(MetOpt, MetLab, Nu, q, K = 1, G, Cx, Cy, DName = "iris", : impossible de changer la valeur d'un lien verrouillé (in English: impossible to change the value of a locked link) thank you --- Nicolas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problem to read data into a package
Hello i have this following error making a package -- Making package svcR adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files installing data files installing man source files installing indices Error in read.table(zfile, header = TRUE) : more column than column names this kind of error is produced when spaces are met in data . in my case there are only tabulations and three columns of real numbers (with 3 digits) i have no idea what it happens thank for help -- Nicolas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
