Re: [R] Bug in package.skeleton, R 2.9.0?
Daniel Klevebring wrote:
> Bump
>
> Anyone?
>
> Thanks
> Daniel
>
> On 13 jul 2009, at 10.57, Daniel Klevebring wrote:
>
>> Dear all,
>>
>> I am using package.skeleton to build a small packages of misc function
>> for personal use. I have recently discovered that the option
>> force=TRUE doesn't seem to do what is meant to do. Here's what I'm
>> doing:
>>
>>> setwd("/Users/danielk/Documents/R/packages/dk")
>>> files <- paste("codebase", dir("codebase", pattern=".R"), sep="/")
>>> package.skeleton(name="dk", force=TRUE, code_files=files)
>> Creating directories ...
>> Creating DESCRIPTION ...
>> Creating Read-and-delete-me ...
>> Copying code files ...
>> Making help files ...
>> Done.
>> Further steps are described in './dk/Read-and-delete-me'.
>> Now, everything seems fine, but changes to files in me codebase
>> folder, doesn't come along if the folder dk/R already contains the
>> files, even though I use force=TRUE. If I remove the dk/R folder or
>> the dk folder altogether, the changes come along so to me it seems
>> that it's the overwrite part that doesn't work as it should - or am I
>> doing something wrong here? To me, it seems that the function
>> safe.dir.create (which is defined in package.skeleton never overwrites
>> folders, yielding force=TRUE useless.
from the help on package.skeleton
force: If 'FALSE' will not overwrite an existing directory.
which could be clearer in that package.skeleton will stop with an error if the
top level
directory, i.e. 'dk' in your case, exists and you had specified force=FALSE.
But it will
not overwrite the existing directory 'dk' with force=TRUE as you observed.
Looking at the code it is clear that file.copy is used to copy the code files
and that has
per default overwrite=FALSE so your existing code files will not be overwritten.
With the current implementation package.skeleton will not do what you intended.
There are many ways to workaround
e.g.
fn <- dir("codebase", pattern=".R", full.names=TRUE)
file.remove( list.files(path=file.path("dk", "R"), pattern="\\.R",
full.names=TRUE))
package.skeleton(name="dk", force=TRUE, code_files=fn)
Matthias
>>
>> See below for sessionInfo.
>>
>> Thanks a bunch
>> Daniel
>>
>>
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.9.0
>>
>> --
>>
>> Contact information:
>>
>> Daniel Klevebring
>> M. Sc. Eng., Ph.D. Student
>> Dept of Gene Technology
>> Royal Institute of Technology, KTH
>> SE-106 91 Stockholm, Sweden
>>
>> Visiting address: Roslagstullsbacken 21, B3
>> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
>> Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
>> SE-10450 Stockholm
>> E-mail: dan...@biotech.kth.se
>> Phone: +46 8 5537 8337 (Office)
>> Phone: +46 704 71 65 91 (Mobile)
>> Web: http://www.biotech.kth.se/genetech/index.html
>> Fax: +46 8 5537 8481
>>
>> --
>>
>> Contact information:
>>
>> Daniel Klevebring
>> M. Sc. Eng., Ph.D. Student
>> Dept of Gene Technology
>> Royal Institute of Technology, KTH
>> SE-106 91 Stockholm, Sweden
>>
>> Visiting address: Roslagstullsbacken 21, B3
>> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
>> Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
>> SE-10450 Stockholm
>> E-mail: dan...@biotech.kth.se
>> Phone: +46 8 5537 8337 (Office)
>> Phone: +46 704 71 65 91 (Mobile)
>> Web: http://www.biotech.kth.se/genetech/index.html
>> Fax: +46 8 5537 8481
>> MSN messenger: klevebr...@msn.com
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>
> --
>
> Contact information:
>
> Daniel Klevebring
> M. Sc. Eng., Ph.D. Student
> Dept of Gene Technology
> Royal Institute of Technology, KTH
> SE-106 91 Stockholm, Sweden
>
> Visiting address: Roslagstullsbacken 21, B3
> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
> Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
> SE-10450 Stockholm
> E-mail: dan...@biotech.kth.se
> Phone: +46 8 5537 8337 (Office)
> Phone: +46 704 71 65 91 (Mobile)
> Web: http://www.biotech.kth.se/genetech/index.html
> Fax: +46 8 5537 8481
> MSN messenger: klevebr...@msn.com
>
>
> [[alternative HTML version deleted]]
>
>
>
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com
Re: [R] Bug in package.skeleton, R 2.9.0?
Bump
Anyone?
Thanks
Daniel
On 13 jul 2009, at 10.57, Daniel Klevebring wrote:
> Dear all,
>
> I am using package.skeleton to build a small packages of misc function
> for personal use. I have recently discovered that the option
> force=TRUE doesn't seem to do what is meant to do. Here's what I'm
> doing:
>
>> setwd("/Users/danielk/Documents/R/packages/dk")
>> files <- paste("codebase", dir("codebase", pattern=".R"), sep="/")
>> package.skeleton(name="dk", force=TRUE, code_files=files)
> Creating directories ...
> Creating DESCRIPTION ...
> Creating Read-and-delete-me ...
> Copying code files ...
> Making help files ...
> Done.
> Further steps are described in './dk/Read-and-delete-me'.
>>
>
> Now, everything seems fine, but changes to files in me codebase
> folder, doesn't come along if the folder dk/R already contains the
> files, even though I use force=TRUE. If I remove the dk/R folder or
> the dk folder altogether, the changes come along so to me it seems
> that it's the overwrite part that doesn't work as it should - or am I
> doing something wrong here? To me, it seems that the function
> safe.dir.create (which is defined in package.skeleton never overwrites
> folders, yielding force=TRUE useless.
>
> See below for sessionInfo.
>
> Thanks a bunch
> Daniel
>
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
>>
>
>
> --
>
> Contact information:
>
> Daniel Klevebring
> M. Sc. Eng., Ph.D. Student
> Dept of Gene Technology
> Royal Institute of Technology, KTH
> SE-106 91 Stockholm, Sweden
>
> Visiting address: Roslagstullsbacken 21, B3
> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
> Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
> SE-10450 Stockholm
> E-mail: dan...@biotech.kth.se
> Phone: +46 8 5537 8337 (Office)
> Phone: +46 704 71 65 91 (Mobile)
> Web: http://www.biotech.kth.se/genetech/index.html
> Fax: +46 8 5537 8481
>
> --
>
> Contact information:
>
> Daniel Klevebring
> M. Sc. Eng., Ph.D. Student
> Dept of Gene Technology
> Royal Institute of Technology, KTH
> SE-106 91 Stockholm, Sweden
>
> Visiting address: Roslagstullsbacken 21, B3
> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
> Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
> SE-10450 Stockholm
> E-mail: dan...@biotech.kth.se
> Phone: +46 8 5537 8337 (Office)
> Phone: +46 704 71 65 91 (Mobile)
> Web: http://www.biotech.kth.se/genetech/index.html
> Fax: +46 8 5537 8481
> MSN messenger: klevebr...@msn.com
>
>
> [[alternative HTML version deleted]]
>
>
--
Contact information:
Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden
Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
SE-10450 Stockholm
E-mail: dan...@biotech.kth.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.biotech.kth.se/genetech/index.html
Fax: +46 8 5537 8481
MSN messenger: klevebr...@msn.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Bug in package.skeleton, R 2.9.0?
Dear all,
I am using package.skeleton to build a small packages of misc function
for personal use. I have recently discovered that the option
force=TRUE doesn't seem to do what is meant to do. Here's what I'm
doing:
> setwd("/Users/danielk/Documents/R/packages/dk")
> files <- paste("codebase", dir("codebase", pattern=".R"), sep="/")
> package.skeleton(name="dk", force=TRUE, code_files=files)
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Copying code files ...
Making help files ...
Done.
Further steps are described in './dk/Read-and-delete-me'.
>
Now, everything seems fine, but changes to files in me codebase
folder, doesn't come along if the folder dk/R already contains the
files, even though I use force=TRUE. If I remove the dk/R folder or
the dk folder altogether, the changes come along so to me it seems
that it's the overwrite part that doesn't work as it should - or am I
doing something wrong here? To me, it seems that the function
safe.dir.create (which is defined in package.skeleton never overwrites
folders, yielding force=TRUE useless.
See below for sessionInfo.
Thanks a bunch
Daniel
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.9.0
>
--
Contact information:
Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden
Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
SE-10450 Stockholm
E-mail: dan...@biotech.kth.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.biotech.kth.se/genetech/index.html
Fax: +46 8 5537 8481
--
Contact information:
Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden
Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
SE-10450 Stockholm
E-mail: dan...@biotech.kth.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.biotech.kth.se/genetech/index.html
Fax: +46 8 5537 8481
MSN messenger: klevebr...@msn.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Bug in package.skeleton, R 2.9.0?
Dear all,
I am using package.skeleton to build a small packages of misc function
for personal use. I have recently discovered that the option
force=TRUE doesn't seem to do what is meant to do. Here's what I'm
doing:
> setwd("/Users/danielk/Documents/R/packages/dk")
> files <- paste("codebase", dir("codebase", pattern=".R"), sep="/")
> package.skeleton(name="dk", force=TRUE, code_files=files)
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Copying code files ...
Making help files ...
Done.
Further steps are described in './dk/Read-and-delete-me'.
>
Now, everything seems fine, but changes to files in me codebase
folder, doesn't come along if the folder dk/R already contains the
files, even though I use force=TRUE. If I remove the dk/R folder or
the dk folder altogether, the changes come along so to me it seems
that it's the overwrite part that doesn't work as it should - or am I
doing something wrong here?
See below for sessionInfo.
Thanks a bunch
Daniel
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.9.0
>
--
Contact information:
Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden
Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075,
SE-10450 Stockholm
E-mail: dan...@biotech.kth.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.biotech.kth.se/genetech/index.html
Fax: +46 8 5537 8481
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
