On 12/02/2016 09:26 AM, Leonardo Collado Torres wrote:
Dear Jurat,
Maybe it'll be helpful to you if you see how other packages have their
data. For example, take a look at one of my packages:
https://github.com/lcolladotor/derfinder
You'll see that I have two directories inside /inst/extdata with some
files that I use in my vignette code. See
https://github.com/lcolladotor/derfinder/tree/master/inst/extdata for
the files and search system.file() inside
https://github.com/lcolladotor/derfinder/blob/master/vignettes/derfinder-quickstart.Rmd
to see how I use it in the vignette.
Regarding your permissions issue, I don't recall right now how to get
this to work with Windows. But basically you can see that error at:
Warning in dir.create(pkgoutdir, mode = "0755") :
cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason 'Permission denied'
Is your user in your windows machine part of the "administrators"
group? If not, that could be why.
Just to clarify, you don't need (and shouldn't) need administrator
privileges to 'R CMD check' a package. The error message above (which
appears as a warning) indicates that Jurat is trying to run
'R CMD check' from inside the C:\Program Files\R\R-devel\bin\x64\
folder, which is of course a very bad idea. As Dan said, 'R CMD check'
should be run in a directory where you have write permissions. Typically
in your home or in a directory below it.
H.
You could otherwise run R CMD build
and upload your tar ball (a .tar.gz file) to
https://builder.r-hub.io/.
Finally, you might want to search the manual of how to create R
extensions for other details.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html
Best,
Leo
On Fri, Dec 2, 2016 at 12:11 PM, Jurat Shayidin <juratb...@gmail.com> wrote:
Dear Dan :
I forgot to commit vignette file, now I pushed new changes, so now error
could be something else. People in stackoverflow suggest me to put all my
external data (a.k.a, bed files) into vignette folder, try to run R CMD
check and see what happen, I did this solution, but it doesn't work. Plus,
I checked file permission of my package parent directory, seems fine to me.
How I check file permission of my package ?
How can I fix this write permission on my machine ? This is not intuitive
to me, Any hint please ?
Herve suggest me don't create inst/extdata directory manually, but I still
can't let external data available for vignette code. FYI, my objective in
vignette file : let external data available for package use, compile
trivial version of vignette with no error, then continue to make it
perfect. Here is updated session of R CMD check :
Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.
C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
"C:\Users\jvrat\Documents\MSPC"
* installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
* installing *source* package 'MSPC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)
C:\Program Files\R\R-devel\bin\x64>R CMD check
"C:\Users\jvrat\Documents\MSPC"
Warning in dir.create(pkgoutdir, mode = "0755") :
cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason 'Permission denied'
ERROR: cannot create check dir 'C:/Program
Files/R/R-devel/bin/x64/MSPC.Rcheck'
C:\Program Files\R\R-devel\bin\x64>R CMD build
"C:\Users\jvrat\Documents\MSPC"
* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command
'"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
"tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
R Markdown v1.
Quitting from lines 60-64 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
C:\Program Files\R\R-devel\bin\x64>
How I fix R CMD check error above ? system.file() still can't detect
external data. Any idea please ? Thanks a lot
Best regards :
Jurat
On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:
See below.
----- Original Message -----
From: "Jurat Shayidin" <juratb...@gmail.com>
To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
bioc-devel@r-project.org>
Sent: Friday, December 2, 2016 8:32:35 AM
Subject: Re: [Bioc-devel] package vignette error : external data can't
be captured when compiling package vignette
Dear Dan :
Really appreciated for your quick respond. Instead, I am using R CMD
check
on my packages, I have an error. Here is whole session detail :
Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.
C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
"C:\Users\jvrat\Documents\MSPC"
* installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
* installing *source* package 'MSPC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)
C:\Program Files\R\R-devel\bin\x64>R CMD check
"C:\Users\jvrat\Documents\MSPC"
Warning in dir.create(pkgoutdir, mode = "0755") :
cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason
'Permission denied'
ERROR: cannot create check dir 'C:/Program
Files/R/R-devel/bin/x64/MSPC.Rcheck'
You need to run R CMD check in a directory where you have write
permissions.
C:\Program Files\R\R-devel\bin\x64>R CMD build
"C:\Users\jvrat\Documents\MSPC"
* checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
* preparing 'MSPC':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command
'"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages=
-e
"tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
R Markdown v1.
Quitting from lines 62-66 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
object 'inputData' not found
Execution halted
Line 61 of the vignette (as it is in Github; it's apparently different on
yur machine based on the error message) is:
total.ERs <- denoise_ERs(peakGRs = inputData, tau.w = 1.0E-04, .fileName =
"noiseER", outDir = "", verbose = FALSE)
As you can see, the peakGRs argument is set to inputData, but inputData is
not defined anywhere.
Dan
C:\Program Files\R\R-devel\bin\x64>
How can I fix this R CMD check error ? Instead people in stackoverflow
remind me that using devtools packages is not stable some times, so I go
for old fashion : use CMD. Plus, still my external data can't available
for
vignette data, and vignette compilation is failed again. I used
system.file() to do this, but not working. Any idea please ? How can I
overcome this problem? Thanks a lot to Bioconductor project team.
Best regards :
Jurat
On Fri, Dec 2, 2016 at 5:20 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:
If your package is in github at https://github.com/julaiti/MSPC , it
looks like there is no inst or extdata folder in that repository.
Maybe it has not yet been added/committed/pushed to git?
Note that everything _under_ inst gets installed when you install the
package, but the inst directory itself goes away.
If in your package source you have the following structure:
inst/extdata/
inst/foo.txt
In the installed package you end up with:
extdata/
foo.txt
HTH
Dan
----- Original Message -----
From: "Jurat Shayidin" <juratb...@gmail.com>
To: "Hervé Pagès" <hpa...@fredhutch.org>, "bioc-devel" <
bioc-devel@r-project.org>
Sent: Friday, December 2, 2016 5:36:28 AM
Subject: Re: [Bioc-devel] package vignette error : external data can't
be captured when compiling package vignette
Dear Hervé :
Thanks again for your response on my issue. I've read your message
very
carefully and did all you suggested to me, still can't fix the
vignette
compilation error. I have developed my package on windows machine
under
devel version of R and Bioc, all unit test works fine to me. I don't
understand why inst/ directory was not created when I build and
install
my
packages, external data can't be read during vignette compilation.
However, my objective is, to build my package vignette with no error
in
the
first place, then continue to edit the context until getting final
version
of vignette file. When I install packages using devtools::install(), I
got
this :
devtools::install()
Installing MSPC
"C:/PROGRA~1/R/R-devel/bin/x64/R" \
--no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
"C:/Users/jvrat/Documents/MSPC" \
--library="C:/Users/jvrat/Documents/R/win-library/3.4" \
--install-tests
* installing *source* package 'MSPC' ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSPC)
Reloading installed MSPC
I believe doing this is right in vignette file after I follow your
advise :
```{r}
library(MSPC)
inputBed <- list.files(system.file("extdata", package = "MSPC"),
full.names
= TRUE)
inputData <- readPeakFile(peakFolder = inputBed)
inputData
```
However, I should not add inst/extdata manually , without this I can't
allow to load external data for package use, and vignette compilation
keep
failed. To be honest, this is my very first time building R packages,
I
don't know how to fix this error. Just out of curiosity, during
package
installation, everything is under the inst/ , but I don't have this
folder.
Why is that ? Is that possible to get further help from Bioconductor
project team to review the package source in github ?
I am stuck with this problem, I searched all possible answer from all
over
the place, cannot fix my issues. I am very sorry if my question is
naive
to
ask here. Could you point me out how to possibly solve this problem?
Thanks
again for your great favor.
Best regards :
Jurat
On Fri, Dec 2, 2016 at 2:04 AM, Hervé Pagès <hpa...@fredhutch.org>
wrote:
Hi,
Make sure you understand the difference between the *package source
tree*, which you control and where you must create the inst/ folder,
and the *package installation folder*, which gets created and
populated by 'R CMD INSTALL'. The exact location of the *package
installation folder* doesn't really matter but if you are curious
you can use the .libPaths() command to see it. The *package
installation
folder* is the subfolder of .libPaths() that has the name of the
package. You can also see it with find.package("mypackage").
During installation, everything that is under the inst/ folder will
get installed *directly* under the *package installation folder*.
So if you created the extdata/ folder under inst/ (as it should be),
extdata/ will end up being installed at
.libPaths()/mypackage/extdata/
The code in your examples can get the path to the *installed*
extdata/
folder with
system.file(package="mypackage", "extdata")
or get the path to any file under extdata/ with e.g.
system.file(package="mypackage", "extdata", "data1.bed")
Don't do
system.file(package="mypackage", "extdata/data1.bed")
even if it works for you because it's not portable (the use of / as
a separator is a platform-dependent thing).
Finally note that you should never try to modify anything that is
under
.libPaths() by hand. Furthermore, and that's a mistake we see
sometimes
with contributed packages, the code in your package should always
treat the *package installation folder* as a read-only folder.
Hope this helps,
H.
On 12/01/2016 04:34 PM, Jurat Shayidin wrote:
Hi BiocDevel :
I am getting vignette error when I building my packages, and
external
data
can't be captured by system.file() . I did unit test all function
of my
packages, it works fine. When I am going to compile package
vignette,
test
input bed file can't be detected. However, I used
devtools::install()command
to install my packages, but installation directory inst/ was not
created
automatically. By R package convention, all external data must be
located
in inst/, so I manually created this folder inst/extdata and paste
my
data, but vignette compilation still failed. According to convention
of R
package, my package structure will be:
myPackage
`- inst
`- extdata
`- data1.bed
`- data2.bed
`- R
`- ...
`- NAMESPACE
`- DESCRIPTION
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Jurat Shahidin
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608
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_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Jurat Shahidin
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608
--
Jurat Shahidin
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
