Re: [Bioc-devel] package download statistics
Sweet Dan, that is good to know. I realize of course you would only have stats for the Bioconductor.org server. That is still pretty useful. -Robert On Fri, Apr 19, 2013 at 1:42 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Fri, Apr 19, 2013 at 8:51 AM, Robert M. Flight rfligh...@gmail.com wrote: Is there any central, web-accessible location for the download statistics for all of the Bioconductor packages? I know each packages web-page has a link to a page with all of the download statistics, but was wondering if there was an easy way to get access to all of the statistics for given packages. There is this page: http://bioconductor.org/packages/stats/ All packages are listed here with the number of downloads for each in the last 12 months. One thing to bear in mind is that the stats we compile are only from downloads on bioconductor.org; we don't have access to the web server logs of other mirrors. Dan The reason is alt-metrics. I thought it would be cool to have a little R package that takes a supplied Bioconductor package name, and compares its download statistics to the download statistics for all the other Bioconductor packages, essentially providing a percentile ranking. Cheers, -Robert Robert M Flight, PhD Bioinformatics PostDoctoral Scholar Center for Regulatory Environmental Analytical Metabolomics (CREAM) Department of Chemistry Rm 309, Chemistry Building University of Louisville 2320 South Brook Street Louisville, KY 40292 PH 502-509-1827 EM robert.fli...@louisville.edu EM rfligh...@gmail.com robertmflight.blogspot.com The most exciting phrase to hear in science, the one that heralds new discoveries, is not Eureka! (I found it!) but That's funny ... - Isaac Asimov [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 13-04-19 10:03 PM, Gabor Grothendieck wrote: On Fri, Apr 19, 2013 at 8:47 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-19 5:37 PM, Kevin Coombes wrote: Having finally found some free time, I was going to use it to update a bunch of R packages from 2.15 to 3.0. I am running Windows 7, 64-bit professional. This is on a brand-new laptop using vanilla settings when installing the operating system. Problem 1: I installed R3.0 to the default location (C:\Program FIles\R\R-3.0.0). The first thing I tried to do was install BioConductor. This failed (permission denied). Thinking that this might be a BioConductor problem, I then tried to install a (semirandom) package from CRAN. This also failed. In both cases, when using the GUI, the error message is almost incomprehensible. You get a pop-up window that *only* says Do you want to use a private library instead? Since this wasn't what I wanted to do I said no. Only after the pop-up closes does the command window print the error message telling me that permission was denied for R to write to its own library location. This is a standard Windows problem, to stop viruses from modifying installed programs. The standard Windows solution to it is to run the installer as an administrator, taking personal responsibility for installing the package/virus. Since this is a laptop, you could probably do this, but it's possible that you are not the administrator on your system. If that's the case, you should ask your administrator to do the install. Dumb Fix to Problem 1: So, I uninstalled R and then reinstalled to a nonstandard location (C:\R\R-3.0.0). Now I can successfully install packages from CRAN and BioConductor (hooray!). But I run directly into: That's another solution, and a third solution is to accept the offer R made, to install your packages somewhere where you as a user have write permission. Problem 2: Emacs Speaks Statistics (ESS) can no longer find the R binary. When R was installed in the default location, ESS worked. When R 2.15 (or earlier) was installed in the same nonstandard location, I could get ESS to find the R binaries by including (setq ess-directory-containing-r C:) in my .emacs file, but that no longer works. Dumb Fix to Problem 2: Hack into ess-site.el and put the complete, explicit path to the correct binary into (setq-default inferior-R-program-name 'FULLPATHHERE) which will break as soon as I upgrade R (assuming I am foolish enough to ever do that again). I can't help you with ESS. Now I am ready to rebuild my R packages. I have this nice perl script that goes through the following procedure: 1. Set the path to include the correct Rtools directory. (For reasons that Gabor Grothendieck has pointed out previously, this is not a permanent part of the path since doing so would override some built-in Windows commands.) Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Only those people who choose not to solve them in the recommended way. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. Hadley -- Chief Scientist, RStudio http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Publishing my Package on CRAN
On 19.04.2013 06:38, liuyipei wrote: Hi, I have a simple package with two functions. It essentially implements estimators and data simulation for a paper I am writing for immunology (and in some sense, ecology). How long is the typical CRAN review process Typically less than 12 hours. -- and how long will it take to get through the process? How selective is it? Depends on how well the package is prepared. Best, Uwe Ligges I have never published a package before, so I am wondering whether you guys think this is a reasonable thing for me to promise in the paper that the package will be available on CRAN. Thank you for your advice in advance! -- View this message in context: http://r.789695.n4.nabble.com/Publishing-my-Package-on-CRAN-tp4664676.html Sent from the R devel mailing list archive at Nabble.com. __ 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
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linux distribution with gcc 4.8 and AddressSanitizer -- solved
It works! After some hours of compilation, reading the docs and testing, I got it now working and was able to reproduce (and fix) the reported error message. Then ingredients of the successful AdressSanitizer (ASAN) system were: - Fedora 19 Alpha RC4 with gcc 4.8 on VirtualBox, - manual installation of several additional libraries especially libasan-devel, - setting of Makevars and a few environment variables, - compilation of R-devel (2013-04-19) with address-sanitizer (and --enable-strict barrier) == the compilation of R itself went through without problems so that R runs without crash. Finally: - compilation and ASAN check of the affected package that reproduced the error message. - bugfix and successful final test. Maybe this was not the most parsimonious approach ;-) but using a suitable self-compiled R seems to be unavoidable. Again, many thanks for your help and the great R system! Thomas P. -- Thomas Petzoldt Technische Universitaet Dresden Faculty of Environmental Sciences Institute of Hydrobiology 01062 Dresden, Germany E-Mail: thomas.petzo...@tu-dresden.de http://tu-dresden.de/Members/thomas.petzoldt __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to control the environment of a formula
On 13-04-19 2:57 PM, Thomas Alexander Gerds wrote:
hmm. I have tested a bit more, and found this perhaps more difficult
solve situation. even though I delete x, since x is part of the output
of the formula, the size of the object is twice as much as it should be:
test - function(x){
x - rnorm(100)
out - list(x=x)
rm(x)
out$f - as.formula(a~b)
out
}
v - test(1)
x - rnorm(100)
save(v,file=~/tmp/v.rda)
save(x,file=~/tmp/x.rda)
system(ls -lah ~/tmp/*.rda)
-rw-rw-r-- 1 tag tag 15M Apr 19 20:52 /home/tag/tmp/v.rda
-rw-rw-r-- 1 tag tag 7,4M Apr 19 20:52 /home/tag/tmp/x.rda
can you solve this as well?
Yes, this is tricky. The problem is that out is in the environment of
out$f, so you get two copies when you save it. (I think you won't have
two copies in memory, because R only makes a copy when it needs to, but
I haven't traced this.)
Here are two solutions, both have some problems.
1. Don't put out in the environment:
test - function(x) {
x - rnorm(100)
out$x - list(x=x)
out$f - a ~ b# the as.formula() was never needed
# temporarily create a new environment
local({
# get a copy of what you want to keep
out - out
# remove everything that you don't need from the formula
rm(list=c(x, out), envir=environment(out$f))
# return the local copy
out
})
}
I don't like this because it is too tricky, but you could probably wrap
the tricky bits into a little function (a variant on return() that
cleans out the environment first), so it's probably what I would use if
I was desperate to save space in saved copies.
2. Never evaluate the formula in the first place, so it doesn't pick up
the environment:
test - function(x) {
x - rnorm(100)
out$x - list(x=x)
out$f - quote(a ~ b)
out
}
This is a lot simpler, but it might not work with some modelling
functions, which would be confused by receiving the model formula
unevaluated. It also has the problems that you get with using
.GlobalEnv as the environment of the formula, but maybe to a slightly
lesser extent: rather than having what is possibly the wrong
environment, it doesn't have one at all.
Duncan Murdoch
thanks!
thomas
Duncan Murdoch murdoch.dun...@gmail.com writes:
On 13-04-18 11:39 AM, Thomas Alexander Gerds wrote:
Dear Duncan
thank you for taking the time to answer my questions! It will be
quite some work to delete all the objects generated inside the
function ... but if there is no other way to avoid a large
environment then this is what I will do.
It's not really that hard. Use names - ls() in the function to get a
list of all of them; remove the names of variables that might be
needed in the formula (and the name of the formula itself); then use
rm(list=names) to delete everything else just before returning it.
Duncan Murdoch
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Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 4/20/2013 12:54 PM, Duncan Murdoch wrote: On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel How do you do that? (More explicitly, what steps would I have to take to redefine things like find.exe and sort.exe in Rtools so that R would know how to find them and use them? I can't figure that out from the earlier parts of these messages.) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On Sat, Apr 20, 2013 at 1:54 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. I certainly was not aware of this and posts in this thread suggest that others were not aware of it either. Perhaps you could provide some details and links. I am sure many people would be interested. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to control the environment of a formula
On Sat, Apr 20, 2013 at 1:44 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 13-04-19 2:57 PM, Thomas Alexander Gerds wrote:
hmm. I have tested a bit more, and found this perhaps more difficult
solve situation. even though I delete x, since x is part of the output
of the formula, the size of the object is twice as much as it should be:
test - function(x){
x - rnorm(100)
out - list(x=x)
rm(x)
out$f - as.formula(a~b)
out
}
v - test(1)
x - rnorm(100)
save(v,file=~/tmp/v.rda)
save(x,file=~/tmp/x.rda)
system(ls -lah ~/tmp/*.rda)
-rw-rw-r-- 1 tag tag 15M Apr 19 20:52 /home/tag/tmp/v.rda
-rw-rw-r-- 1 tag tag 7,4M Apr 19 20:52 /home/tag/tmp/x.rda
can you solve this as well?
Yes, this is tricky. The problem is that out is in the environment of
out$f, so you get two copies when you save it. (I think you won't have two
copies in memory, because R only makes a copy when it needs to, but I
haven't traced this.)
Here are two solutions, both have some problems.
1. Don't put out in the environment:
test - function(x) {
x - rnorm(100)
out$x - list(x=x)
out$f - a ~ b# the as.formula() was never needed
# temporarily create a new environment
local({
# get a copy of what you want to keep
out - out
# remove everything that you don't need from the formula
rm(list=c(x, out), envir=environment(out$f))
# return the local copy
out
})
}
I don't like this because it is too tricky, but you could probably wrap the
tricky bits into a little function (a variant on return() that cleans out
the environment first), so it's probably what I would use if I was desperate
to save space in saved copies.
2. Never evaluate the formula in the first place, so it doesn't pick up the
environment:
test - function(x) {
x - rnorm(100)
out$x - list(x=x)
out$f - quote(a ~ b)
out
}
This is a lot simpler, but it might not work with some modelling functions,
which would be confused by receiving the model formula unevaluated. It also
has the problems that you get with using .GlobalEnv as the environment of
the formula, but maybe to a slightly lesser extent: rather than having what
is possibly the wrong environment, it doesn't have one at all.
An approach along the lines of Duncan's last solution that works with
lm but may or may not work with other regression-style functions is to
use a character string:
fit - lm(demand ~ Time, BOD)
As long as you are only saving the input you should be OK but if you
are saving the output of lm then you are back to the same problem
since the lm object will contain a formula.
class(formula(fit))
[1] formula
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Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 13-04-20 2:02 PM, Kevin Coombes wrote: On 4/20/2013 12:54 PM, Duncan Murdoch wrote: On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel How do you do that? (More explicitly, what steps would I have to take to redefine things like find.exe and sort.exe in Rtools so that R would know how to find them and use them? I can't figure that out from the earlier parts of these messages.) Rename them to whatever you want in the Rtools install, then edit the definitions. I think currently they are in src/gnuwin32/Makefile and src/gnuwin32/MkRules (one in each), but I'd suggest you just search files named M* for the strings sort and find, in case I've got it wrong, or it has changed since the last time I looked. If you try to build R itself rather than just packages, you may need to do more edits, because some of the makefiles for things like the jpeg libraries weren't written by us, and may have these commands hard-coded. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On Sat, Apr 20, 2013 at 2:21 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 2:02 PM, Kevin Coombes wrote: On 4/20/2013 12:54 PM, Duncan Murdoch wrote: On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel How do you do that? (More explicitly, what steps would I have to take to redefine things like find.exe and sort.exe in Rtools so that R would know how to find them and use them? I can't figure that out from the earlier parts of these messages.) Rename them to whatever you want in the Rtools install, then edit the definitions. I think currently they are in src/gnuwin32/Makefile and src/gnuwin32/MkRules (one in each), but I'd suggest you just search files named M* for the strings sort and find, in case I've got it wrong, or it has changed since the last time I looked. If you try to build R itself rather than just packages, you may need to do more edits, because some of the makefiles for things like the jpeg libraries weren't written by us, and may have these commands hard-coded. Are you suggesting that R itself be rebuild? Rtools be rebuilt? Some clarity on this and the process to do it would be helpful. I was really looking for a way to do this with an out of the box R installation since from a practical viewpoint few are going to want to build their own software. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Publishing my Package on CRAN
If you're not aware of it, you should know of: http://cran.r-project.org/web/packages/policies.html /Henrik On Sat, Apr 20, 2013 at 8:42 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 19.04.2013 06:38, liuyipei wrote: Hi, I have a simple package with two functions. It essentially implements estimators and data simulation for a paper I am writing for immunology (and in some sense, ecology). How long is the typical CRAN review process Typically less than 12 hours. -- and how long will it take to get through the process? How selective is it? Depends on how well the package is prepared. Best, Uwe Ligges I have never published a package before, so I am wondering whether you guys think this is a reasonable thing for me to promise in the paper that the package will be available on CRAN. Thank you for your advice in advance! -- View this message in context: http://r.789695.n4.nabble.com/Publishing-my-Package-on-CRAN-tp4664676.html Sent from the R devel mailing list archive at Nabble.com. __ 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 13-04-20 2:39 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 2:21 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 2:02 PM, Kevin Coombes wrote: On 4/20/2013 12:54 PM, Duncan Murdoch wrote: On 13-04-20 12:30 PM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 11:49 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-04-20 11:09 AM, Gabor Grothendieck wrote: On Sat, Apr 20, 2013 at 10:45 AM, Hadley Wickham h.wick...@gmail.com wrote: Just curious: how often do you use the Windows find command? We have put instructions in place for people to run the install process with a renamed Rtools find command (which I think is the only conflict). The issue is that more users who want to use the command line commands are familiar with the Unix variant (which came first, by the way) than the Windows one, so renaming the Rtools one would cause trouble for more people. Its not just find - its also sort. And really R has no business clobbering built in Windows commands. This is just wrong and really causes anyone who does any significant amount of Windows batch programming (or uses batch programs of any complexity) endless problems. Which is presumably why Rtools doesn't modify the path by default. Better solutions (e.g. Rstudio and devtools) temporarily set the path on when you're calling R CMD *. I am well aware of the various kludges to address this including my own batchfiles ( http://batchfiles.googlecode.com ) which handles this by temporarily changing the path as well; however, the real problem is that Rtools does not play nice with Windows and that needs to be addressed directly. It has been. You ignored it. Duncan Murdoch If some change to address this has been made that would be great but there is no mention of it on the Rtools page in the change history section (the only documented change relates to the png/tiff/jpeg libraries), there was no announcement that I saw and Rtools\bin still contains find and sort so what specifically is the change? It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel How do you do that? (More explicitly, what steps would I have to take to redefine things like find.exe and sort.exe in Rtools so that R would know how to find them and use them? I can't figure that out from the earlier parts of these messages.) Rename them to whatever you want in the Rtools install, then edit the definitions. I think currently they are in src/gnuwin32/Makefile and src/gnuwin32/MkRules (one in each), but I'd suggest you just search files named M* for the strings sort and find, in case I've got it wrong, or it has changed since the last time I looked. If you try to build R itself rather than just packages, you may need to do more edits, because some of the makefiles for things like the jpeg libraries weren't written by us, and may have these commands hard-coded. Are you suggesting that R itself be rebuild? Rtools be rebuilt? Some clarity on this and the process to do it would be helpful. I was really looking for a way to do this with an out of the box R installation since from a practical viewpoint few are going to want to build their own software. No. No. Can't help you. So? Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On 4/20/2013 1:21 PM, Duncan Murdoch wrote: On 13-04-20 2:02 PM, Kevin Coombes wrote: On 4/20/2013 12:54 PM, Duncan Murdoch wrote: It's not a change to Rtools, it's a change is to the build system in R: it allows you to rename sort or find in your own copy of Rtools, and R will use whatever you specify. You were informed of this when I did it in 2007, and I've mentioned it when the topic comes up here, most recently in the message quoted above. That's a long time ago, so I don't remember if you tried it then, but I've never heard a complaint from anyone else that it doesn't work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel How do you do that? (More explicitly, what steps would I have to take to redefine things like find.exe and sort.exe in Rtools so that R would know how to find them and use them? I can't figure that out from the earlier parts of these messages.) Rename them to whatever you want in the Rtools install, then edit the definitions. I think currently they are in src/gnuwin32/Makefile and src/gnuwin32/MkRules (one in each), but I'd suggest you just search files named M* for the strings sort and find, in case I've got it wrong, or it has changed since the last time I looked. If you try to build R itself rather than just packages, you may need to do more edits, because some of the makefiles for things like the jpeg libraries weren't written by us, and may have these commands hard-coded. Duncan Murdoch To most Windows users, the Rtools install would seem to refer to getting the bundled Rtools30.exe from the CRAN web site, double-clicking on it, selecting the options form the GUI windows that appear, and clicking install. There is no option in this procedure to change the names of find or sort. As far as I can tell, the steps you are recommending take place in an earlier build step. This would require the user who wants to do this to rebuild Rtools in its entirety, which is more trouble than it is likely to be worth. Especially when you can avoid the problem by using your own batch script or perl script to reset the path on those relatively rare occasions when you need to use Rtools. Since buiilding Rtools for a Windows machine is something than CRAN does on a regular basis, why can't they just change the names there (and not bother the UNIX users, and probably not even bother the UNIX users who find themselves banished to the Windows wilderness). Just call them unixfind and unixsort and everyone will be able to figure it out __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
As far as I can tell, the steps you are recommending take place in an earlier build step. This would require the user who wants to do this to rebuild Rtools in its entirety, which is more trouble than it is likely to be worth. Especially when you can avoid the problem by using your own batch script or perl script to reset the path on those relatively rare occasions when you need to use Rtools. Since buiilding Rtools for a Windows machine is something than CRAN does on a regular basis, why can't they just change the names there (and not bother the UNIX users, and probably not even bother the UNIX users who find themselves banished to the Windows wilderness). Just call them unixfind and unixsort and everyone will be able to figure it out Because the point of Rtools is to make windows more like linux, rather than less? I really don't understand the complaints in this thread - I have regularly had classes of 10-20 windows users build a package with no prior experience, and simply downloading and installing Rtools. In my opinion Rtools uses the right defaults, and with a bit of extra scripting work (painful at first, but only needs to be done once, e.g. https://github.com/hadley/devtools/blob/master/R/rtools.r) it's painless to use from R. Hadley -- Chief Scientist, RStudio http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
On Sat, Apr 20, 2013 at 9:13 PM, Hadley Wickham h.wick...@gmail.com wrote: As far as I can tell, the steps you are recommending take place in an earlier build step. This would require the user who wants to do this to rebuild Rtools in its entirety, which is more trouble than it is likely to be worth. Especially when you can avoid the problem by using your own batch script or perl script to reset the path on those relatively rare occasions when you need to use Rtools. Since buiilding Rtools for a Windows machine is something than CRAN does on a regular basis, why can't they just change the names there (and not bother the UNIX users, and probably not even bother the UNIX users who find themselves banished to the Windows wilderness). Just call them unixfind and unixsort and everyone will be able to figure it out Because the point of Rtools is to make windows more like linux, rather than less? I really don't understand the complaints in this thread - I have regularly had classes of 10-20 windows users build a package with no prior experience, and simply downloading and installing Rtools. In my opinion Rtools uses the right defaults, and with a bit of extra scripting work (painful at first, but only needs to be done once, e.g. https://github.com/hadley/devtools/blob/master/R/rtools.r) it's painless to use from R. The problem is that if you don't just use the PC for running R but use it to run other programs too then any program and that utilizes Windows batch scripts making use of find.exe or sort.exe likely won't work if Rtools is on your path. The fact that devtools, batchfiles and Rcpp have workarounds mitigates it somewhat but the problem should be fixed so it works out-of-the-box once and for all. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
