Greetings. I am new to R, but have quite a bit of experience
programming with other languages (e.g., Perl, Java, Python, shell
scripting). I'm now working on a project where I need to use R. A
colleague wrote a number of small scripts that work fine in Rstudio,
but a couple of them don't work when run using Rscript (which we're
planning on doing). The behavior is basically the same on a few
different machines (two of them are Linux, one I think is a Mac). To
run the scripts using Rscript, we put one of the following lines at
the top of the script:
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
or called the script using Rscript:
Rscript scriptname
In all cases, the behavior is the same.
Here's one of the scripts:
#!/usr/bin/env Rscript
library(apcluster)
options(stringsAsFactors = FALSE)
args <- commandArgs(TRUE)
num <- args[1]
numClusters <- num
mydata <- read.csv("input_data.csv")
xData <- mydata[, 1]
yData <- mydata[, 2]
fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
#Leave the rest commented for now
#output <- data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3])))
#write.csv <- write.table(output, file = "output_AP.csv", sep = ",", row.names = FALSE, col.names = FALSE)
Here's a call to the script:
$ ./affinity_propagation.R 3
Attaching
The following object is masked package::
heatmap
Trying p = -15.41969
Number of clusters: 17
Error in tmpk - K : non-numeric argument to binary operator
Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK -> .local
Execution halted
The line with the expression "tmpk - K" is from the code for the
apclusterK() function (from the apcluster library). The
definition/value of tmpk is set using a call to the function length().
I mention this because the failure we're getting with the other script
also seems to involve an expression with call to length(). Here's the
error from calling that script:
$ ./spectral_clustering.R 3
Loading required package: methods
Error in length(tmpsig) * nc : non-numeric argument to binary operator
Calls: specc -> specc -> .local -> matrix
Execution halted
The script is calling the specc() function in the kernlab library.
Any ideas what's going on here, why it's not working and what we can
do to get it to work? Is there something that needs to be set or run
in .Renviron or .Rprofile, say?
Thanks.
Milt Epstein
Programmer in Computational Genomics
Institute for Genomic Biology (IGB)
University of Illinois at Urbana-Champaign (UIUC)
mepstein at illinois.edu
script works in Rstudio but not with Rscript
5 messages · Henrik Bengtsson, Milt Epstein, William Dunlap
Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik
On Apr 8, 2015 07:41, "Milt Epstein" <mepstein at illinois.edu> wrote:
Greetings. I am new to R, but have quite a bit of experience
programming with other languages (e.g., Perl, Java, Python, shell
scripting). I'm now working on a project where I need to use R. A
colleague wrote a number of small scripts that work fine in Rstudio,
but a couple of them don't work when run using Rscript (which we're
planning on doing). The behavior is basically the same on a few
different machines (two of them are Linux, one I think is a Mac). To
run the scripts using Rscript, we put one of the following lines at
the top of the script:
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
or called the script using Rscript:
Rscript scriptname
In all cases, the behavior is the same.
Here's one of the scripts:
#!/usr/bin/env Rscript
library(apcluster)
options(stringsAsFactors = FALSE)
args <- commandArgs(TRUE)
num <- args[1]
numClusters <- num
mydata <- read.csv("input_data.csv")
xData <- mydata[, 1]
yData <- mydata[, 2]
fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
#Leave the rest commented for now
#output <- data.frame(xData, yData, c(as.data.frame(fit[1]),
as.data.frame(fit[2]), as.data.frame(fit[3])))
#write.csv <- write.table(output, file = "output_AP.csv", sep = ",",
row.names = FALSE, col.names = FALSE)
Here's a call to the script:
$ ./affinity_propagation.R 3
Attaching
The following object is masked package::
heatmap
Trying p = -15.41969
Number of clusters: 17
Error in tmpk - K : non-numeric argument to binary operator
Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK ->
.local
Execution halted
The line with the expression "tmpk - K" is from the code for the
apclusterK() function (from the apcluster library). The
definition/value of tmpk is set using a call to the function length().
I mention this because the failure we're getting with the other script
also seems to involve an expression with call to length(). Here's the
error from calling that script:
$ ./spectral_clustering.R 3
Loading required package: methods
Error in length(tmpsig) * nc : non-numeric argument to binary operator
Calls: specc -> specc -> .local -> matrix
Execution halted
The script is calling the specc() function in the kernlab library.
Any ideas what's going on here, why it's not working and what we can
do to get it to work? Is there something that needs to be set or run
in .Renviron or .Rprofile, say?
Thanks.
Milt Epstein
Programmer in Computational Genomics
Institute for Genomic Biology (IGB)
University of Illinois at Urbana-Champaign (UIUC)
mepstein at illinois.edu
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with "R -f script". The longer answer: Note that the script is currently set up to be called with a command line argument, "./affinity_propagation.R 3". So first I tried "R -f affinity_propagation.R 3". That failed, but because it wasn't using the "3" as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using "./affinity_propagation.R" -- and it worked! "R -f affinity_propagation.R" also worked. Then I noticed the --args command line option for R, and I ran "R -f affinity_propagation.R --args 3" on the original script, and it failed, the same error as I described below. Also, when you say "Try loading methods", do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error. So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num <- as.integer(args[1]) rather than: num <- args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepstein at illinois.edu
On Wed, 8 Apr 2015, Henrik Bengtsson wrote:
Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, "Milt Epstein" <mepstein at illinois.edu> wrote:
Greetings. I am new to R, but have quite a bit of experience
programming with other languages (e.g., Perl, Java, Python, shell
scripting). I'm now working on a project where I need to use R. A
colleague wrote a number of small scripts that work fine in Rstudio,
but a couple of them don't work when run using Rscript (which we're
planning on doing). The behavior is basically the same on a few
different machines (two of them are Linux, one I think is a Mac). To
run the scripts using Rscript, we put one of the following lines at
the top of the script:
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
or called the script using Rscript:
Rscript scriptname
In all cases, the behavior is the same.
Here's one of the scripts:
#!/usr/bin/env Rscript
library(apcluster)
options(stringsAsFactors = FALSE)
args <- commandArgs(TRUE)
num <- args[1]
numClusters <- num
mydata <- read.csv("input_data.csv")
xData <- mydata[, 1]
yData <- mydata[, 2]
fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
#Leave the rest commented for now
#output <- data.frame(xData, yData, c(as.data.frame(fit[1]),
as.data.frame(fit[2]), as.data.frame(fit[3])))
#write.csv <- write.table(output, file = "output_AP.csv", sep = ",",
row.names = FALSE, col.names = FALSE)
Here's a call to the script:
$ ./affinity_propagation.R 3
Attaching
The following object is masked package::
heatmap
Trying p = -15.41969
Number of clusters: 17
Error in tmpk - K : non-numeric argument to binary operator
Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK ->
.local
Execution halted
The line with the expression "tmpk - K" is from the code for the
apclusterK() function (from the apcluster library). The
definition/value of tmpk is set using a call to the function length().
I mention this because the failure we're getting with the other script
also seems to involve an expression with call to length(). Here's the
error from calling that script:
$ ./spectral_clustering.R 3
Loading required package: methods
Error in length(tmpsig) * nc : non-numeric argument to binary operator
Calls: specc -> specc -> .local -> matrix
Execution halted
The script is calling the specc() function in the kernlab library.
Any ideas what's going on here, why it's not working and what we can
do to get it to work? Is there something that needs to be set or run
in .Renviron or .Rprofile, say?
Thanks.
Milt Epstein
Programmer in Computational Genomics
Institute for Genomic Biology (IGB)
University of Illinois at Urbana-Champaign (UIUC)
mepstein at illinois.edu
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
args <- commandArgs(TRUE) num <- args[1]
and then you get a complaint about something not being numeric. commandArgs() returns a character vector so try num <- as.numeric(args[1]) and you may as well preface it with stopifnot(length(args)>0) Bill Dunlap TIBCO Software wdunlap tibco.com
On Wed, Apr 8, 2015 at 11:20 AM, Milt Epstein <mepstein at illinois.edu> wrote:
OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with "R -f script". The longer answer: Note that the script is currently set up to be called with a command line argument, "./affinity_propagation.R 3". So first I tried "R -f affinity_propagation.R 3". That failed, but because it wasn't using the "3" as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using "./affinity_propagation.R" -- and it worked! "R -f affinity_propagation.R" also worked. Then I noticed the --args command line option for R, and I ran "R -f affinity_propagation.R --args 3" on the original script, and it failed, the same error as I described below. Also, when you say "Try loading methods", do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error. So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num <- as.integer(args[1]) rather than: num <- args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepstein at illinois.edu On Wed, 8 Apr 2015, Henrik Bengtsson wrote:
Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, "Milt Epstein" <mepstein at illinois.edu> wrote:
Greetings. I am new to R, but have quite a bit of experience
programming with other languages (e.g., Perl, Java, Python, shell
scripting). I'm now working on a project where I need to use R. A
colleague wrote a number of small scripts that work fine in Rstudio,
but a couple of them don't work when run using Rscript (which we're
planning on doing). The behavior is basically the same on a few
different machines (two of them are Linux, one I think is a Mac). To
run the scripts using Rscript, we put one of the following lines at
the top of the script:
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
or called the script using Rscript:
Rscript scriptname
In all cases, the behavior is the same.
Here's one of the scripts:
#!/usr/bin/env Rscript
library(apcluster)
options(stringsAsFactors = FALSE)
args <- commandArgs(TRUE)
num <- args[1]
numClusters <- num
mydata <- read.csv("input_data.csv")
xData <- mydata[, 1]
yData <- mydata[, 2]
fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
#Leave the rest commented for now
#output <- data.frame(xData, yData, c(as.data.frame(fit[1]),
as.data.frame(fit[2]), as.data.frame(fit[3])))
#write.csv <- write.table(output, file = "output_AP.csv", sep = ",",
row.names = FALSE, col.names = FALSE)
Here's a call to the script:
$ ./affinity_propagation.R 3
Attaching
The following object is masked package::
heatmap
Trying p = -15.41969
Number of clusters: 17
Error in tmpk - K : non-numeric argument to binary operator
Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK
->
.local Execution halted The line with the expression "tmpk - K" is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc -> specc -> .local -> matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepstein at illinois.edu
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
On Wed, Apr 8, 2015 at 11:20 AM, Milt Epstein <mepstein at illinois.edu> wrote:
OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with "R -f script". The longer answer: Note that the script is currently set up to be called with a command line argument, "./affinity_propagation.R 3". So first I tried "R -f affinity_propagation.R 3". That failed, but because it wasn't using the "3" as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using "./affinity_propagation.R" -- and it worked! "R -f affinity_propagation.R" also worked. Then I noticed the --args command line option for R, and I ran "R -f affinity_propagation.R --args 3" on the original script, and it failed, the same error as I described below. Also, when you say "Try loading methods", do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error.
Yes, that's what I meant. My suggestion was just a guess given that it is not that uncommon to see cases where a script works with 'R' but not with 'Rscript'. From your answers/tests, it's seems clear that your problem now has to do with parsing arguments. /Henrik
So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num <- as.integer(args[1]) rather than: num <- args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepstein at illinois.edu On Wed, 8 Apr 2015, Henrik Bengtsson wrote:
Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, "Milt Epstein" <mepstein at illinois.edu> wrote:
Greetings. I am new to R, but have quite a bit of experience
programming with other languages (e.g., Perl, Java, Python, shell
scripting). I'm now working on a project where I need to use R. A
colleague wrote a number of small scripts that work fine in Rstudio,
but a couple of them don't work when run using Rscript (which we're
planning on doing). The behavior is basically the same on a few
different machines (two of them are Linux, one I think is a Mac). To
run the scripts using Rscript, we put one of the following lines at
the top of the script:
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
or called the script using Rscript:
Rscript scriptname
In all cases, the behavior is the same.
Here's one of the scripts:
#!/usr/bin/env Rscript
library(apcluster)
options(stringsAsFactors = FALSE)
args <- commandArgs(TRUE)
num <- args[1]
numClusters <- num
mydata <- read.csv("input_data.csv")
xData <- mydata[, 1]
yData <- mydata[, 2]
fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
#Leave the rest commented for now
#output <- data.frame(xData, yData, c(as.data.frame(fit[1]),
as.data.frame(fit[2]), as.data.frame(fit[3])))
#write.csv <- write.table(output, file = "output_AP.csv", sep = ",",
row.names = FALSE, col.names = FALSE)
Here's a call to the script:
$ ./affinity_propagation.R 3
Attaching
The following object is masked package::
heatmap
Trying p = -15.41969
Number of clusters: 17
Error in tmpk - K : non-numeric argument to binary operator
Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK ->
.local
Execution halted
The line with the expression "tmpk - K" is from the code for the
apclusterK() function (from the apcluster library). The
definition/value of tmpk is set using a call to the function length().
I mention this because the failure we're getting with the other script
also seems to involve an expression with call to length(). Here's the
error from calling that script:
$ ./spectral_clustering.R 3
Loading required package: methods
Error in length(tmpsig) * nc : non-numeric argument to binary operator
Calls: specc -> specc -> .local -> matrix
Execution halted
The script is calling the specc() function in the kernlab library.
Any ideas what's going on here, why it's not working and what we can
do to get it to work? Is there something that needs to be set or run
in .Renviron or .Rprofile, say?
Thanks.
Milt Epstein
Programmer in Computational Genomics
Institute for Genomic Biology (IGB)
University of Illinois at Urbana-Champaign (UIUC)
mepstein at illinois.edu
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.