[Rd] RcppArmadillo compilation error: R CMD SHLIB returns status 1
Dear all,
running the example by D. Eddebuettel
(http://dirk.eddelbuettel.com/blog/2011/04/23/) I get an error message.
Specifically, the R code I was taking from the above example is
### BEGIN EXAMPLE ###
suppressMessages(require(RcppArmadillo))
suppressMessages(require(Rcpp))
suppressMessages(require(inline))
code <- '
arma::mat coeff = Rcpp::as(a);
arma::mat errors = Rcpp::as(e);
int m = errors.n_rows; int n = errors.n_cols;
arma::mat simdata(m,n);
simdata.row(0) = arma::zeros(1,n);
for (int row=1; row
4: #include
5:
6:
7: #ifndef BEGIN_RCPP
8: #define BEGIN_RCPP
9: #endif
10:
11: #ifndef END_RCPP
12: #define END_RCPP
13: #endif
14:
15: using namespace Rcpp;
16:
17:
18: // user includes
19:
20:
21: // declarations
22: extern "C" {
23: SEXP file33765791( SEXP a, SEXP e) ;
24: }
25:
26: // definition
27:
28: SEXP file33765791( SEXP a, SEXP e ){
29: BEGIN_RCPP
30:
31:arma::mat coeff = Rcpp::as(a);
32:arma::mat errors = Rcpp::as(e);
33:int m = errors.n_rows; int n = errors.n_cols;
34:arma::mat simdata(m,n);
35:simdata.row(0) = arma::zeros(1,n);
36:for (int row=1; row file33765791.cpp.err.txt' returned status 1
I am working under R 2.14.0 and as the pros among you might guess, I am new to
using the C++ interfaces within R. I think all I have to do is to edit some
settings on my Windows 7 machine here, but the error message is too cryptic to
me. Alas, I could also not find any thread or help topic that deals with this
online. I appreciate any direct reply or reference where I can find a solution
to this.
Please let me know in case I am leaving out some essential details here.
Many thanks,
Paul
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Re: [Rd] RcppArmadillo compilation error: R CMD SHLIB returns status 1
On 05/12/2011 1:22 PM, Paul Viefers wrote:
Dear all,
running the example by D. Eddebuettel
(http://dirk.eddelbuettel.com/blog/2011/04/23/) I get an error message.
Specifically, the R code I was taking from the above example is
### BEGIN EXAMPLE ###
suppressMessages(require(RcppArmadillo))
suppressMessages(require(Rcpp))
suppressMessages(require(inline))
code<- '
arma::mat coeff = Rcpp::as(a);
arma::mat errors = Rcpp::as(e);
int m = errors.n_rows; int n = errors.n_cols;
arma::mat simdata(m,n);
simdata.row(0) = arma::zeros(1,n);
for (int row=1; row
4: #include
5:
6:
7: #ifndef BEGIN_RCPP
8: #define BEGIN_RCPP
9: #endif
10:
11: #ifndef END_RCPP
12: #define END_RCPP
13: #endif
14:
15: using namespace Rcpp;
16:
17:
18: // user includes
19:
20:
21: // declarations
22: extern "C" {
23: SEXP file33765791( SEXP a, SEXP e) ;
24: }
25:
26: // definition
27:
28: SEXP file33765791( SEXP a, SEXP e ){
29: BEGIN_RCPP
30:
31:arma::mat coeff = Rcpp::as(a);
32:arma::mat errors = Rcpp::as(e);
33:int m = errors.n_rows; int n = errors.n_cols;
34:arma::mat simdata(m,n);
35:simdata.row(0) = arma::zeros(1,n);
36:for (int row=1; row file33765791.cpp.err.txt' returned status 1
I am working under R 2.14.0 and as the pros among you might guess, I am new to
using the C++ interfaces within R. I think all I have to do is to edit some
settings on my Windows 7 machine here, but the error message is too cryptic to
me. Alas, I could also not find any thread or help topic that deals with this
online. I appreciate any direct reply or reference where I can find a solution
to this.
Please let me know in case I am leaving out some essential details here.
If you put the program source into a file (e.g. fn.cpp) and in a Windows
cmd shell you run
R CMD SHLIB fn.cpp
what do you get? I would guess you've got a problem with your setup of
the compiler or other tools, and this would likely show it.
Duncan Murdoch
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[Rd] warning for inefficiently compressed datasets
Hi,
Recently added to doc/NEWS.Rd:
'R CMD check' now gives a warning rather than a note if it finds
inefficiently compressed datasets. With 'bzip2' and 'xz' compression
having been available since R 2.10.0, there is no excuse for not
using them.
Why isn't a note enough for this?
Generally speaking, warnings are for things that are dangerous,
or unsafe, or unportable, or for anything that could potentially
cause trouble. I don't see how using gzip instead of bzip2 or xz
could fall into that category (and BTW gzip is the default for
save() and for 'R CMD build' resave-data feature).
The problem is that bzip2 and xz compressions are slower and also
require more memory than gzip. Bioconductor has big data packages
and sometimes it makes sense to use gzip and not bzip2 or xz. For
example, when loading Human chromosome 1 from disk, bzip2 and xz
are 7 and 3.4 times slower than gzip, respectively:
> system.time(load("chr1-gzip.rda"))
user system elapsed
1.210 0.180 1.384
> system.time(load("chr1-bzip2.rda"))
user system elapsed
9.500 0.160 9.674
> system.time(load("chr1-xz.rda"))
user system elapsed
4.460.204.69
hpages@latitude:~/testing$ ls -lhtr chr1-*.rda
-rw-r--r-- 1 hpages hpages 61M 2011-12-06 12:13 chr1-gzip.rda
-rw-r--r-- 1 hpages hpages 55M 2011-12-06 12:15 chr1-bzip2.rda
-rw-r--r-- 1 hpages hpages 49M 2011-12-06 12:25 chr1-xz.rda
This is with R-2.14.0 on a 64-bit Ubuntu laptop with 8GB of RAM.
The size on disk doesn't really matter and it doesn't matter either
that the source tarball for the full Human genome ends up being 20%
bigger when using gzip instead of xz: the 20% extra time it takes to
download it (which needs to be done only once) will largely be
compensated by the fact that most analyses will run faster e.g. in
40-45 sec. instead of more than 2 minutes (for many short analyses,
loading the chromosomes into memory is the bottleneck).
Is there a way to turn this warning off? If not, could an option be
added to 'R CMD check' to turn this warning off? Something along the
lines of the --no-resave-data option for 'R CMD build'.
Thanks,
H.
--
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...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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