Aaron,
Thanks for taking the time to report a bug.
On 5 August 2008 at 08:05, Aaron Culich wrote:
| Package: r-base-dev
| Version: 2.7.1-2
| Severity: important
|
| When installing an R package it fails to create the .so file. This
| happens with my own packages, as well as any I download from CRAN, for
Unlikely. Many of us do that all the time, plus the Debian autobuilder
rebuilds some 50 or 60 sixty packages across a dozen architectures. This
works.
| example I have the problem with MCMCpack:
|
| % R CMD INSTALL -l ./lib MCMCpack
What may have been your problem is the '-l ./lib'. You are generally advised
(see R Admin manual from the three r-doc-* packages) to _not_ install into
your source directory. More common is something like
$ cd src/R/packages ## or whereever your sources are
$ R CMD INSTALL -l ~/R/lib MCMCpack ## note that lib is somewhere
else
| g++ -I/usr/share/R/include -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0
-DHAVE_TRUNC -fpic -g -O2 -c MCMCprobitres.cc -o MCMCprobitres.o
| g++ -I/usr/share/R/include -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0
-DHAVE_TRUNC -fpic -g -O2 -c MCMCregress.cc -o MCMCregress.o
| make: `MCMCSVDreg.o' is up to date.
| g++ -I/usr/share/R/include -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0
-DHAVE_TRUNC -fpic -g -O2 -c MCMCtobit.cc -o MCMCtobit.o
| cp: cannot stat `*.so': No such file or directory
| chmod: cannot access `/tmp/lib/MCMCpack/libs/*': No such file or directory
| ERROR: compilation failed for package 'MCMCpack'
| ** Removing '/tmp/lib/MCMCpack'
|
| Note that it is missing the usual link line that would be something like:
|
| g++ -shared -Wl,-O1 -o MCMCpack.so ...
That's all hidden from you and me as R does that.
Lastly, MCMCpack is in Debian as
[EMAIL PROTECTED]:~> apt-cache show r-cran-mcmcpack
Package: r-cran-mcmcpack
Priority: optional
Section: math
Installed-Size: 2784
Maintainer: Chris Lawrence <[EMAIL PROTECTED]>
Architecture: i386
Source: mcmcpack
Version: 0.9-4-1
Depends: libc6 (>= 2.7-1), libgcc1 (>= 1:4.1.1-21), libstdc++6 (>= 4.2.1-4),
r-base-core (>> 2.5.0), r-cran-coda (>> 0.11-3), r-cran-vr (>> 7.2.8)
Suggests: r-cran-bayesm, r-cran-eco, r-cran-mnp
Filename: pool/main/m/mcmcpack/r-cran-mcmcpack_0.9-4-1_i386.deb
Size: 656866
MD5sum: d724c56445ffdb09407a82876bad82fe
SHA1: 2ce58fbd02325edca761e7ac8354ed2f8f8901d8
SHA256: fede3112030b9d102668f85ecf95a05f679072c77af936951c6376e0bdc67c51
Description: GNU R routines for Markov chain Monte Carlo model estimation
This is a set of routines for GNU R that implement various
statistical and econometric models using Markov chain Monte Carlo
(MCMC) estimation, which allows "solving" models that would otherwise
be intractable with traditional techniques, particularly problems in
Bayesian statistics (where one or more "priors" are used as part of
the estimation procedure, instead of an assumption of ignorance about
the "true" point estimates), although MCMC can also be used to solve
frequentist statistical problems with uninformative priors. MCMC
techniques are also preferable over direct estimation in the presence
of missing data.
.
Currently implemented are a number of ecological inference (EI)
routines (for estimating individual-level attributes or behavior from
aggregate data, such as electoral returns or census results), as well
as models for traditional linear panel and cross-sectional data, some
visualization routines for EI diagnostics, two item-response theory
(or ideal-point estimation) models, metric, ordinal, and
mixed-response factor analysis, and models for Gaussian (linear) and
Poisson regression, logistic regression (or logit), and binary and
ordinal-response probit models.
.
The suggested packages (r-cran-bayesm, -eco, and -mnp) contain
additional models that may also be useful for those interested in
this package.
Homepage: http://mcmcpack.wustl.edu/
Tag: devel::lang:r, devel::library, field::statistics, implemented-in::r,
role::app-data, suite::gnu
so I am also CCing Chris. I doubt it is broken but you never know.
| I haven't changed any of the R configuration files, and it doesn't
| even work on my R package's src directory when I leave out the
| Makevars file altogether. Not sure if this is a problem with the
| Debian version or an issue upstream.
I don't follow.
Package building 'just works'. Maybe this is just a simple 'how do I do
this' type question we can sort out.
Dirk
| -- System Information:
| Debian Release: lenny/sid
| APT prefers unstable
| APT policy: (500, 'unstable')
| Architecture: i386 (i686)
|
| Kernel: Linux 2.6.25-2-686 (SMP w/2 CPU cores)
| Locale: LANG=en_US.ISO-8859-15, LC_CTYPE=en_US.ISO-8859-15
(charmap=ISO-8859-15)
| Shell: /bin/sh linked to /bin/bash
|
| Versions of packages r-base-dev depends on:
| ii build-essential 11.3 informational list of
build-essent
| ii dpatch 2.0.29 patch maintenance system for
Debia
| ii g++ 4:4.3.1-2 The GNU C++ compiler
| ii gcc 4:4.3.1-2 The GNU C compiler
| ii gfortran 4:4.3.1-2 The GNU Fortran 95 compiler
| ii libblas-dev 1.2-2 Basic Linear Algebra Subroutines
3
| ii libbz2-dev 1.0.5-0.1 high-quality block-sorting file
co
| ii libjpeg62-dev 6b-14 Development files for the IJG
JPEG
| ii liblapack-dev 3.1.1-1 library of linear algebra
routines
| ii libncurses5-dev 5.6+20080621-2 developer's libraries and docs
for
| ii libpcre3-dev 7.6-2 Perl 5 Compatible Regular
Expressi
| ii libpng12-dev 1.2.27-1 PNG library - development
| ii libreadline5-dev 5.2-3 GNU readline and history
libraries
| ii r-base-core 2.7.1-2 GNU R core of statistical
computin
| ii zlib1g-dev 1:1.2.3.3.dfsg-12 compression library - development
|
| r-base-dev recommends no packages.
|
| Versions of packages r-base-dev suggests:
| pn cdbs <none> (no description available)
| ii debhelper 7.0.13 helper programs for debian/rules
|
| -- no debconf information
|
|
--
Three out of two people have difficulties with fractions.
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