Adam,
It seems that your attachment didn't make it through.
That aside, my experience with strange errors like those (random type
not implemented ones) has been that you may be looking at a memory
problem on you machine. Given that you can't replicate on another
platform (and the .csv file didn't come through), I would think it
wise to start there.
My 2c. And I love bacon too :)
Jeff
On Fri, Aug 7, 2009 at 1:10 PM, <a...@ilovebacon.org> wrote:
> This message is in MIME format. The first part should be readable text,
> while the remaining parts are likely unreadable without MIME-aware tools.
>
> --1660387551-1458482416-1249639718=:2997
> Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; FORMAT=flowed
> Content-ID: <pine.lnx.4.64.0908071039211.2...@parser.ilovebacon.org>
>
> Hello,
>
> There appears to be a bug in the nlm function, which I discovered
> when trying to run an SEM. The SEM is not bizarre; the covariance matrix is
> solve-able and the eigenvalues are greater than zero, and I do not believe
> the "sem" package per se to be the problem (as nlm keeps being the part that
> fails, though I can't replicate this with other nlm tasks). I apologize if
> I have put too many much information in this message; I'm not a programmer
> by trade so I don't really know what's going on here, which hampers my
> ability to write consise bug reports.
>
> Here is the code I use:
>
> library(sem)
> ice.S <- read.csv("iceS.csv") # attached
> rownames(ice.S) <- ice.S[,1]
> ice.S[,1] <- NULL
> ice.S <- as.matrix(ice.S)
> ice.ram <- specify.model("ice.ram") # attached
> ice.N <- 342
> ice.sem <- sem(ram=ice.ram, S=ice.S, N=ice.N)
>
> ...at this point, any number of problems could occur. I have seen the
> following.
>
> 1) Simple lack of convergence. (might be my model's fault.)
> 2) Error in nlm(if (analytic.gradient) objective.2 else objective.1, start,
> :
> type 31 is unimplemented in 'type2char'
> 3) *** caught segfault ***
> address 0xc019c87b, cause 'memory not mapped'
>
> Traceback:
> 1: nlm(if (analytic.gradient) objective.2 else objective.1, start,
> hessian = TRUE, iterlim = maxiter, print.level = if (debug) 2 else 0,
> typsize = typsize, ...)
> 2: sem.default(ram = ram, S = S, N = N, param.names = pars, var.names =
> vars, fixed.x = fixed.x, debug = debug, ...)
> 3: sem(ram = ram, S = S, N = N, param.names = pars, var.names = vars,
> fixed.x = fixed.x, debug = debug, ...)
> 4: sem.mod(ram = ice.ram, S = ice.S, N = ice.N)
> 5: sem(ram = ice.ram, S = ice.S, N = ice.N)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 1
> aborting ...
> Segmentation fault
> swiss:data$
>
> (no core was dumped).
>
> Trying with debug mode provides other interesting errors:
>
>> ice.sem <- sem(ram=ice.ram, S=ice.S, N=ice.N, debug=TRUE)
>
> ...gets up to some iteration (not always 15), and then R dies ungracefully,
> and exits to the shell:
>
> iteration = 15
> Step:
> [1] 1.253132e-02 1.183343e-02 -7.651342e-03 -2.490800e-03 2.278938e-03
> [6] 3.197431e-04 6.137849e-04 -2.496882e-03 -1.065829e-03 -2.118179e-03
> [11] 2.942936e-03 -1.335936e-03 -3.665618e-03 3.090566e-03 8.534956e-04
> [16] -1.440421e-03 -5.230877e-04 -1.053686e-04 -9.771005e-04 -4.269216e-04
> [21] 7.261694e-05 -1.039668e-03 -8.409151e-03 -3.497456e-03 2.216899e-03
> [26] -4.633520e-03 -4.052130e-03 -4.746537e-03 -1.589622e-03 -2.523766e-04
> Parameter:
> [1] -0.76604614 -1.19639662 0.83456888 0.72540413 0.08482452 0.56180393
> [7] 0.50615814 0.55728015 0.83796696 0.88371335 -0.70465116 0.85251098
> [13] -0.18346956 0.66857787 0.57012481 0.39116561 0.91237990 0.63951482
> [19] 0.26601566 0.29240836 0.44710919 0.94734056 6.52039015 0.02524762
> [25] -0.01614603 2.88198219 0.03442452 3.52272237 1.44698423 -0.72964745
> Function Value
> [1] -15175.94
> Gradient:
> [1] -2.085412e+07 -3.819717e+07 3.883989e+07 1.352594e+00 -4.283329e+00
> [6] -1.437250e+00 -6.558913e-01 1.358276e+00 7.930865e+05 -1.293853e+06
> [11] -5.816627e+03 5.908197e+05 -2.705742e+08 -1.194400e+07 -4.007083e+07
> [16] -4.143068e+07 -6.159782e-01 1.044274e-01 -8.591048e+00 -2.083471e+00
> [21] -7.548753e-01 -5.418994e-01 -2.799228e+02 -1.321739e+07 -3.517728e+07
> [26] -7.106654e+02 -7.335293e+06 -7.335285e+05 3.117764e-01 -2.234989e+04
>
> Abort trap
> swiss:data$
>
> ...I have also seen convergence reached, and nlm then die with this message:
>
> Error in nlm(if (analytic.gradient) objective.2 else objective.1, start,
> :
> type 27 is unimplemented in 'type2char'
>
> (similar to above, but now referring to type 27)
>
> I have shown this effect (or something similar...never know how it'll fail
> next) on the following platforms:
>
>> version
> _
> platform i386-apple-darwin9.7.0
> arch i386
> os darwin9.7.0
> system i386, darwin9.7.0
> status
> major 2
> minor 9.1
> year 2009
> month 06
> day 26
> svn rev 48839
> language R
> version.string R version 2.9.1 (2009-06-26)
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin9.8.0
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] sem_0.9-17
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.9.1 tools_2.9.1
>
> (I admit to having compiled this version of R myself (to link to a
> hand-compiled ATLAS), though no errors were thrown in the compilation stage.
> I compiled using this config string, at first...
>
> ./configure --prefix=/usr/local --with-x --disable-R-framework
> --enable-threads=posix --with-blas="/usr/local/lib/libptf77blas.a
> /usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
> --with-lapack="/usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a
> /usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
> --without-aqua CFLAGS="-O3 -mtune=nocona -m32" CXXFLAGS="-O3 -mtune=nocona
> -m32" FFLAGS="-O3 -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1
> -l gfortran" F77FLAGS="-O3 -mtune=nocona -m32
> -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" FCFLAGS="-O3
> -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran"
> LDFLAGS="-m32 -L/sw/lib" CPPFLAGS="-I/sw/include" CC=gcc-4.2 F77=gfortran-4.2
> FC=gfortran-4.2 CXX=g++-4.2 OBJC=gcc-4.2
>
> ...though I have also recompiled using simply this:
>
> ./configure --prefix=/usr/local --with-x --disable-R-framework
>
> ...and then re-installed SEM, and I got a few other, different error
> messages and core dumps, "including type 11 is unimplemented in 'type2char'"
> and "cannot coerce type 'weakref' to vector of type 'double'". Running with
> debug=TRUE also segfaults sometimes, even after achieving "Current iterate
> is probably solution" status.)
>
>> version
> _
> platform x86_64-unknown-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major 2
> minor 9.1
> year 2009
> month 06
> day 26
> svn rev 48839
> language R
> version.string R version 2.9.1 (2009-06-26)
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] sem_0.9-17
>
> ...however, THIS platform does NOT show the bug:
>
>> version
> _
> platform powerpc-unknown-linux-gnu
> arch powerpc
> os linux-gnu
> system powerpc, linux-gnu
> status
> major 2
> minor 9.1
> year 2009
> month 06
> day 26
> svn rev 48839
> language R
> version.string R version 2.9.1 (2009-06-26)
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> powerpc-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] sem_0.9-17
>>
>
> ...for this system, the model simply repeatedly fails to converge, whether
> debug is set or not.
>
> I have also tried altering my model. This has resulted in the same bugs, but
> instead of "every so often simply not converging," it actually converges and
> appears to be the model I asked R to solve...but this is rare.
>
> Please let me know if I can provide any other info.
>
> Cordially,
> Adam D. I. Kramer
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>
> --1660387551-1458482416-1249639718=:2997--
>
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>
--
Jeffrey Ryan
jeffrey.r...@insightalgo.com
ia: insight algorithmics
www.insightalgo.com
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