I'm attempting to convert my code from the Cartpole environment to other classic environments in Open AI Gym, such as MountainCar. However, I keep getting this runtime error. Could someone please assist me in resolving this issue?
Cartpole:
Observation space: Box([-4.8000002e+00 -3.4028235e+38 -4.1887903e-01 -3.4028235e+38], [4.8000002e+00 3.4028235e+38 4.1887903e-01 3.4028235e+38], (4,), float32)
Action space: Discrete(2)
MountainCar
Observation space: Box([-1.2 -0.07], [0.6 0.07], (2,), float32)
Action space: Discrete(3)
Related
I am new to sage and have got a code (link to code) which should run.
I am still getting an error message in the decoding part. The error trace looks like this:
in decode(y)
--> sigma[i+1+1] = sigma[i+1]*(z)\
-(delta[i+1]/delta[mu+1])*z^(i-mu)*sigma[mu+1]*(z);
in sage.structure.element.Element.__mul__
if BOTH_ARE_ELEMNT(cl):
--> return coercion_model.bin_op(left, right, mul)
in sage.structure.coerce.CoercionModel_cache_maps.bin_op
--> action = self.get_action(xp,yp,op,x,y)
...... some more traces (don't actually know if they are important)
TypeError: positive characteristics not allowed in symbolic computations
Does anybody know if there is something wrong in this code snipped? Due to previous errors, I changed the following to get to where I am at the moment:
.coeffs() changed to .coefficients(sparse=False) due to a warning message.
in the code line sigma[i+1+1] = sigma[i+1](z)\
-(delta[i+1]/delta[mu+1])*z^(i-mu)*sigma[mu+1](z); where the error occurs, i needed to insert * eg. sigma[i+1]*(z)
I would be grateful for any guess what could be wrong!
Your issue is that you are multiplying things not of characteristic zero (like elements related to Phi.<x> = GF(2^m)) with elements of symbolic computation like z which you have explicitly defined as a symbolic variable
Phi.<x> = GF(2^m)
PR = PolynomialRing(Phi,'z')
z = var('z')
Basically, the z you get from PR is not the same one as from var('z'). I recommend naming it something else. You should be able to access this with PR.gen() or maybe PR(z).
I'd be able to be more detailed, but I encourage you next time to paste a fully (non-)working example; trying to slog through a big worksheet is not the easiest thing to track all this down. Finally, good luck, hope Sage ends up being useful for you!
I am trying to analyze data from flow cytometry, where there is a package that was developed like 10 years ago. It requires a few dependencies packages that I was able to install all.
Now when I tried to run it with the first function to create a gate frame for a winlist processed fcs file.
create_gate_frame(frame = archframe1x36x16, inputfile =c("facsdata/TrungTran/Gelfree-8-lane7-5_1_1_A5.fcs"), popdesc = "frames/popdescriptions/array1xpopdesc.txt").
I just got the following errors that I don't know how to solve. So, any help would be very much appreciated.
uneven number of tokens: 1013
The last keyword is dropped.
uneven number of tokens: 1013
The last keyword is dropped.
Error in mat[, c(scatters, dims1, dims2, PE)] : subscript out of bounds
Before watch the mail list, I'm confused with the lack of "size" of symbol table in the Mach-o file. And I found the solution in source file posted in that E-Mail, which note that:
//Mach-O symbol table does have size in it
//so need to scan ahead to find symbol with next highest address.
But when I parse out the symbol table in a Mach-O file (I got the symbol table from the symtab_command and the following nlists) and trying to calculate the size of one global symbol as the same way, I was confused again when I compared the symbol table from the output of dwarfdump (dwarfdump -ae). The end address of the symbol in the symbol table from the dwarfdump is different from the result my program's output. Is there some problem with the symbol table I parsed out? Or is there some other way to work out it?
Some of the output from my program:
<start address> <section index> <method>
0x0006d030 1 ___arclite_objc_autoreleasePoolPop
0x0006d048 1 _patch_lazy_pointers
0x0006d1f0 1 ___arclite_objc_autoreleasePoolPush
The corresponding part of the output from dwarfdump:
0x0014a37b: [0x0006d030 - 0x0006d046) __arclite_objc_autoreleasePoolPop
0x0014a122: [0x0006d048 - 0x0006d1ee) patch_lazy_pointers
0x0014a3a0: [0x0006d1f0 - 0x0006d212) __arclite_objc_autoreleasePoolPush
So if I use the way in the "MachONormalizedFileToAtoms.cpp" to calculate the end address of the symbol (look ahead to find symbol with next highest address), the result must be different from the output of dwarfdump. And does anyone know how dwarfdump calculate it?
Thank you!
From the answer by Nick Kledzik:
The compiler often aligns functions to start at aligned address (e.g. 8 or 16 bytes). So, there is padding bytes (usually NOPs) after the end of a function and before the start of the next function.
dwarfdump has access to the debug info which does have size info for functions. So dwarfdump can show the size of a function without the alignment padding at the end. Whereas the linker just looks at the next symbol address. There is not much point in the linker digging through the debug info to get a function’s true size, because when writing the output, the linker has to align the next function which would just add back the pad bytes.
I hope that can help others who has the same confusion.
Hi I am new to scilab and don't have much mathematical background.
I have been following code for another example and am being shown error 10000 for the following code:
function [z]=f(x,y)
z=0.026*(1.0-(y/ym))*y;
endfunction;
ym=12000;
x0=1950;y0=2555;xn=5;h=10;
x=[x0:h:xn];
y=ode("rk",y0,x0,x,f);
disp("x y")
disp("--------")
disp([x'y']);
function z=fe(x)
z=ym/(1-(1-ym/y0)*e^(-k*(t-t0)));
endfunction;
xe=(x0:h/10:xn);
n=length(xe)
for i=1:n
ye(i)=fe(xe(i));
end;
plot (x,y,'ro',xe, ye,'-b');legend ('rk4','Exact',3);
xtitle('solving dy/dx=k(1-y/ym)y','x','y');
I have worked through several other error messages. I am lost and don't know if the problem is in the code or the way I set up the problem. The following is the current error message:
!--error 10000
plot: Wrong size for input argument #2: A non empty matrix expected.
at line 57 of function checkXYPair called by :
at line 235 of function plot called by :
plot (x,y,'ro',xe, ye,'-b');legend ('rk4','Exact',3);
at line 25 of exec file called by :
I would appreciate any help.
Thanks
Start by adding clear as first statement, this will erase all variables before running your function. In the above script you don't declare ye.
Also the statement x=[x0:h:xn]; is strange with those values for x0,h and xn. You are now trying to get a list of x-values starting at 1950 and with positive steps of 10 up until 5 is reached.
I would recommend to try each line and see if the outcome is as expected. You do not need to know everything about the code, but probaly x and y should contain at least some values. The error is telling you that it expected a non-empty matrix for argument 2. This is y, so essentially it is telling you y is empty.
I am trying to scan for possible SNPs and indels by aligning scaffolds to subsequences from a reference genome. (the raw reads are not available). I am using R/bioconductor and the `pairwiseAlignment function from the Biostrings package.
This was working fine for smaller scaffolds, but failed when I tried to align as 56kbp scaffold with the error message:
Error in QualityScaledXStringSet.pairwiseAlignment(pattern = pattern,
: cannot allocate memory block of size 17179869183.7 Gb
I am not sure if this is a bug or not ? ; I was under the impression that the Needleman-Wunsch algorithm used by pairwiseAlignment is an O(n*m) which I thought would imply the computational demand to be on the order of 3.1E9 operations (56K * 56k ~= 3.1E9). It seems the Needleman-Wunsch similarity matrix should as well take up on the order of 3.1 gigs of memory as well. Not sure if I'm not remembering big-o notation correctly or that is actually the memory overhead that would be needed to build the alignment given the overhead of the R scripting environment.
Does anybody have suggestions for a better alignment algorithm to use for aligning longer sequences? An initial alignment was already done using BLAST to find the region of the reference genome to align. I am not entirely confident BLAST's reliability for correctly placing indels and I have not yet been able to find an api as good as that provided by biostrings for parsing the raw BLAST alignments.
By the way, here is a code snippet that replicates the problem:
library("Biostrings")
scaffold_set = read.DNAStringSet(scaffold_file_name) #scaffold_set is a DNAStringSet instance
scafseq = scaffold_set[[scaffold_name]] #scaf_seq is a "DNAString" instance
genome = read.DNAStringSet(genome_file_name)[[1]] #genome is a "DNAString" instance
#qstart, qend, substart, subend are all from intial BLAST alignment step
scaf_sub = subseq(scafseq, start=qstart, end=qend) #56170-letter "DNAString" instance
genomic_sub = subseq(genome, start=substart, end=subend) #56168-letter "DNAString" instance
curalign = pairwiseAlignment(pattern = scaf_sub, subject = genomic_sub)
#that last line gives the error:
#Error in .Call2("XStringSet_align_pairwiseAlignment", pattern, subject, :
#cannot allocate memory block of size 17179869182.9 Gb
The error does not happen with shorter alignments (hundreds of bases).
I have not yet found the length cutoff where the error starts happening
So I use Clustal as an alignment tool. Not sure about the specific performance, but it has never given me issues when doing multiple sequence alignments of large quantity. Here is a script that runs a whole directory of .fasta files and aligns them. You can modify the flags on the system call to suit your input/output needs. Just look at the clustal documentation. This is in Perl, I don't use R too much for alignments. You need to edit the executable path in the script to match where clustal is on your computer.
#!/usr/bin/perl
use warnings;
print "Please type the list file name of protein fasta files to align (end the directory path with a / or this will fail!): ";
$directory = <STDIN>;
chomp $directory;
opendir (DIR,$directory) or die $!;
my #file = readdir DIR;
closedir DIR;
my $add="_align.fasta";
foreach $file (#file) {
my $infile = "$directory$file";
(my $fileprefix = $infile) =~ s/\.[^.]+$//;
my $outfile="$fileprefix$add";
system "/Users/Wes/Desktop/eggNOG_files/clustalw-2.1-macosx/clustalw2 -INFILE=$infile -OUTFILE=$outfile -OUTPUT=FASTA -tree";
}