I have a C source code and also its llvm bit code. Please tell me how to slice the bitcode if I give a particular line from the source code as slicing target. I am actually trying to get the branch and jump instructions or their line numbers in bit code which will allow the program to reach that block where this source code line is present in bit code format. Please tell me if it is possible at all.
Related
I am using JupyterLab to build a bioinformatics pipeline that uses both bash and python scripts.
The first bash script results gives a lot of feedback on every step of the process. However, this feedback is not helpful (unless there was an error) and makes the document less readable.
I would like to be able to hide this cell's output by default, but also to be able to open it when necessary to troubleshoot. I know it's possible to click 3 times on the output to collapse it; I was just wondering whether there is a way to do so by default.
I tried to add the tag specified on here (https://jupyterbook.org/features/hiding.html#Hiding-outputs) to the cell, but it does not seem to work for me.
Thanks for your help.
You may just want to suppress the output using %%capture cell magic as illustrated here. Then you simply remove that magic command from the first line of the cell for times you want to see the output, such as when troubleshooting.
If you want to make it so every time you run the cell, you can later decide to review what was captured you can use the %%capture magic command more as it was meant to be used. By assigning what is captured you can also do something like what the %%bash cell magic allows with handling output streams (see here), too. As described and illustrated here using the utils object you can easily get the stdout and/or stderr as a string, see http://ipython.readthedocs.io/en/stable/api/generated/IPython.utils.capture.html.
So say you put the following at the top of you cell to assign what was captured to out:
%%capture out
You can review the stdout stream later with the following:
print(out.stdout)
Or if you just want part of it, something like print(out.stdout[1:500]). I have some fancier handling illustrated in some blocks of code here.
would you please help me? if I have a code including some loops and IFs, how can I debug inside FOR or IF, line by line.
for example
I can use shift+enter for every line. but when it is used for a For all loop will run. Is there any facility to debug inside a loop line by line?
thanks
You can run line by line in e.g. Juno by just highlighting the line, that will not run the entire loop. I'd recommend doing that.
With regards to an actual debugger, there is not currently one available for julia-1.x. But there's Rebugger.jl, it's use is quite advanced though.
I must predicate this by saying that I am still quite new to RStudio/R so I hope this is not user error. However when debugging I am getting some strange results whilst in debug mode.
1) The code jumps to another part of the code without apparently being called.
2) When this happens the highlighter only partially highlights the code it jumps to but the arrow in the margin points to this partially highlighted line
3) The code then returns to place it jumped away from originally
I get the warning "Debug location is approximate because source source code is not available". Is this related to the problem?
You can replicate the results by installing the package dlm:
https://cran.r-project.org/web/packages/dlm/dlm.pdf
p<-3
G=diag(c(0.9963,0.9478,0.7740))
W=diag(c(0.0026^2,0.0027^2,0.0035^2))
C0_est=solve(diag(p)-G%*%t(G))*W
mod2<-dlm(m0=c(0.0501,-0.0251,-0.0116),C0=C0_est,FF=X,V=0.000000001*diag(m),GG=diag(c(0.9963,0.9478,0.7740)),W=diag(c(0.0026^2,0.0027^2,0.0035^2)))
debugonce(dlmForecast)
dlmForecast(mod2, nAhead=5, sampleNew=2)
When you step through using F10 you will find that the code jumps to L7 from Lines 28,32, 54 and 57 and to L4 from line 47.
Q1.) Why does this partial highlighting of the line being debugged mean?
Q2.) What causeses the code to jump backward and forwards like this with no apparent function call?
Kind Regards
Baz
Most R packages don't include copies of the package's source code (the keep.source option controls this behavior; you can read more about it here). When you debug code from this kind of package, RStudio has to guess at both what the code looked like originally and where the current execution point is in that code. This process includes some heuristics and does occasionally misinterpret the execution point. So what you're seeing is not the actual execution point jumping around, but RStudio making the wrong guess about where it is in the deparsed code.
Code from your own R scripts (and from packages with keep.source) have source references (see R journal article) which allow RStudio to line up the code and execution point precisely.
I wasn't able to reproduce this with your example (it appears to reference a variable m that it doesn't declare); if you can resolve that and send it to me (jonathan at rstudio dot com) I'll see if we can improve the heuristics so this case works better.
I'm trying to get package references resolved during a build, using GNAT Programming Suite (hosted on Win XP). In the Builder Results, I get errors like this one:
file "ac_configuration_s.ada" not found
Clicking on the error takes me to a line like this:
with
Ac_Configuration,
Dispense_Timer,
...
The first item (Ac_Configuration) isn't resolved, but the second item (Dispense_Time) is resolved. I have several others that do or don't resolve. All of the files in question (spec and body) are identified as source files.
When I hover my mouse over the line with the error, a popup shows up that offers this:
(Cross-references info not up to date. This is a guess.)
Ac_Configuration
local package declared at D_Ac_Config_S.Ada:85
The guess is correct, but I don't know how to use this. How do I get this to correctly build?
Update
Here is teh call to gcc
gcc -c "-gnatec=C:\Source\build\GNAT-TEMP-000001.TMP" -I- -gnatA
-x ada "-gnatem=C:\Source\build\GNAT-TEMP-000002.TMP" "C:\Source\C_Cbt_Main_B.Ada"
I don't see a reference to teh "miimal" switch.
In this case, there is no corresponding body file file D_Ac_Config_S.Ada. So the is no body file to compile separately.
When I right click on the package reference inside the with, I can goto the declaration of Ac_Configuration and every other package name that is the source of an error. So these lreferences are being resolved somehow.
By the way, I have not used ADA before, so I'm still trying to understand everything.
It looks as though you're using _s.ada as the suffix for specs, and I'm guessing _b.ada for bodies?
GNAT may have difficulty with this naming convention. It's possible, using a GNAT Project file (.gpr), to alter GNAT's default convention ({unit-name}.ads for specs, {unit-name}.adb for bodies) but the rules (see "Spec_Suffix") say "It cannot start with an underscore followed by an alphanumeric character" (I haven't tried this, but you can see that it would confuse the issue if you had a package Foo_S, for example).
LATER: It turns out that GNAT (GPL, 4.7, 4.8) is quite happy with your suffixes!
If the package Ac_Configuration is really a local package declared at line 85 of D_Ac_Config_S.Ada, then there's your problem; you can only with a library unit, which in this case would be D_Ac_Config.
with D_Ac_Config;
...
package Foo is
...
Bar : D_Ac_Config.Ac_Configuration.Baz;
I wonder whether D_Ac_Config_S.Ada (for example) actually contains multiple Ada units? (if so, compiling that file should result in a compilation error such as end of file expected, file can have only one compilation unit). GNAT doesn't support this at compile time, providing instead a utility gnatchop.
Would it be possible to just gnatchop all the source and be done with it?
Hm, I think it sounds like the compiler's got a bad set of objects/ALIs it's working with, hence the cross-reference not up to date error. (Usually the compiler's good about keeping things up to date; but you may want to check to see if the "minimal recompilation" switch is set for the project.)
Have you tried compiling just the ["owning"] file D_Ac_Config_S.Ada? (i.e. if it were a spec, go to the corresponding body and compile that.) That should force its ALI/object files to be updated.
Then try building as normal.
-- PS: you might have to clean first.
I have got a memory image, that i can't find the source for and I want to get the code out of it again. What do i have to do to achieve that? I can obviously load the image, but then i'd need to guess the function names.
You may get "interesting" symbols with (apropos ""), and the function names with WITH-PACKAGE-ITERATOR and FBOUNDP. But the source code is (probably) lost: try DISASSEMBLE on functions and see the information which is there.
In addition to DISASSEMBLE, you might try EXT:UNCOMPILE. Note, however, that it will only work on functions compiled in an interactive session (i.e., from REPL), not on those loaded from a compiled .fas file.
So, the suggested procedure is:
LIST-ALL-PACKAGES - figure out which packages are interesting.
DO-EXTERNAL-SYMBOLS - figure out which symbols in the interesting packages are interesting.
DISASSEMBLE or EXT:UNCOMPILE on those interesting symbols.
However, the easiest way is to contact your vendor. Remember, CLISP is distributed under the GNU GPL.