On 04/01/2018 03:53 PM, campos wrote:
Dear Martin,
I am trying to fix this problem but I am really lost... Do you mean C++
code? Becasue there is no C code in the whole package. I really don't
know what the problem might be.
Please keep the conversation on the bioc-devel mailing list, so that
others can learn or help.
I use Linux, not Mac, but C (which I used to mean your C++ code) errors
often occur on all platforms but are only visible as a segfault on one.
I created the vignette R code with
cd vignettes
R CMD Stangle STAN-knitr.Rmd
This produces a file STAN-knitr.R. I then ran your R code with valgrind
R -d valgrind -f STAN-knitr.R
this runs much slower than without valgrind. The first error reported by
valgrind was
> ##
----STAN-PoiLog-----------------------------------------------------------
> nStates = 10
> hmm_poilog = initHMM(trainRegions, nStates, "PoissonLogNormal",
sizeFactors)
> hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
sizeFactors=sizeFactors, maxIters=10)
[1] 6
==22304== Invalid write of size 4
==22304== at 0x4B489316: HMM::BaumWelch[abi:cxx11](double***, int*,
int, int, int**, int*, int*, int*, int, int, int**, double***, SEXPREC*,
SEXPREC*, int, double, double, int, int) (HMM.cpp:998)
==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
==22304== by 0x4F81BA6: bcEval (eval.c:6771)
==22304== by 0x4F6E963: Rf_eval (eval.c:624)
==22304== by 0x4F71188: R_execClosure (eval.c:1764)
==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
==22304== by 0x4F74B12: do_set (eval.c:2774)
==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
==22304== by 0x4FB7BEE: Rf_ReplIteration (main.c:258)
==22304== Address 0x238b28f4 is 4 bytes inside a block of size 5 alloc'd
==22304== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==22304== by 0x4B4892E5: HMM::BaumWelch[abi:cxx11](double***, int*,
int, int, int**, int*, int*, int*, int, int, int**, double***, SEXPREC*,
SEXPREC*, int, double, double, int, int) (HMM.cpp:995)
==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
==22304== by 0x4F81BA6: bcEval (eval.c:6771)
==22304== by 0x4F6E963: Rf_eval (eval.c:624)
==22304== by 0x4F71188: R_execClosure (eval.c:1764)
==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
==22304== by 0x4F74B12: do_set (eval.c:2774)
==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
'Invalid write' suggests that you are writing after the end of memory
that you'd allocated. I looked at the C code at the line where the error
occurs as indicated in the stack trace, HMM.cpp:998 which is the
assigment myStateBucks[i] = 0 in the loop
int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1);
for(i=0; i<=ncores; i++)
{
myStateBuckets[i] = 0;
}
The argument to malloc (where he memory was allocated, at line 995)
should be the number of bytes to allocate and it should have been memory
for ncores + 1 'int'
malloc(sizeof(int) * (ncores + 1))
rather than what you wrote, which is memory for ncores ints plus 1 byte.
C++ code would avoid the need for such explicit memory management, e.g.,
using a vector from the standard template library
std::vector<int> myStateBuckets(ncores);
There were may other valgrind errors, but I do not know whether these
are from similar programming errors, or a consequence of this one.
Martin
Thanks,
Rafael
On 03/29/2018 01:07 PM, campos wrote:
Dear bioc-devel team,
I have made some changes in the package STAN and although it seems to
install correctly, I have problems with timeout and error in
windows... Could someone help me to improve the time?
https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/
it looks like, with your most recent commit (at the top of the page,
'Snapshot Date', 'Last Commit', 'Last Changed Date'), the package
built on Windows and Linux.
There is a segfault on Mac, which is likely a programming error in
your C code. It could be debugged perhaps using valgrind or similar
tools, but the first step would be to isolate the code to something
more easily reproduced than the full vignette. It would also help to
clean up the C code so that it compiles without warnings with the
-Wall -pedantic flags
Martin
Best,
Rafael
On 28.03.2018 01:08, Martin Morgan wrote:
When I try and install the version on the master branch of the
Bioconductor git repository I get
STAN master$ Rdev --vanilla CMD INSTALL .
* installing to library ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
...
** testing if installed package can be loaded
Error: package or namespace load failed for 'STAN' in
namespaceExport(ns, exports):
undefined exports: viterbi2Gviz
This comes about in a rather interesting way because the body of
plotViterbi is not defined
plotViterbi <- function(viterbi, regions, gen, chrom, from, to,
statecols, col)
#'
...
Can you please commit a version of the package that installs?
Martin
On 03/27/2018 06:42 PM, campos wrote:
Dear bioc-devel team,
I am developing the STAN packages and I am running into problems
when trying to build my package. The problem is the following:
Error in vignette_type(Outfile) :
Vignette product 'STAN.tex' does not have a known filename
extension ('NA')
ERROR: installing vignettes failed
* removing '/tmp/Rtmp925Iru/Rinst63471ff1efdc/STAN'
I tried to build the package in old versions (which they used to
work) and I run in other problems but in this case is:
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
quiet, :
Running 'texi2dvi' on 'STAN.tex' failed.
LaTeX errors:
! LaTeX Error: File `beramono.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Could you help me with this problem?
Thank you very much,
Rafael
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