[Bioc-devel] vignette problems

Hi Martin,

when I run now valgrind seems that there are no problems. I pushed 
yesterday the changes, was I still on time for the new release? We want 
to publish the changes and it would be really helpful if the package is 
running on Bioconductor.

Thank you very much,

Rafael


On 02.04.2018 02:51, Martin Morgan wrote:

On 04/01/2018 08:06 PM, Martin Morgan wrote:

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);

oops, std::vector<int> myStateBuckets(ncores + 1); !

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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