[Bioc-devel] vignette problems
Aha! now I see all the changes! so, now everything should be fine and it should run on mac as well right? here: https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/malbec2-checksrc.html there is only the linux and windows machine, there is no info about the mac. Thousand thanks again Martin, you have been of great help. Best, Rafael
On 11.04.2018 16:52, Martin Morgan wrote:
On 04/11/2018 10:47 AM, campos wrote:
Hi Martin, when I run git status I get this: On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working directory clean shouldn't I see that my version in my machine is some commits behind? ??$git remote -v origin??? git at git.bioconductor.org:packages/STAN (fetch) origin??? git at git.bioconductor.org:packages/STAN (push)
maybe your version is current; I have ~/b/git/STAN master$ git log --oneline -n10 06dbdae Merge remote-tracking branch 'upstream/master' 6e070d4 version 2.7.3 b8e2123 make destructors for polymorhpic base classes virtual 18ac6ba mismatch new[] / delete[] 985768b restore EmissionFactory::createEmissionFunctionMixed 8b749db provide return value for non-void functions 26ca36e update poor printf statements 0bb83ab clear 'unused variable' -Wall -pedantic warnings a3b7666 remove vignette product STAN-knitr.R 1c4f140 upgrade version 2.7.3 if you don't, then I guess `git pull` or more pedantically `git fetch origin; git merge origin/master master`. Martin
Thanks a lot, Rafa On 11.04.2018 16:43, Martin Morgan wrote:
On 04/11/2018 09:58 AM, campos wrote:
Hi Martin, thank you very much for your time and effort! I pulled the branch to my computer updated the DESCRIPTION file and pushed the changes. That should be enough right?
actually I seemed to have messed up the git commit, but I fixed it from my end; you should git pull and not worry about pushing any further commits for the moment.
Best, Rafa PS: If you ever stop by Cologne please let me know. I owe you a beer or two!
tasty! Martin
On 10.04.2018 23:44, Martin Morgan wrote:
Hi -- I'm not sure what you mean; the 'devel' builld report does not include mac (the build system experienced problems with disk space last night, so the build did not complete) https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/ and STAN failed in Release https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/ HOWEVER, I spent some time with your package. First, I compiled it with compiler flages -Wall -pedantic, which makes the compiler quite sensitive. I did this by creating, on my Linux, a file ??? $ cat ~/.R/Makevars ??? CFLAGS = -g -O0 -Wall -pedantic ??? CXXFLAGS = -g -O0 -Wall -pedantic and then installing the package from the source directory ??? STAN master$ rm -f src/*o && R CMD INSTALL . There were a number of minor issues (unused variables, incorrect printf formatting [and use of printf() rather than Rprintf()]) as well as somewhat more substantial problems (virtual destructors for polymorphic base classes); a few problems remain, of the form ??? RWrapper.cpp:950:5: warning: control reaches end of non-void function [-Wreturn-type] ???? } where the problem is obvious -- no return value if parallel != 0 -- but also innocuous, since it seems from inspection that in fact this function is always invoked with parallel == 0 ??? HMM* createHMM(int parallel, int K, InitialProbability* initProb, TransitionMatrix* transMat, EmissionFunction** myEmissions) ??? { ??????? if(parallel == 0) ??????? { ??????????? return new HMM(K, initProb, transMat, myEmissions); ??????? } ??? } You should fix these problems, e.g., by removing the parallel argument from the function and body. After cleaning up as best I could, I install the package again and ran the vignette through valgrind ??? STAN master$ R CMD INSTALL . ??? ... ??? STAN master$ cd vignettes ??? STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw ??? STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw ??? STAN/vignettes master$ R -d valgrind -f STAN-knitr.R leading to an about mismatched new[] / delete[] -- memory allocated by 'new x[]' must be deleted with 'delete[]', but the package code had simply 'delete'. With these changes, the vignette builds without segfaulting or valgrind errors on my machine, and on the Mac builder; I did not check the full build and check of the package. The changes are summarized in the following commits: ??? STAN master$ git log --oneline ??? a719f42 version bump ??? b8e2123 make destructors for polymorhpic base classes virtual ??? 18ac6ba mismatch new[] / delete[] ??? 985768b restore EmissionFactory::createEmissionFunctionMixed ??? 8b749db provide return value for non-void functions ??? 26ca36e update poor printf statements ??? 0bb83ab clear 'unused variable' -Wall -pedantic warnings ??? a3b7666 remove vignette product STAN-knitr.R You should pull these down to your local git repository, e.g., for me I have ??? STAN master$ git remote -v ??? origin??? git at git.bioconductor.org:packages/STAN (fetch) ??? origin??? git at git.bioconductor.org:packages/STAN (push) So I would ??? STAN master$ git pull origin master to incorporate the changes. It would be good to port these changes to the RELEASE_3_6 branch; remember to bump the version of the RELEASE_3_6 branch to 2.6.1. Unfortunately, I pushed the changes after tonight's builds started, so the effect of the changes will not be reported until Thursday mid-morning, Eastern time, if the build system does not have problems. Martin On 04/10/2018 02:14 PM, campos wrote:
Hi Martin, it seems like mac is ok now. What has changed?? Thank you very much, Rafael On 10.04.2018 11:33, Martin Morgan wrote:
On 04/10/2018 05:27 AM, campos wrote:
Hi Martin, Thank you very much, I am a bit concerned about the option of: Last?Changed?Date: 2018-04-05?09:37:37?-0400?(Thu,?05?Apr?2018) I did a change yesterday and push it, why isn't it visible?
Notice that at the top of the build report it says ? This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09 Apr 2018). ? Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018) If you pushed after the snapshot date then your changes are not yet visible. Martin
Best, Rafa On 09.04.2018 16:44, Martin Morgan wrote:
I'll try to provide you with a pull request addressing issues. Martin On 04/09/2018 08:42 AM, campos wrote:
Dear devel team, I am still puzzled with the problems with mac compiling. I am really lost and have no idea how to continue or how to be able to check about this problems with my linux machine in order to fix it faster. Could you please help me with that?? Best, Rafael On 05.04.2018 14:29, Shepherd, Lori wrote:
In order for changes to be propagated a version bump in the DESCRIPTION file is needed.? Please bump the version in the DESCRIPTION file to 2.7.2. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ------------------------------------------------------------------------ *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of campos <campos at mpipz.mpg.de> *Sent:* Thursday, April 5, 2018 7:45:57 AM *To:* Morgan, Martin; bioc-devel *Subject:* Re: [Bioc-devel] vignette problems Hey Martin, I pushed new changes since last friday but in https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ says that the last change date was friday. Any idea what is the problem? I have tried to fix the problems with memory and all you told me. Best, Rafael On 03.04.2018 17:06, Martin Morgan wrote:
Please use 'reply all' so that the mailing list remains
engaged.
Check out the release schedule http://bioconductor.org/developers/release-schedule/ in particular Wednesday April 25 - Deadline for packages passing ??R CMD build?? and ??R
CMD check??
without errors or warnings. so you still have time to get your package in order. Using the same techniques as before, I still see valgrind
problems,
the first being
hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
sizeFactors=sizeFactors, maxIters=10) ==24916== Invalid write of size 4 ==24916==??? at 0x4BA93FD7: TransitionMatrix::updateAuxiliaries(double**, double***,
double*,
int*, int, int**, int, double, int)
(TransitionMatrix.cpp:292)
==24916==??? by 0x4BA77934:
HMM::updateSampleAux(double***, int*, int,
double**, double**, double**, double***, double*, int*,
int*, int*,
int**, double***, SEXPREC*, SEXPREC*, int, double, int,
int, int)
(HMM.cpp:771) ==24916==??? by 0x4BA7896D:
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:1076)
==24916==??? by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494) ==24916==??? by 0x4F2992D: R_doDotCall (dotcode.c:692) ==24916==??? by 0x4F339D5: do_dotcall (dotcode.c:1252) ==24916==??? by 0x4F81BA6: bcEval (eval.c:6771) ==24916==??? by 0x4F6E963: Rf_eval (eval.c:624) ==24916==??? by 0x4F71188: R_execClosure (eval.c:1764) ==24916==??? by 0x4F70E7C: Rf_applyClosure (eval.c:1692) ==24916==??? by 0x4F6F18B: Rf_eval (eval.c:747) ==24916==??? by 0x4F74B12: do_set (eval.c:2774) ==24916==? Address 0x2e73a294 is 4 bytes inside a block of
size 5 alloc'd
==24916==??? at 0x4C2DB8F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==24916==??? by 0x4BA93FA6: TransitionMatrix::updateAuxiliaries(double**, double***,
double*,
int*, int, int**, int, double, int)
(TransitionMatrix.cpp:289)
==24916==??? by 0x4BA77934:
HMM::updateSampleAux(double***, int*, int,
double**, double**, double**, double***, double*, int*,
int*, int*,
int**, double***, SEXPREC*, SEXPREC*, int, double, int,
int, int)
(HMM.cpp:771) ==24916==??? by 0x4BA7896D:
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:1076)
==24916==??? by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494) ==24916==??? by 0x4F2992D: R_doDotCall (dotcode.c:692) ==24916==??? by 0x4F339D5: do_dotcall (dotcode.c:1252) ==24916==??? by 0x4F81BA6: bcEval (eval.c:6771) ==24916==??? by 0x4F6E963: Rf_eval (eval.c:624) ==24916==??? by 0x4F71188: R_execClosure (eval.c:1764) ==24916==??? by 0x4F70E7C: Rf_applyClosure (eval.c:1692) ==24916==??? by 0x4F6F18B: Rf_eval (eval.c:747) ==24916== This seems to be the exact same code as in the problem
that you fixed
at another location. Actually, I would guess that all of
these
grep --color -nH -e ")\*ncores+1" * HMM.cpp:784:??? int *myStateBuckets =
(int*)malloc(sizeof(int)*ncores+1);
MultivariateGaussian.cpp:295:??? int *myDimBuckets = (int*)malloc(sizeof(int)*ncores+1); MultivariateGaussian.cpp:475:??? int *myDimBuckets = (int*)malloc(sizeof(int)*ncores+1); TransitionMatrix.cpp:132:??????? int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1); TransitionMatrix.cpp:289:??? int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1); are the same problem. Also, usually code that has been
copy/pasted
like this can instead be refactored to? a single function
call, so a
bug can be fixed in one place. I still see a number of compiler warnings, the first of
which is
STAN master$ R CMD INSTALL . Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite
for help
* installing to library '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.7' * installing *source* package 'STAN' ... ** libs g++ -I"/home/mtmorgan/bin/R-3-5-branch/include" -DNDEBUG -I/usr/local/include? -D_RDLL_ -fopenmp -fpic -g -O0 -Wall
-pedantic
-c HMM.cpp -o HMM.o HMM.cpp: In member function ?virtual void HMM::calcEmissionProbs(double***, double**, int*, int,
int**, int*,
int*, int**, int, int, int*)?: HMM.cpp:112:15: warning: unused variable ?j?
[-Wunused-variable]
???????? int i,j,t,k; ?????????????? ^ It really pays to clean these up; most are harmless, but
they obscure
the more important warnings. Martin On 04/03/2018 09:58 AM, campos wrote:
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?
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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