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? 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-boun...@r-project.org> on behalf of >>> campos <cam...@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? >>> >>>>>>> >>> >>>>>>> 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 >>> >>>>>>>>> >>> >>>>>>>>> _______________________________________________ >>> >>>>>>>>> Bioc-devel@r-project.org mailing list >>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> This email message may contain legally privileged and/or >>> >>>>>>>> confidential information.� If you are not the intended >>> >>>>>>>> recipient(s), or the employee or agent responsible for the >>> >>>>>>>> delivery of this message to the intended recipient(s), you are >>> >>>>>>>> hereby notified that any disclosure, copying, distribution, or >>> >>>>>>>> use of this email message is prohibited.� If you have received >>> >>>>>>>> this message in error, please notify the sender immediately by >>> >>>>>>>> e-mail and delete this email message from your computer. 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