Thanks! another question, is there any way to check if the changes that I have done pass the checks for all PC like on the webpage? I do not have mac or windows so I feel like I have to wait to the next day to check if my changes worked out.
Thank you very much, 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. Thank > >>>>>>>> you. > >>>>>>> > >>>>>> > >>>>>> > >>>>>> 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. Thank you. > >>>>> > >>>> > >>>> > >>>> This email message may contain legally privileged > >>>> and/or...{{dropped:2}} > >>>> > >>>> _______________________________________________ > >>>> 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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