Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 64/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AneuFinder 1.33.0 (landing page) Aaron Taudt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the AneuFinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AneuFinder.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: AneuFinder |
Version: 1.33.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AneuFinder_1.33.0.tar.gz |
StartedAt: 2024-08-26 20:28:36 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:40:28 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 711.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AneuFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AneuFinder_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘AneuFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AneuFinder’ version ‘1.33.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘AneuFinder’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Aneufinder: multiple local function definitions for ‘parallel.helper’ with different formal arguments * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed simulateReads 51.364 2.711 54.078 refineBreakpoints 46.043 0.452 46.495 heatmapAneuploidies 40.444 1.125 41.569 correctGC 24.278 3.331 27.613 plotHeterogeneity 27.021 0.296 27.317 heatmapGenomewideClusters 22.906 0.232 23.138 karyotypeMeasures 20.562 0.189 20.750 heatmapGenomewide 19.257 0.272 19.536 annotateBreakpoints 15.621 0.784 16.874 getBreakpoints 10.758 0.195 10.954 consensusSegments 7.644 0.095 7.741 getSCEcoordinates 4.790 0.155 5.321 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck/00check.log’ for details.
AneuFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AneuFinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘AneuFinder’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_interface.cpp -o R_interface.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c densities.cpp -o densities.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c loghmm.cpp -o loghmm.o loghmm.cpp:320: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 320 | #pragma omp parallel for | loghmm.cpp:480: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 480 | #pragma omp parallel for | loghmm.cpp:518: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 518 | #pragma omp parallel for | loghmm.cpp:583: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 583 | #pragma omp parallel for | g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scalehmm.cpp -o scalehmm.o scalehmm.cpp:384: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 384 | #pragma omp parallel for | scalehmm.cpp:400: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 400 | #pragma omp parallel for | scalehmm.cpp:694: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 694 | #pragma omp parallel for | scalehmm.cpp:732: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 732 | #pragma omp parallel for | scalehmm.cpp:791: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 791 | #pragma omp parallel for | g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utility.cpp -o utility.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-AneuFinder/00new/AneuFinder/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AneuFinder)
AneuFinder.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(AneuFinder) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: cowplot Loading required package: AneuFinderData Please visit https://github.com/ataudt/aneufinder for the latest bugfixes and features. > > test_check("AneuFinder") number of states = 11 number of bins = 6183 maximum number of iterations = 1000 maximum running time = none epsilon = 0.1 data mean = 58.8193, data variance = 486.587 Iteration log(P) dlog(P) Diff in posterior Time in sec 0 -inf - - 0 1 -24789.866771 inf 6183.000000 0 2 -23822.331670 967.535101 601.762712 0 3 -23761.771285 60.560384 131.281549 0 4 -23745.235666 16.535619 119.461404 0 5 -23738.238770 6.996896 63.831344 0 6 -23735.137871 3.100899 48.587399 0 7 -23733.451273 1.686598 29.803499 0 8 -23732.421572 1.029701 21.580983 0 9 -23731.674903 0.746669 14.186707 0 10 -23731.069920 0.604983 9.975381 0 11 -23730.527674 0.542246 7.021040 0 12 -23730.007090 0.520584 4.942881 0 13 -23729.480035 0.527055 3.803030 0 14 -23728.932681 0.547354 2.653912 0 15 -23728.372455 0.560226 2.141742 0 16 -23727.839017 0.533439 1.244299 0 17 -23727.367012 0.472005 1.109390 0 18 -23726.947097 0.419914 0.529456 0 19 -23726.552750 0.394348 0.602730 0 Iteration log(P) dlog(P) Diff in posterior Time in sec 20 -23726.169459 0.383291 0.302116 0 21 -23725.791510 0.377949 0.389827 0 22 -23725.416462 0.375048 0.244787 0 23 -23725.043233 0.373229 0.307572 0 24 -23724.671334 0.371899 0.240956 0 25 -23724.300551 0.370783 0.275223 0 26 -23723.930786 0.369765 0.245508 0 27 -23723.561998 0.368789 0.262164 0 28 -23723.194164 0.367834 0.248735 0 29 -23722.827276 0.366888 0.256570 0 30 -23722.461329 0.365947 0.250428 0 31 -23722.096319 0.365010 0.254042 0 32 -23721.732244 0.364076 0.251213 0 33 -23721.369100 0.363144 0.252844 0 34 -23721.006885 0.362214 0.251549 0 35 -23720.645598 0.361287 0.252622 0 36 -23720.285236 0.360362 0.252383 0 37 -23719.925796 0.359440 0.253123 0 38 -23719.567277 0.358519 0.253290 0 39 -23719.209677 0.357600 0.254027 0 Iteration log(P) dlog(P) Diff in posterior Time in sec 40 -23718.852994 0.356683 0.254590 0 41 -23718.497228 0.355766 0.255400 0 42 -23718.142378 0.354850 0.256151 0 43 -23717.788445 0.353933 0.257145 0 44 -23717.435431 0.353014 0.258100 0 45 -23717.083339 0.352092 0.259094 0 46 -23716.732173 0.351166 0.260034 0 47 -23716.381938 0.350235 0.260935 0 48 -23716.032640 0.349298 0.261735 0 49 -23715.684287 0.348353 0.262424 0 50 -23715.336886 0.347401 0.262956 0 51 -23714.990445 0.346441 0.263312 0 52 -23714.644972 0.345473 0.263463 0 53 -23714.300474 0.344498 0.263396 0 54 -23713.956958 0.343516 0.263103 0 55 -23713.614428 0.342530 0.262584 0 56 -23713.272887 0.341540 0.261849 0 57 -23712.932339 0.340548 0.260917 0 58 -23712.592783 0.339556 0.259810 0 59 -23712.254217 0.338565 0.258559 0 Iteration log(P) dlog(P) Diff in posterior Time in sec 60 -23711.916641 0.337576 0.257196 0 61 -23711.580050 0.336591 0.255754 0 62 -23711.244442 0.335609 0.254264 0 63 -23710.909811 0.334631 0.252755 0 64 -23710.576153 0.333657 0.251252 0 65 -23710.243465 0.332688 0.249777 0 66 -23709.911743 0.331722 0.248349 0 67 -23709.580982 0.330761 0.247090 0 68 -23709.251180 0.329802 0.245906 0 69 -23708.922334 0.328846 0.244786 0 70 -23708.594441 0.327893 0.243757 0 71 -23708.267498 0.326942 0.242885 0 72 -23707.941505 0.325993 0.242069 0 73 -23707.616459 0.325046 0.241304 0 74 -23707.292358 0.324101 0.240590 0 75 -23706.969202 0.323156 0.239921 0 76 -23706.646989 0.322213 0.239394 0 77 -23706.325719 0.321271 0.239012 0 78 -23706.005389 0.320329 0.238641 0 79 -23705.686000 0.319389 0.238282 0 Iteration log(P) dlog(P) Diff in posterior Time in sec 80 -23705.367551 0.318449 0.237931 0 81 -23705.050040 0.317511 0.237592 0 82 -23704.733468 0.316573 0.237265 0 83 -23704.417832 0.315635 0.236943 0 84 -23704.103134 0.314699 0.236626 0 85 -23703.789371 0.313763 0.236312 0 86 -23703.476543 0.312828 0.236001 0 87 -23703.164650 0.311893 0.235693 0 88 -23702.853691 0.310959 0.235387 0 89 -23702.543664 0.310026 0.235083 0 90 -23702.234570 0.309094 0.234781 0 91 -23701.926408 0.308163 0.234480 0 92 -23701.619176 0.307232 0.234179 0 93 -23701.312874 0.306302 0.233879 0 94 -23701.007502 0.305372 0.233580 0 95 -23700.703059 0.304444 0.233281 1 96 -23700.399543 0.303516 0.232982 1 97 -23700.096954 0.302589 0.232683 1 98 -23699.795291 0.301663 0.232384 1 99 -23699.494554 0.300737 0.232086 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 100 -23699.194741 0.299813 0.231789 1 101 -23698.895853 0.298889 0.231491 1 102 -23698.597887 0.297966 0.231193 1 103 -23698.300843 0.297044 0.230895 1 104 -23698.004721 0.296122 0.230596 1 105 -23697.709519 0.295202 0.230296 1 106 -23697.415236 0.294282 0.229997 1 107 -23697.121873 0.293364 0.229697 1 108 -23696.829427 0.292446 0.229396 1 109 -23696.537897 0.291529 0.229095 1 110 -23696.247284 0.290613 0.228793 1 111 -23695.957586 0.289698 0.228491 1 112 -23695.668802 0.288784 0.228189 1 113 -23695.380931 0.287871 0.227886 1 114 -23695.093972 0.286959 0.227582 1 115 -23694.807925 0.286047 0.227278 1 116 -23694.522788 0.285137 0.226973 1 117 -23694.238560 0.284228 0.226668 1 118 -23693.955240 0.283320 0.226362 1 119 -23693.672828 0.282412 0.226056 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 120 -23693.391322 0.281506 0.225749 1 121 -23693.110721 0.280601 0.225443 1 122 -23692.831025 0.279696 0.225136 1 123 -23692.552232 0.278793 0.224828 1 124 -23692.274340 0.277891 0.224520 1 125 -23691.997350 0.276990 0.224212 1 126 -23691.721261 0.276090 0.223903 1 127 -23691.446070 0.275191 0.223593 1 128 -23691.171777 0.274293 0.223283 1 129 -23690.898380 0.273396 0.222972 1 130 -23690.625880 0.272501 0.222661 1 131 -23690.354274 0.271606 0.222349 1 132 -23690.083561 0.270713 0.222037 1 133 -23689.813741 0.269820 0.221724 1 134 -23689.544812 0.268929 0.221411 1 135 -23689.276773 0.268039 0.221097 1 136 -23689.009623 0.267150 0.220783 1 137 -23688.743361 0.266262 0.220469 1 138 -23688.477985 0.265376 0.220154 1 139 -23688.213495 0.264490 0.219838 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 140 -23687.949889 0.263606 0.219522 1 141 -23687.687165 0.262723 0.219206 1 142 -23687.425324 0.261841 0.218889 1 143 -23687.164363 0.260961 0.218571 1 144 -23686.904282 0.260081 0.218253 1 145 -23686.645079 0.259203 0.217935 1 146 -23686.386752 0.258326 0.217616 1 147 -23686.129301 0.257451 0.217297 1 148 -23685.872725 0.256576 0.216977 1 149 -23685.617022 0.255703 0.216657 1 150 -23685.362190 0.254831 0.216336 1 151 -23685.108229 0.253961 0.216015 1 152 -23684.855137 0.253092 0.215694 1 153 -23684.602914 0.252224 0.215372 1 154 -23684.351557 0.251357 0.215049 1 155 -23684.101065 0.250492 0.214727 1 156 -23683.851437 0.249628 0.214403 1 157 -23683.602672 0.248765 0.214080 1 158 -23683.354769 0.247904 0.213756 1 159 -23683.107725 0.247044 0.213432 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 160 -23682.861540 0.246185 0.213107 1 161 -23682.616213 0.245328 0.212782 1 162 -23682.371741 0.244472 0.212456 1 163 -23682.128124 0.243617 0.212131 1 164 -23681.885360 0.242764 0.211806 1 165 -23681.643448 0.241912 0.211480 1 166 -23681.402387 0.241062 0.211154 1 167 -23681.162174 0.240213 0.210828 1 168 -23680.922809 0.239365 0.210502 1 169 -23680.684291 0.238519 0.210175 1 170 -23680.446617 0.237674 0.209848 1 171 -23680.209786 0.236831 0.209520 1 172 -23679.973797 0.235989 0.209192 1 173 -23679.738649 0.235148 0.208864 1 174 -23679.504339 0.234309 0.208536 1 175 -23679.270868 0.233472 0.208207 1 176 -23679.038232 0.232636 0.207878 1 177 -23678.806431 0.231801 0.207548 1 178 -23678.575463 0.230968 0.207219 1 179 -23678.345326 0.230136 0.206889 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 180 -23678.116020 0.229306 0.206559 1 181 -23677.887543 0.228478 0.206228 1 182 -23677.659892 0.227650 0.205897 1 183 -23677.433067 0.226825 0.205566 1 184 -23677.207067 0.226001 0.205235 1 185 -23676.981889 0.225178 0.204903 1 186 -23676.757532 0.224357 0.204571 1 187 -23676.533994 0.223537 0.204239 1 188 -23676.311275 0.222719 0.203906 1 189 -23676.089372 0.221903 0.203574 1 190 -23675.868284 0.221088 0.203241 1 191 -23675.648009 0.220275 0.202907 1 192 -23675.428546 0.219463 0.202574 1 193 -23675.209893 0.218653 0.202240 1 194 -23674.992049 0.217844 0.201906 1 195 -23674.775012 0.217037 0.201572 1 196 -23674.558781 0.216232 0.201237 1 197 -23674.343353 0.215428 0.200902 1 198 -23674.128727 0.214626 0.200567 1 199 -23673.914902 0.213825 0.200232 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 200 -23673.701877 0.213026 0.199897 1 201 -23673.489648 0.212228 0.199562 1 202 -23673.278216 0.211433 0.199226 1 203 -23673.067577 0.210638 0.198890 1 204 -23672.857731 0.209846 0.198554 1 205 -23672.648676 0.209055 0.198218 1 206 -23672.440411 0.208266 0.197882 1 207 -23672.232933 0.207478 0.197545 1 208 -23672.026241 0.206692 0.197208 1 209 -23671.820333 0.205908 0.196871 1 210 -23671.615208 0.205125 0.196534 1 211 -23671.410864 0.204344 0.196198 1 212 -23671.207299 0.203565 0.195861 1 213 -23671.004512 0.202787 0.195525 1 214 -23670.802501 0.202011 0.195188 1 215 -23670.601265 0.201237 0.194851 1 216 -23670.400800 0.200464 0.194514 1 217 -23670.201107 0.199693 0.194176 1 218 -23670.002183 0.198924 0.193839 1 219 -23669.804027 0.198156 0.193501 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 220 -23669.606636 0.197391 0.193163 1 221 -23669.410010 0.196627 0.192826 1 222 -23669.214145 0.195864 0.192488 1 223 -23669.019042 0.195104 0.192149 1 224 -23668.824697 0.194345 0.191811 1 225 -23668.631110 0.193587 0.191473 1 226 -23668.438278 0.192832 0.191134 1 227 -23668.246200 0.192078 0.190795 1 228 -23668.054874 0.191326 0.190456 2 229 -23667.864298 0.190576 0.190118 2 230 -23667.674471 0.189827 0.189779 2 231 -23667.485390 0.189081 0.189439 2 232 -23667.297055 0.188336 0.189100 2 233 -23667.109462 0.187592 0.188761 2 234 -23666.922612 0.186851 0.188421 2 235 -23666.736501 0.186111 0.188082 2 236 -23666.551128 0.185373 0.187744 2 237 -23666.366491 0.184637 0.187405 2 238 -23666.182588 0.183902 0.187066 2 239 -23665.999419 0.183170 0.186727 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 240 -23665.816980 0.182439 0.186388 2 241 -23665.635270 0.181710 0.186049 2 242 -23665.454288 0.180982 0.185710 2 243 -23665.274031 0.180257 0.185370 2 244 -23665.094498 0.179533 0.185031 2 245 -23664.915686 0.178811 0.184692 2 246 -23664.737595 0.178091 0.184352 2 247 -23664.560223 0.177373 0.184013 2 248 -23664.383566 0.176656 0.183674 2 249 -23664.207625 0.175942 0.183335 2 250 -23664.032396 0.175229 0.182996 2 251 -23663.857879 0.174517 0.182657 2 252 -23663.684071 0.173808 0.182318 2 253 -23663.510970 0.173101 0.181979 2 254 -23663.338575 0.172395 0.181641 2 255 -23663.166884 0.171691 0.181302 2 256 -23662.995894 0.170989 0.180963 2 257 -23662.825605 0.170289 0.180624 2 258 -23662.656015 0.169591 0.180285 2 259 -23662.487121 0.168894 0.179946 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 260 -23662.318921 0.168199 0.179607 2 261 -23662.151414 0.167507 0.179268 2 262 -23661.984599 0.166816 0.178929 2 263 -23661.818473 0.166126 0.178590 2 264 -23661.653034 0.165439 0.178251 2 265 -23661.488280 0.164754 0.177912 2 266 -23661.324210 0.164070 0.177573 2 267 -23661.160822 0.163388 0.177234 2 268 -23660.998114 0.162708 0.176895 2 269 -23660.836084 0.162030 0.176556 2 270 -23660.674730 0.161354 0.176217 2 271 -23660.514051 0.160679 0.175879 2 272 -23660.354044 0.160007 0.175540 2 273 -23660.194708 0.159336 0.175202 2 274 -23660.036041 0.158667 0.174864 2 275 -23659.878041 0.158000 0.174526 2 276 -23659.720706 0.157335 0.174188 2 277 -23659.564034 0.156672 0.173851 2 278 -23659.408024 0.156010 0.173513 2 279 -23659.252673 0.155351 0.173175 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 280 -23659.097980 0.154693 0.172838 2 281 -23658.943943 0.154037 0.172500 2 282 -23658.790560 0.153383 0.172162 2 283 -23658.637828 0.152731 0.171825 2 284 -23658.485747 0.152081 0.171488 2 285 -23658.334315 0.151433 0.171150 2 286 -23658.183528 0.150786 0.170813 2 287 -23658.033387 0.150142 0.170476 2 288 -23657.883888 0.149499 0.170139 2 289 -23657.735030 0.148858 0.169802 2 290 -23657.586811 0.148219 0.169465 2 291 -23657.439229 0.147582 0.169128 2 292 -23657.292283 0.146947 0.168792 2 293 -23657.145969 0.146313 0.168455 2 294 -23657.000288 0.145682 0.168119 2 295 -23656.855235 0.145052 0.167783 2 296 -23656.710811 0.144424 0.167447 2 297 -23656.567013 0.143798 0.167111 2 298 -23656.423838 0.143174 0.166775 2 299 -23656.281286 0.142552 0.166439 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 300 -23656.139354 0.141932 0.166104 2 301 -23655.998040 0.141314 0.165768 2 302 -23655.857343 0.140697 0.165433 2 303 -23655.717260 0.140083 0.165098 2 304 -23655.577790 0.139470 0.164763 2 305 -23655.438931 0.138859 0.164428 2 306 -23655.300681 0.138250 0.164094 2 307 -23655.163038 0.137643 0.163759 2 308 -23655.026000 0.137038 0.163425 2 309 -23654.889566 0.136434 0.163091 2 310 -23654.753733 0.135833 0.162757 2 311 -23654.618500 0.135233 0.162423 2 312 -23654.483864 0.134635 0.162089 2 313 -23654.349825 0.134040 0.161755 2 314 -23654.216379 0.133446 0.161422 2 315 -23654.083526 0.132854 0.161089 2 316 -23653.951262 0.132263 0.160756 2 317 -23653.819587 0.131675 0.160423 2 318 -23653.688499 0.131088 0.160090 2 319 -23653.557995 0.130504 0.159757 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 320 -23653.428074 0.129921 0.159425 2 321 -23653.298734 0.129340 0.159092 2 322 -23653.169973 0.128761 0.158760 2 323 -23653.041789 0.128184 0.158428 2 324 -23652.914180 0.127609 0.158097 2 325 -23652.787145 0.127035 0.157765 2 326 -23652.660681 0.126464 0.157434 2 327 -23652.534787 0.125894 0.157103 2 328 -23652.409461 0.125326 0.156771 2 329 -23652.284700 0.124760 0.156441 2 330 -23652.160504 0.124196 0.156110 2 331 -23652.036870 0.123634 0.155780 2 332 -23651.913797 0.123074 0.155452 2 333 -23651.791282 0.122515 0.155124 2 334 -23651.669323 0.121958 0.154796 2 335 -23651.547920 0.121404 0.154469 2 336 -23651.427069 0.120851 0.154142 2 337 -23651.306769 0.120300 0.153815 2 338 -23651.187019 0.119750 0.153488 2 339 -23651.067816 0.119203 0.153161 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 340 -23650.949159 0.118657 0.152835 2 341 -23650.831045 0.118114 0.152509 2 342 -23650.713473 0.117572 0.152183 2 343 -23650.596442 0.117032 0.151857 2 344 -23650.479948 0.116494 0.151534 2 345 -23650.363991 0.115957 0.151210 2 346 -23650.248568 0.115423 0.150887 2 347 -23650.133678 0.114890 0.150564 2 348 -23650.019319 0.114359 0.150242 2 349 -23649.905488 0.113830 0.149919 2 350 -23649.792185 0.113303 0.149597 2 351 -23649.679407 0.112778 0.149275 2 352 -23649.567153 0.112254 0.148953 2 353 -23649.455420 0.111733 0.148632 2 354 -23649.344207 0.111213 0.148310 2 355 -23649.233512 0.110695 0.147989 2 356 -23649.123334 0.110179 0.147668 2 357 -23649.013670 0.109664 0.147348 2 358 -23648.904518 0.109152 0.147027 2 359 -23648.795877 0.108641 0.146707 2 Iteration log(P) dlog(P) Diff in posterior Time in sec 360 -23648.687745 0.108132 0.146387 2 361 -23648.580120 0.107625 0.146067 2 362 -23648.473000 0.107120 0.145748 2 363 -23648.366384 0.106616 0.145429 2 364 -23648.260270 0.106114 0.145110 2 365 -23648.154656 0.105614 0.144791 2 366 -23648.049539 0.105116 0.144473 2 367 -23647.944919 0.104620 0.144154 2 368 -23647.840794 0.104126 0.143836 2 369 -23647.737161 0.103633 0.143519 3 370 -23647.634019 0.103142 0.143201 3 371 -23647.531366 0.102653 0.142884 3 372 -23647.429201 0.102165 0.142567 3 373 -23647.327521 0.101680 0.142251 3 374 -23647.226325 0.101196 0.141934 3 375 -23647.125611 0.100714 0.141618 3 376 -23647.025378 0.100234 0.141302 3 377 -23646.925622 0.099755 0.140986 3 Convergence reached! number of states = 12 number of bins = 6183 maximum number of iterations = 1000 maximum running time = none epsilon = 0.1 data mean = 58.8193, data variance = 486.587 Iteration log(P) dlog(P) Diff in posterior Time in sec 0 -inf - - 0 1 -24380.580428 inf 6183.000000 0 2 -23357.275929 1023.304498 686.821642 0 3 -23260.421975 96.853955 172.471538 0 4 -23232.483517 27.938458 143.506687 0 5 -23222.142294 10.341223 76.049323 0 6 -23217.735527 4.406767 58.626866 0 7 -23215.521320 2.214207 35.912568 0 8 -23214.276947 1.244373 27.484487 0 9 -23213.395549 0.881398 18.765222 0 10 -23212.605307 0.790242 15.594210 0 11 -23211.762729 0.842578 12.269888 0 12 -23210.839848 0.922881 11.279480 0 13 -23209.921053 0.918795 9.624877 0 14 -23209.118734 0.802320 8.968506 0 15 -23208.463874 0.654860 7.927086 0 16 -23207.924958 0.538916 7.683630 0 17 -23207.463600 0.461358 7.238144 0 18 -23207.046263 0.417337 7.327465 0 19 -23206.646001 0.400262 7.466156 0 Iteration log(P) dlog(P) Diff in posterior Time in sec 20 -23206.242687 0.403315 7.882758 0 21 -23205.828261 0.414426 8.254388 0 22 -23205.414415 0.413846 8.474710 0 23 -23205.032476 0.381939 8.244365 0 24 -23204.714716 0.317760 7.544341 0 25 -23204.473698 0.241018 6.506549 0 26 -23204.300805 0.172894 5.379661 0 27 -23204.178183 0.122622 4.308309 0 28 -23204.088739 0.089444 3.383929 0 Convergence reached! number of states = 11 number of bins = 5442 maximum number of iterations = 1000 maximum running time = none epsilon = 0.1 data mean = 63.9717, data variance = 1059.32 Iteration log(P) dlog(P) Diff in posterior Time in sec 0 -inf - - 0 1 -21177.150641 inf 5442.000000 0 2 -20711.054012 466.096629 390.505270 0 3 -20693.275989 17.778024 85.372131 0 4 -20690.239855 3.036134 33.071291 0 5 -20689.163935 1.075919 26.872093 0 6 -20688.762950 0.400986 12.127422 0 7 -20688.580230 0.182719 8.966009 0 8 -20688.472739 0.107491 4.304038 0 9 -20688.396085 0.076655 3.087959 0 Convergence reached! number of states = 12 number of bins = 5442 maximum number of iterations = 1000 maximum running time = none epsilon = 0.1 data mean = 63.9717, data variance = 1059.32 Iteration log(P) dlog(P) Diff in posterior Time in sec 0 -inf - - 0 1 -20778.885904 inf 5442.000000 0 2 -20214.840926 564.044978 503.589244 0 3 -20185.942950 28.897975 137.261825 0 4 -20179.925587 6.017363 51.421390 0 5 -20177.170587 2.755000 36.836764 0 6 -20175.645594 1.524994 18.722502 0 7 -20174.658989 0.986605 13.124839 0 8 -20173.895734 0.763255 11.327572 1 9 -20173.167941 0.727793 9.948167 1 10 -20172.282987 0.884954 11.162019 1 11 -20170.984261 1.298726 12.412190 1 12 -20169.145246 1.839014 14.930161 1 13 -20166.835634 2.309613 16.942694 1 14 -20163.895031 2.940602 18.691149 1 15 -20160.410970 3.484061 18.008358 1 16 -20157.717749 2.693221 14.496841 1 17 -20156.213293 1.504456 10.220281 1 18 -20155.444668 0.768625 7.026993 1 19 -20155.094478 0.350190 4.771865 1 Iteration log(P) dlog(P) Diff in posterior Time in sec 20 -20154.925350 0.169128 3.076403 1 21 -20154.827513 0.097837 1.932927 1 Convergence reached! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ] > > proc.time() user system elapsed 15.517 0.527 16.034
AneuFinder.Rcheck/AneuFinder-Ex.timings
name | user | system | elapsed | |
Aneufinder | 0 | 0 | 0 | |
annotateBreakpoints | 15.621 | 0.784 | 16.874 | |
bam2GRanges | 0.330 | 0.027 | 0.360 | |
bed2GRanges | 0.753 | 0.031 | 0.786 | |
binReads | 2.217 | 0.113 | 2.330 | |
blacklist | 1.807 | 0.024 | 1.832 | |
clusterByQuality | 2.242 | 0.048 | 2.296 | |
clusterHMMs | 0.397 | 0.008 | 0.405 | |
collapseBins | 2.257 | 0.092 | 2.348 | |
colors | 0.073 | 0.001 | 0.074 | |
compareMethods | 0.611 | 0.006 | 0.617 | |
consensusSegments | 7.644 | 0.095 | 7.741 | |
correctGC | 24.278 | 3.331 | 27.613 | |
export | 0 | 0 | 0 | |
filterSegments | 0.291 | 0.008 | 0.299 | |
findCNVs | 4.110 | 0.423 | 4.534 | |
findCNVs.strandseq | 4.192 | 0.216 | 4.407 | |
fixedWidthBins | 0.064 | 0.000 | 0.064 | |
getBreakpoints | 10.758 | 0.195 | 10.954 | |
getDistinctColors | 0.106 | 0.004 | 0.111 | |
getQC | 1.525 | 0.004 | 1.529 | |
getSCEcoordinates | 4.790 | 0.155 | 5.321 | |
heatmapAneuploidies | 40.444 | 1.125 | 41.569 | |
heatmapGenomewide | 19.257 | 0.272 | 19.536 | |
heatmapGenomewideClusters | 22.906 | 0.232 | 23.138 | |
importBed | 1.118 | 0.011 | 1.131 | |
karyotypeMeasures | 20.562 | 0.189 | 20.750 | |
loadFromFiles | 3.181 | 0.031 | 3.213 | |
plotHeterogeneity | 27.021 | 0.296 | 27.317 | |
plot_pca | 0.962 | 0.012 | 0.974 | |
refineBreakpoints | 46.043 | 0.452 | 46.495 | |
simulateReads | 51.364 | 2.711 | 54.078 | |
subsetByCNVprofile | 4.765 | 0.028 | 4.793 | |
variableWidthBins | 3.809 | 0.052 | 3.861 | |