Back to Multiple platform build/check report for BioC 3.19:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-12-07 12:27:10 -0500 (Thu, 07 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4609
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" 4369
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4375
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 4262
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 64/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.31.0  (landing page)
Aaron Taudt
Snapshot Date: 2023-12-06 14:00:17 -0500 (Wed, 06 Dec 2023)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: devel
git_last_commit: b8d11a4
git_last_commit_date: 2023-10-24 10:48:50 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for AneuFinder on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: AneuFinder
Version: 1.31.0
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings AneuFinder_1.31.0.tar.gz
StartedAt: 2023-12-07 06:13:35 -0000 (Thu, 07 Dec 2023)
EndedAt: 2023-12-07 06:20:03 -0000 (Thu, 07 Dec 2023)
EllapsedTime: 388.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AneuFinder.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings AneuFinder_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.31.0’
* 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++ (GCC) 10.3.1’
* 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 R 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 ... ERROR
Running examples in ‘AneuFinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: consensusSegments
> ### Title: Make consensus segments
> ### Aliases: consensusSegments
> 
> ### ** Examples
> 
> ## Get results from a small-cell-lung-cancer
> lung.folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
> lung.files <- list.files(lung.folder, full.names=TRUE)
> ## Get consensus segments and states
> consensusSegments(lung.files)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.


Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/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/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/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/R/R-devel/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/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/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)

Tests output

AneuFinder.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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              1
        11       -23730.527674            0.542246            7.021040              1
        12       -23730.007090            0.520584            4.942881              1
        13       -23729.480035            0.527055            3.803030              1
        14       -23728.932681            0.547354            2.653912              1
        15       -23728.372455            0.560226            2.141742              1
        16       -23727.839017            0.533439            1.244299              1
        17       -23727.367012            0.472005            1.109390              1
        18       -23726.947097            0.419914            0.529456              1
        19       -23726.552750            0.394348            0.602730              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23726.169459            0.383291            0.302116              1
        21       -23725.791510            0.377949            0.389827              1
        22       -23725.416462            0.375048            0.244787              1
        23       -23725.043233            0.373229            0.307572              1
        24       -23724.671334            0.371899            0.240956              1
        25       -23724.300551            0.370783            0.275223              1
        26       -23723.930786            0.369765            0.245508              1
        27       -23723.561998            0.368789            0.262164              1
        28       -23723.194164            0.367834            0.248735              1
        29       -23722.827276            0.366888            0.256570              1
        30       -23722.461329            0.365947            0.250428              1
        31       -23722.096319            0.365010            0.254042              1
        32       -23721.732244            0.364076            0.251213              1
        33       -23721.369100            0.363144            0.252844              1
        34       -23721.006885            0.362214            0.251549              1
        35       -23720.645598            0.361287            0.252622              1
        36       -23720.285236            0.360362            0.252383              1
        37       -23719.925796            0.359440            0.253123              1
        38       -23719.567277            0.358519            0.253290              1
        39       -23719.209677            0.357600            0.254027              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        40       -23718.852994            0.356683            0.254590              1
        41       -23718.497228            0.355766            0.255400              1
        42       -23718.142378            0.354850            0.256151              1
        43       -23717.788445            0.353933            0.257145              1
        44       -23717.435431            0.353014            0.258100              1
        45       -23717.083339            0.352092            0.259094              1
        46       -23716.732173            0.351166            0.260034              1
        47       -23716.381938            0.350235            0.260935              1
        48       -23716.032640            0.349298            0.261735              1
        49       -23715.684287            0.348353            0.262424              1
        50       -23715.336886            0.347401            0.262956              1
        51       -23714.990445            0.346441            0.263312              1
        52       -23714.644972            0.345473            0.263463              1
        53       -23714.300474            0.344498            0.263396              1
        54       -23713.956958            0.343516            0.263103              1
        55       -23713.614428            0.342530            0.262584              1
        56       -23713.272887            0.341540            0.261849              1
        57       -23712.932339            0.340548            0.260917              1
        58       -23712.592783            0.339556            0.259810              1
        59       -23712.254217            0.338565            0.258559              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        60       -23711.916641            0.337576            0.257196              1
        61       -23711.580050            0.336591            0.255754              1
        62       -23711.244442            0.335609            0.254264              1
        63       -23710.909811            0.334631            0.252755              1
        64       -23710.576153            0.333657            0.251252              1
        65       -23710.243465            0.332688            0.249777              1
        66       -23709.911743            0.331722            0.248349              1
        67       -23709.580982            0.330761            0.247090              1
        68       -23709.251180            0.329802            0.245906              1
        69       -23708.922334            0.328846            0.244786              2
        70       -23708.594441            0.327893            0.243757              2
        71       -23708.267498            0.326942            0.242885              2
        72       -23707.941505            0.325993            0.242069              2
        73       -23707.616459            0.325046            0.241304              2
        74       -23707.292358            0.324101            0.240590              2
        75       -23706.969202            0.323156            0.239921              2
        76       -23706.646989            0.322213            0.239394              2
        77       -23706.325719            0.321271            0.239012              2
        78       -23706.005389            0.320329            0.238641              2
        79       -23705.686000            0.319389            0.238282              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        80       -23705.367551            0.318449            0.237931              2
        81       -23705.050040            0.317511            0.237592              2
        82       -23704.733468            0.316573            0.237265              2
        83       -23704.417832            0.315635            0.236943              2
        84       -23704.103134            0.314699            0.236626              2
        85       -23703.789371            0.313763            0.236312              2
        86       -23703.476543            0.312828            0.236001              2
        87       -23703.164650            0.311893            0.235693              2
        88       -23702.853691            0.310959            0.235387              2
        89       -23702.543664            0.310026            0.235083              2
        90       -23702.234570            0.309094            0.234781              2
        91       -23701.926408            0.308163            0.234480              2
        92       -23701.619176            0.307232            0.234179              2
        93       -23701.312874            0.306302            0.233879              2
        94       -23701.007502            0.305372            0.233580              2
        95       -23700.703059            0.304444            0.233281              2
        96       -23700.399543            0.303516            0.232982              2
        97       -23700.096954            0.302589            0.232683              2
        98       -23699.795291            0.301663            0.232384              2
        99       -23699.494554            0.300737            0.232086              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       100       -23699.194741            0.299813            0.231789              2
       101       -23698.895853            0.298889            0.231491              2
       102       -23698.597887            0.297966            0.231193              2
       103       -23698.300843            0.297044            0.230895              2
       104       -23698.004721            0.296122            0.230596              2
       105       -23697.709519            0.295202            0.230296              2
       106       -23697.415236            0.294282            0.229997              2
       107       -23697.121873            0.293364            0.229697              2
       108       -23696.829427            0.292446            0.229396              2
       109       -23696.537897            0.291529            0.229095              2
       110       -23696.247284            0.290613            0.228793              2
       111       -23695.957586            0.289698            0.228491              2
       112       -23695.668802            0.288784            0.228189              2
       113       -23695.380931            0.287871            0.227886              2
       114       -23695.093972            0.286959            0.227582              2
       115       -23694.807925            0.286047            0.227278              2
       116       -23694.522788            0.285137            0.226973              2
       117       -23694.238560            0.284228            0.226668              2
       118       -23693.955240            0.283320            0.226362              2
       119       -23693.672828            0.282412            0.226056              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              2
       121       -23693.110721            0.280601            0.225443              2
       122       -23692.831025            0.279696            0.225136              2
       123       -23692.552232            0.278793            0.224828              2
       124       -23692.274340            0.277891            0.224520              2
       125       -23691.997350            0.276990            0.224212              2
       126       -23691.721261            0.276090            0.223903              2
       127       -23691.446070            0.275191            0.223593              2
       128       -23691.171777            0.274293            0.223283              3
       129       -23690.898380            0.273396            0.222972              3
       130       -23690.625880            0.272501            0.222661              3
       131       -23690.354274            0.271606            0.222349              3
       132       -23690.083561            0.270713            0.222037              3
       133       -23689.813741            0.269820            0.221724              3
       134       -23689.544812            0.268929            0.221411              3
       135       -23689.276773            0.268039            0.221097              3
       136       -23689.009623            0.267150            0.220783              3
       137       -23688.743361            0.266262            0.220469              3
       138       -23688.477985            0.265376            0.220154              3
       139       -23688.213495            0.264490            0.219838              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       140       -23687.949889            0.263606            0.219522              3
       141       -23687.687165            0.262723            0.219206              3
       142       -23687.425324            0.261841            0.218889              3
       143       -23687.164363            0.260961            0.218571              3
       144       -23686.904282            0.260081            0.218253              3
       145       -23686.645079            0.259203            0.217935              3
       146       -23686.386752            0.258326            0.217616              3
       147       -23686.129301            0.257451            0.217297              3
       148       -23685.872725            0.256576            0.216977              3
       149       -23685.617022            0.255703            0.216657              3
       150       -23685.362190            0.254831            0.216336              3
       151       -23685.108229            0.253961            0.216015              3
       152       -23684.855137            0.253092            0.215694              3
       153       -23684.602914            0.252224            0.215372              3
       154       -23684.351557            0.251357            0.215049              3
       155       -23684.101065            0.250492            0.214727              3
       156       -23683.851437            0.249628            0.214403              3
       157       -23683.602672            0.248765            0.214080              3
       158       -23683.354769            0.247904            0.213756              3
       159       -23683.107725            0.247044            0.213432              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       160       -23682.861540            0.246185            0.213107              3
       161       -23682.616213            0.245328            0.212782              3
       162       -23682.371741            0.244472            0.212456              3
       163       -23682.128124            0.243617            0.212131              3
       164       -23681.885360            0.242764            0.211806              3
       165       -23681.643448            0.241912            0.211480              3
       166       -23681.402387            0.241062            0.211154              3
       167       -23681.162174            0.240213            0.210828              3
       168       -23680.922809            0.239365            0.210502              3
       169       -23680.684291            0.238519            0.210175              3
       170       -23680.446617            0.237674            0.209848              3
       171       -23680.209786            0.236831            0.209520              3
       172       -23679.973797            0.235989            0.209192              3
       173       -23679.738649            0.235148            0.208864              3
       174       -23679.504339            0.234309            0.208536              3
       175       -23679.270868            0.233472            0.208207              3
       176       -23679.038232            0.232636            0.207878              3
       177       -23678.806431            0.231801            0.207548              3
       178       -23678.575463            0.230968            0.207219              3
       179       -23678.345326            0.230136            0.206889              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       180       -23678.116020            0.229306            0.206559              3
       181       -23677.887543            0.228478            0.206228              3
       182       -23677.659892            0.227650            0.205897              3
       183       -23677.433067            0.226825            0.205566              3
       184       -23677.207067            0.226001            0.205235              3
       185       -23676.981889            0.225178            0.204903              3
       186       -23676.757532            0.224357            0.204571              3
       187       -23676.533994            0.223537            0.204239              3
       188       -23676.311275            0.222719            0.203906              4
       189       -23676.089372            0.221903            0.203574              4
       190       -23675.868284            0.221088            0.203241              4
       191       -23675.648009            0.220275            0.202907              4
       192       -23675.428546            0.219463            0.202574              4
       193       -23675.209893            0.218653            0.202240              4
       194       -23674.992049            0.217844            0.201906              4
       195       -23674.775012            0.217037            0.201572              4
       196       -23674.558781            0.216232            0.201237              4
       197       -23674.343353            0.215428            0.200902              4
       198       -23674.128727            0.214626            0.200567              4
       199       -23673.914902            0.213825            0.200232              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              4
       201       -23673.489648            0.212228            0.199562              4
       202       -23673.278216            0.211433            0.199226              4
       203       -23673.067577            0.210638            0.198890              4
       204       -23672.857731            0.209846            0.198554              4
       205       -23672.648676            0.209055            0.198218              4
       206       -23672.440411            0.208266            0.197882              4
       207       -23672.232933            0.207478            0.197545              4
       208       -23672.026241            0.206692            0.197208              4
       209       -23671.820333            0.205908            0.196871              4
       210       -23671.615208            0.205125            0.196534              4
       211       -23671.410864            0.204344            0.196198              4
       212       -23671.207299            0.203565            0.195861              4
       213       -23671.004512            0.202787            0.195525              4
       214       -23670.802501            0.202011            0.195188              4
       215       -23670.601265            0.201237            0.194851              4
       216       -23670.400800            0.200464            0.194514              4
       217       -23670.201107            0.199693            0.194176              4
       218       -23670.002183            0.198924            0.193839              4
       219       -23669.804027            0.198156            0.193501              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              4
       221       -23669.410010            0.196627            0.192826              4
       222       -23669.214145            0.195864            0.192488              4
       223       -23669.019042            0.195104            0.192149              4
       224       -23668.824697            0.194345            0.191811              4
       225       -23668.631110            0.193587            0.191473              4
       226       -23668.438278            0.192832            0.191134              4
       227       -23668.246200            0.192078            0.190795              4
       228       -23668.054874            0.191326            0.190456              4
       229       -23667.864298            0.190576            0.190118              4
       230       -23667.674471            0.189827            0.189779              4
       231       -23667.485390            0.189081            0.189439              4
       232       -23667.297055            0.188336            0.189100              4
       233       -23667.109462            0.187592            0.188761              4
       234       -23666.922612            0.186851            0.188421              4
       235       -23666.736501            0.186111            0.188082              4
       236       -23666.551128            0.185373            0.187744              4
       237       -23666.366491            0.184637            0.187405              4
       238       -23666.182588            0.183902            0.187066              4
       239       -23665.999419            0.183170            0.186727              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       240       -23665.816980            0.182439            0.186388              4
       241       -23665.635270            0.181710            0.186049              4
       242       -23665.454288            0.180982            0.185710              4
       243       -23665.274031            0.180257            0.185370              4
       244       -23665.094498            0.179533            0.185031              4
       245       -23664.915686            0.178811            0.184692              4
       246       -23664.737595            0.178091            0.184352              4
       247       -23664.560223            0.177373            0.184013              5
       248       -23664.383566            0.176656            0.183674              5
       249       -23664.207625            0.175942            0.183335              5
       250       -23664.032396            0.175229            0.182996              5
       251       -23663.857879            0.174517            0.182657              5
       252       -23663.684071            0.173808            0.182318              5
       253       -23663.510970            0.173101            0.181979              5
       254       -23663.338575            0.172395            0.181641              5
       255       -23663.166884            0.171691            0.181302              5
       256       -23662.995894            0.170989            0.180963              5
       257       -23662.825605            0.170289            0.180624              5
       258       -23662.656015            0.169591            0.180285              5
       259       -23662.487121            0.168894            0.179946              5
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              5
       261       -23662.151414            0.167507            0.179268              5
       262       -23661.984599            0.166816            0.178929              5
       263       -23661.818473            0.166126            0.178590              5
       264       -23661.653034            0.165439            0.178251              5
       265       -23661.488280            0.164754            0.177912              5
       266       -23661.324210            0.164070            0.177573              5
       267       -23661.160822            0.163388            0.177234              5
       268       -23660.998114            0.162708            0.176895              5
       269       -23660.836084            0.162030            0.176556              5
       270       -23660.674730            0.161354            0.176217              5
       271       -23660.514051            0.160679            0.175879              5
       272       -23660.354044            0.160007            0.175540              5
       273       -23660.194708            0.159336            0.175202              5
       274       -23660.036041            0.158667            0.174864              5
       275       -23659.878041            0.158000            0.174526              5
       276       -23659.720706            0.157335            0.174188              5
       277       -23659.564034            0.156672            0.173851              5
       278       -23659.408024            0.156010            0.173513              5
       279       -23659.252673            0.155351            0.173175              5
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       280       -23659.097980            0.154693            0.172838              5
       281       -23658.943943            0.154037            0.172500              5
       282       -23658.790560            0.153383            0.172162              5
       283       -23658.637828            0.152731            0.171825              5
       284       -23658.485747            0.152081            0.171488              5
       285       -23658.334315            0.151433            0.171150              5
       286       -23658.183528            0.150786            0.170813              5
       287       -23658.033387            0.150142            0.170476              5
       288       -23657.883888            0.149499            0.170139              5
       289       -23657.735030            0.148858            0.169802              5
       290       -23657.586811            0.148219            0.169465              5
       291       -23657.439229            0.147582            0.169128              5
       292       -23657.292283            0.146947            0.168792              5
       293       -23657.145969            0.146313            0.168455              5
       294       -23657.000288            0.145682            0.168119              5
       295       -23656.855235            0.145052            0.167783              5
       296       -23656.710811            0.144424            0.167447              5
       297       -23656.567013            0.143798            0.167111              5
       298       -23656.423838            0.143174            0.166775              5
       299       -23656.281286            0.142552            0.166439              5
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       300       -23656.139354            0.141932            0.166104              5
       301       -23655.998040            0.141314            0.165768              5
       302       -23655.857343            0.140697            0.165433              5
       303       -23655.717260            0.140083            0.165098              5
       304       -23655.577790            0.139470            0.164763              5
       305       -23655.438931            0.138859            0.164428              5
       306       -23655.300681            0.138250            0.164094              5
       307       -23655.163038            0.137643            0.163759              5
       308       -23655.026000            0.137038            0.163425              6
       309       -23654.889566            0.136434            0.163091              6
       310       -23654.753733            0.135833            0.162757              6
       311       -23654.618500            0.135233            0.162423              6
       312       -23654.483864            0.134636            0.162089              6
       313       -23654.349825            0.134040            0.161755              6
       314       -23654.216379            0.133446            0.161422              6
       315       -23654.083526            0.132854            0.161089              6
       316       -23653.951262            0.132263            0.160756              6
       317       -23653.819587            0.131675            0.160423              6
       318       -23653.688499            0.131088            0.160090              6
       319       -23653.557995            0.130504            0.159757              6
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       320       -23653.428074            0.129921            0.159425              6
       321       -23653.298734            0.129340            0.159092              6
       322       -23653.169973            0.128761            0.158760              6
       323       -23653.041789            0.128184            0.158428              6
       324       -23652.914180            0.127609            0.158097              6
       325       -23652.787145            0.127035            0.157765              6
       326       -23652.660681            0.126464            0.157434              6
       327       -23652.534787            0.125894            0.157103              6
       328       -23652.409461            0.125326            0.156771              6
       329       -23652.284700            0.124760            0.156441              6
       330       -23652.160504            0.124196            0.156110              6
       331       -23652.036870            0.123634            0.155780              6
       332       -23651.913797            0.123074            0.155452              6
       333       -23651.791282            0.122515            0.155124              6
       334       -23651.669323            0.121958            0.154796              6
       335       -23651.547920            0.121404            0.154469              6
       336       -23651.427069            0.120851            0.154142              6
       337       -23651.306769            0.120300            0.153815              6
       338       -23651.187019            0.119750            0.153488              6
       339       -23651.067816            0.119203            0.153161              6
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       340       -23650.949159            0.118657            0.152835              6
       341       -23650.831045            0.118114            0.152509              6
       342       -23650.713473            0.117572            0.152183              6
       343       -23650.596442            0.117032            0.151857              6
       344       -23650.479948            0.116494            0.151534              6
       345       -23650.363991            0.115957            0.151210              6
       346       -23650.248568            0.115423            0.150887              6
       347       -23650.133678            0.114890            0.150564              6
       348       -23650.019319            0.114359            0.150242              6
       349       -23649.905488            0.113830            0.149919              6
       350       -23649.792185            0.113303            0.149597              6
       351       -23649.679407            0.112778            0.149275              6
       352       -23649.567153            0.112254            0.148953              6
       353       -23649.455420            0.111733            0.148632              6
       354       -23649.344207            0.111213            0.148310              6
       355       -23649.233512            0.110695            0.147989              6
       356       -23649.123334            0.110179            0.147668              6
       357       -23649.013670            0.109664            0.147348              6
       358       -23648.904518            0.109152            0.147027              6
       359       -23648.795877            0.108641            0.146707              6
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              6
       361       -23648.580120            0.107625            0.146067              6
       362       -23648.473000            0.107120            0.145748              6
       363       -23648.366384            0.106616            0.145429              6
       364       -23648.260270            0.106114            0.145110              6
       365       -23648.154656            0.105614            0.144791              6
       366       -23648.049539            0.105116            0.144473              7
       367       -23647.944919            0.104620            0.144154              7
       368       -23647.840794            0.104126            0.143836              7
       369       -23647.737161            0.103633            0.143519              7
       370       -23647.634019            0.103142            0.143201              7
       371       -23647.531366            0.102653            0.142884              7
       372       -23647.429201            0.102165            0.142567              7
       373       -23647.327521            0.101680            0.142251              7
       374       -23647.226325            0.101196            0.141934              7
       375       -23647.125611            0.100714            0.141618              7
       376       -23647.025378            0.100234            0.141302              7
       377       -23646.925622            0.099755            0.140986              7
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           12.269889              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              1
        23       -23205.032476            0.381939            8.244365              1
        24       -23204.714716            0.317760            7.544341              1
        25       -23204.473698            0.241018            6.506549              1
        26       -23204.300805            0.172894            5.379661              1
        27       -23204.178183            0.122622            4.308309              1
        28       -23204.088739            0.089444            3.383929              1
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              0
         9       -20173.167941            0.727793            9.948167              0
        10       -20172.282987            0.884954           11.162019              0
        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 
 23.510   2.141  26.144 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0010.0000.000
annotateBreakpoints20.849 4.55027.992
bam2GRanges0.4060.0190.436
bed2GRanges1.3650.0241.391
binReads2.8420.0042.853
blacklist2.5480.0282.593
clusterByQuality3.8240.8025.255
clusterHMMs0.5980.0150.661
collapseBins3.6310.0883.730
colors0.0530.0040.058
compareMethods0.7800.0120.794