Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:05 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for AneuFinder on nebbiolo2


To the developers/maintainers of the AneuFinder package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 54/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.22.0  (landing page)
Aaron Taudt
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_14
git_last_commit: ea0beb3
git_last_commit_date: 2021-10-26 12:26:30 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AneuFinder
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AneuFinder_1.22.0.tar.gz
StartedAt: 2022-01-25 06:21:01 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 06:31:56 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 655.0 seconds
RetCode: 0
Status:   OK  
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AneuFinder_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AneuFinder.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.22.0’
* 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
* 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 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             64.801  4.204  69.038
refineBreakpoints         59.764  0.760  60.524
heatmapAneuploidies       55.275  0.467  55.743
plotHeterogeneity         36.572  0.152  36.725
heatmapGenomewideClusters 34.274  0.136  34.410
correctGC                 28.837  3.681  33.292
karyotypeMeasures         30.034  0.112  30.146
heatmapGenomewide         29.880  0.112  30.000
annotateBreakpoints       17.745  0.764  18.811
getBreakpoints            12.530  0.116  12.646
consensusSegments         10.947  0.020  10.967
subsetByCNVprofile         7.154  0.096   7.250
getSCEcoordinates          6.746  0.216   6.969
findCNVs.strandseq         5.916  0.120   6.037
variableWidthBins          5.372  0.059   5.431
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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++14 -I"/home/biocbuild/bbs-3.14-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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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 version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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              1
        87       -23703.164650            0.311893            0.235693              1
        88       -23702.853691            0.310959            0.235387              1
        89       -23702.543664            0.310026            0.235083              1
        90       -23702.234570            0.309094            0.234781              1
        91       -23701.926408            0.308163            0.234480              1
        92       -23701.619176            0.307232            0.234179              1
        93       -23701.312874            0.306302            0.233879              1
        94       -23701.007502            0.305372            0.233580              1
        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              2
       218       -23670.002183            0.198924            0.193839              2
       219       -23669.804027            0.198156            0.193501              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              2
       221       -23669.410010            0.196627            0.192826              2
       222       -23669.214145            0.195864            0.192488              2
       223       -23669.019042            0.195104            0.192149              2
       224       -23668.824697            0.194345            0.191811              2
       225       -23668.631110            0.193587            0.191473              2
       226       -23668.438278            0.192832            0.191134              2
       227       -23668.246200            0.192078            0.190795              2
       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              3
       357       -23649.013670            0.109664            0.147348              3
       358       -23648.904518            0.109152            0.147027              3
       359       -23648.795877            0.108641            0.146707              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              3
       361       -23648.580120            0.107625            0.146067              3
       362       -23648.473000            0.107120            0.145748              3
       363       -23648.366384            0.106616            0.145429              3
       364       -23648.260270            0.106114            0.145110              3
       365       -23648.154656            0.105614            0.144791              3
       366       -23648.049539            0.105116            0.144473              3
       367       -23647.944919            0.104620            0.144154              3
       368       -23647.840794            0.104126            0.143836              3
       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              1
        18       -23207.046263            0.417337            7.327465              1
        19       -23206.646001            0.400262            7.466156              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23206.242687            0.403315            7.882758              1
        21       -23205.828261            0.414426            8.254388              1
        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              0
        12       -20169.145246            1.839014           14.930161              0
        13       -20166.835634            2.309613           16.942694              0
        14       -20163.895031            2.940602           18.691149              0
        15       -20160.410970            3.484061           18.008358              0
        16       -20157.717749            2.693221           14.496841              0
        17       -20156.213293            1.504456           10.220281              0
        18       -20155.444668            0.768625            7.026993              0
        19       -20155.094478            0.350190            4.771865              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -20154.925350            0.169128            3.076403              0
        21       -20154.827513            0.097837            1.932927              0
Convergence reached!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 20.257   0.620  20.862 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder000
annotateBreakpoints17.745 0.76418.811
bam2GRanges0.4410.0080.451
bed2GRanges0.7610.0520.814
binReads1.9560.0081.964
blacklist2.2240.0082.231
clusterByQuality4.1250.0374.167
clusterHMMs0.5410.0000.540
collapseBins1.8180.0001.819
colors0.0660.0040.071
compareMethods0.7380.0120.750
consensusSegments10.947 0.02010.967
correctGC28.837 3.68133.292
export000
filterSegments0.3590.0040.362
findCNVs4.4500.2684.718
findCNVs.strandseq5.9160.1206.037
fixedWidthBins0.0960.0000.096
getBreakpoints12.530 0.11612.646
getDistinctColors0.1150.0000.115
getQC2.5040.0042.508
getSCEcoordinates6.7460.2166.969
heatmapAneuploidies55.275 0.46755.743
heatmapGenomewide29.880 0.11230.000
heatmapGenomewideClusters34.274 0.13634.410
importBed1.1390.0001.139
karyotypeMeasures30.034 0.11230.146
loadFromFiles4.2460.0084.255
plotHeterogeneity36.572 0.15236.725
plot_pca1.2450.0121.258
refineBreakpoints59.764 0.76060.524
simulateReads64.801 4.20469.038
subsetByCNVprofile7.1540.0967.250
variableWidthBins5.3720.0595.431