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This page was generated on 2021-09-24 15:05:39 -0400 (Fri, 24 Sep 2021).

CHECK results for AneuFinder on nebbiolo1

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 56/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.20.0  (landing page)
Aaron Taudt
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_13
git_last_commit: 1c7aed6
git_last_commit_date: 2021-05-19 12:19:05 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: AneuFinder
Version: 1.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AneuFinder_1.20.0.tar.gz
StartedAt: 2021-09-23 08:49:12 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 08:59:06 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 594.0 seconds
RetCode: 0
Status:   OK  
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AneuFinder_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/AneuFinder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.20.0’
* 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
heatmapAneuploidies       62.580  0.167  62.752
refineBreakpoints         53.911  0.159  54.072
simulateReads             44.569  3.689  48.282
plotHeterogeneity         35.211  0.168  35.381
heatmapGenomewideClusters 31.843  0.408  32.253
correctGC                 25.283  3.308  28.598
heatmapGenomewide         28.269  0.043  28.357
karyotypeMeasures         26.795  0.294  27.091
annotateBreakpoints       16.114  0.217  16.635
getBreakpoints            12.777  0.164  12.942
consensusSegments         10.171  0.112  10.283
getSCEcoordinates          7.354  0.088   7.643
subsetByCNVprofile         6.502  0.015   6.521
findCNVs.strandseq         5.495  0.079   5.575
variableWidthBins          5.392  0.009   5.401
* 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-3.13-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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              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              1
        70       -23708.594441            0.327893            0.243757              1
        71       -23708.267498            0.326942            0.242885              1
        72       -23707.941505            0.325993            0.242069              1
        73       -23707.616459            0.325046            0.241304              1
        74       -23707.292358            0.324101            0.240590              1
        75       -23706.969202            0.323156            0.239921              1
        76       -23706.646989            0.322213            0.239394              1
        77       -23706.325719            0.321271            0.239012              1
        78       -23706.005389            0.320329            0.238641              1
        79       -23705.686000            0.319389            0.238282              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        80       -23705.367551            0.318449            0.237931              1
        81       -23705.050040            0.317511            0.237592              1
        82       -23704.733468            0.316573            0.237265              1
        83       -23704.417832            0.315635            0.236943              1
        84       -23704.103134            0.314699            0.236626              1
        85       -23703.789371            0.313763            0.236312              1
        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              2
       157       -23683.602672            0.248765            0.214080              2
       158       -23683.354769            0.247904            0.213756              2
       159       -23683.107725            0.247044            0.213432              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       160       -23682.861540            0.246185            0.213107              2
       161       -23682.616213            0.245328            0.212782              2
       162       -23682.371741            0.244472            0.212456              2
       163       -23682.128124            0.243617            0.212131              2
       164       -23681.885360            0.242764            0.211806              2
       165       -23681.643448            0.241912            0.211480              2
       166       -23681.402387            0.241062            0.211154              2
       167       -23681.162174            0.240213            0.210828              2
       168       -23680.922809            0.239365            0.210502              2
       169       -23680.684291            0.238519            0.210175              2
       170       -23680.446617            0.237674            0.209848              2
       171       -23680.209786            0.236831            0.209520              2
       172       -23679.973797            0.235989            0.209192              2
       173       -23679.738649            0.235148            0.208864              2
       174       -23679.504339            0.234309            0.208536              2
       175       -23679.270868            0.233472            0.208207              2
       176       -23679.038232            0.232636            0.207878              2
       177       -23678.806431            0.231801            0.207548              2
       178       -23678.575463            0.230968            0.207219              2
       179       -23678.345326            0.230136            0.206889              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       180       -23678.116020            0.229306            0.206559              2
       181       -23677.887543            0.228478            0.206228              2
       182       -23677.659892            0.227650            0.205897              2
       183       -23677.433067            0.226825            0.205566              2
       184       -23677.207067            0.226001            0.205235              2
       185       -23676.981889            0.225178            0.204903              2
       186       -23676.757532            0.224357            0.204571              2
       187       -23676.533994            0.223537            0.204239              2
       188       -23676.311275            0.222719            0.203906              2
       189       -23676.089372            0.221903            0.203574              2
       190       -23675.868284            0.221088            0.203241              2
       191       -23675.648009            0.220275            0.202907              2
       192       -23675.428546            0.219463            0.202574              2
       193       -23675.209893            0.218653            0.202240              2
       194       -23674.992049            0.217844            0.201906              2
       195       -23674.775012            0.217037            0.201572              2
       196       -23674.558781            0.216232            0.201237              2
       197       -23674.343353            0.215428            0.200902              2
       198       -23674.128727            0.214626            0.200567              2
       199       -23673.914902            0.213825            0.200232              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              2
       201       -23673.489648            0.212228            0.199562              2
       202       -23673.278216            0.211433            0.199226              2
       203       -23673.067577            0.210638            0.198890              2
       204       -23672.857731            0.209846            0.198554              2
       205       -23672.648676            0.209055            0.198218              2
       206       -23672.440411            0.208266            0.197882              2
       207       -23672.232933            0.207478            0.197545              2
       208       -23672.026241            0.206692            0.197208              2
       209       -23671.820333            0.205908            0.196871              2
       210       -23671.615208            0.205125            0.196534              2
       211       -23671.410864            0.204344            0.196198              2
       212       -23671.207299            0.203565            0.195861              2
       213       -23671.004512            0.202787            0.195525              2
       214       -23670.802501            0.202011            0.195188              2
       215       -23670.601265            0.201237            0.194851              2
       216       -23670.400800            0.200464            0.194514              2
       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              3
       262       -23661.984599            0.166816            0.178929              3
       263       -23661.818473            0.166126            0.178590              3
       264       -23661.653034            0.165439            0.178251              3
       265       -23661.488280            0.164754            0.177912              3
       266       -23661.324210            0.164070            0.177573              3
       267       -23661.160822            0.163388            0.177234              3
       268       -23660.998114            0.162708            0.176895              3
       269       -23660.836084            0.162030            0.176556              3
       270       -23660.674730            0.161354            0.176217              3
       271       -23660.514051            0.160679            0.175879              3
       272       -23660.354044            0.160007            0.175540              3
       273       -23660.194708            0.159336            0.175202              3
       274       -23660.036041            0.158667            0.174864              3
       275       -23659.878041            0.158000            0.174526              3
       276       -23659.720706            0.157335            0.174188              3
       277       -23659.564034            0.156672            0.173851              3
       278       -23659.408024            0.156010            0.173513              3
       279       -23659.252673            0.155351            0.173175              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       280       -23659.097980            0.154693            0.172838              3
       281       -23658.943943            0.154037            0.172500              3
       282       -23658.790560            0.153383            0.172162              3
       283       -23658.637828            0.152731            0.171825              3
       284       -23658.485747            0.152081            0.171488              3
       285       -23658.334315            0.151433            0.171150              3
       286       -23658.183528            0.150786            0.170813              3
       287       -23658.033387            0.150142            0.170476              3
       288       -23657.883888            0.149499            0.170139              3
       289       -23657.735030            0.148858            0.169802              3
       290       -23657.586811            0.148219            0.169465              3
       291       -23657.439229            0.147582            0.169128              3
       292       -23657.292283            0.146947            0.168792              3
       293       -23657.145969            0.146313            0.168455              3
       294       -23657.000288            0.145682            0.168119              3
       295       -23656.855235            0.145052            0.167783              3
       296       -23656.710811            0.144424            0.167447              3
       297       -23656.567013            0.143798            0.167111              3
       298       -23656.423838            0.143174            0.166775              3
       299       -23656.281286            0.142552            0.166439              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       300       -23656.139354            0.141932            0.166104              3
       301       -23655.998040            0.141314            0.165768              3
       302       -23655.857343            0.140697            0.165433              3
       303       -23655.717260            0.140083            0.165098              3
       304       -23655.577790            0.139470            0.164763              3
       305       -23655.438931            0.138859            0.164428              3
       306       -23655.300681            0.138250            0.164094              3
       307       -23655.163038            0.137643            0.163759              3
       308       -23655.026000            0.137038            0.163425              3
       309       -23654.889566            0.136434            0.163091              3
       310       -23654.753733            0.135833            0.162757              3
       311       -23654.618500            0.135233            0.162423              3
       312       -23654.483864            0.134635            0.162089              3
       313       -23654.349825            0.134040            0.161755              3
       314       -23654.216379            0.133446            0.161422              3
       315       -23654.083526            0.132854            0.161089              3
       316       -23653.951262            0.132263            0.160756              3
       317       -23653.819587            0.131675            0.160423              3
       318       -23653.688499            0.131088            0.160090              3
       319       -23653.557995            0.130504            0.159757              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       320       -23653.428074            0.129921            0.159425              3
       321       -23653.298734            0.129340            0.159092              3
       322       -23653.169973            0.128761            0.158760              3
       323       -23653.041789            0.128184            0.158428              3
       324       -23652.914180            0.127609            0.158097              3
       325       -23652.787145            0.127035            0.157765              3
       326       -23652.660681            0.126464            0.157434              3
       327       -23652.534787            0.125894            0.157103              4
       328       -23652.409461            0.125326            0.156771              4
       329       -23652.284700            0.124760            0.156441              4
       330       -23652.160504            0.124196            0.156110              4
       331       -23652.036870            0.123634            0.155780              4
       332       -23651.913797            0.123074            0.155452              4
       333       -23651.791282            0.122515            0.155124              4
       334       -23651.669323            0.121958            0.154796              4
       335       -23651.547920            0.121404            0.154469              4
       336       -23651.427069            0.120851            0.154142              4
       337       -23651.306769            0.120300            0.153815              4
       338       -23651.187019            0.119750            0.153488              4
       339       -23651.067816            0.119203            0.153161              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       340       -23650.949159            0.118657            0.152835              4
       341       -23650.831045            0.118114            0.152509              4
       342       -23650.713473            0.117572            0.152183              4
       343       -23650.596442            0.117032            0.151857              4
       344       -23650.479948            0.116494            0.151534              4
       345       -23650.363991            0.115957            0.151210              4
       346       -23650.248568            0.115423            0.150887              4
       347       -23650.133678            0.114890            0.150564              4
       348       -23650.019319            0.114359            0.150242              4
       349       -23649.905488            0.113830            0.149919              4
       350       -23649.792185            0.113303            0.149597              4
       351       -23649.679407            0.112778            0.149275              4
       352       -23649.567153            0.112254            0.148953              4
       353       -23649.455420            0.111733            0.148632              4
       354       -23649.344207            0.111213            0.148310              4
       355       -23649.233512            0.110695            0.147989              4
       356       -23649.123334            0.110179            0.147668              4
       357       -23649.013670            0.109664            0.147348              4
       358       -23648.904518            0.109152            0.147027              4
       359       -23648.795877            0.108641            0.146707              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              4
       361       -23648.580120            0.107625            0.146067              4
       362       -23648.473000            0.107120            0.145748              4
       363       -23648.366384            0.106616            0.145429              4
       364       -23648.260270            0.106114            0.145110              4
       365       -23648.154656            0.105614            0.144791              4
       366       -23648.049539            0.105116            0.144473              4
       367       -23647.944919            0.104620            0.144154              4
       368       -23647.840794            0.104126            0.143836              4
       369       -23647.737161            0.103633            0.143519              4
       370       -23647.634019            0.103142            0.143201              4
       371       -23647.531366            0.102653            0.142884              4
       372       -23647.429201            0.102165            0.142567              4
       373       -23647.327521            0.101680            0.142251              4
       374       -23647.226325            0.101196            0.141934              4
       375       -23647.125611            0.100714            0.141618              4
       376       -23647.025378            0.100234            0.141302              4
       377       -23646.925622            0.099755            0.140986              4
Convergence reached!
number of states = 12
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24380.580428                 inf         6183.000000              0
         2       -23357.275929         1023.304498          686.821642              0
         3       -23260.421975           96.853955          172.471538              0
         4       -23232.483517           27.938458          143.506687              0
         5       -23222.142294           10.341223           76.049323              0
         6       -23217.735527            4.406767           58.626866              0
         7       -23215.521320            2.214207           35.912568              0
         8       -23214.276947            1.244373           27.484487              0
         9       -23213.395549            0.881398           18.765222              0
        10       -23212.605307            0.790242           15.594210              0
        11       -23211.762729            0.842578           12.269888              0
        12       -23210.839848            0.922881           11.279480              0
        13       -23209.921053            0.918795            9.624877              0
        14       -23209.118734            0.802320            8.968506              0
        15       -23208.463874            0.654860            7.927086              0
        16       -23207.924958            0.538916            7.683630              0
        17       -23207.463600            0.461358            7.238144              0
        18       -23207.046263            0.417337            7.327465              0
        19       -23206.646001            0.400262            7.466156              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23206.242687            0.403315            7.882758              0
        21       -23205.828261            0.414426            8.254388              0
        22       -23205.414415            0.413846            8.474710              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              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 
 18.674   0.456  19.118 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0010.0000.000
annotateBreakpoints16.114 0.21716.635
bam2GRanges0.4110.0120.440
bed2GRanges0.8190.0200.840
binReads2.5550.0362.591
blacklist2.3500.2082.558
clusterByQuality2.1330.2122.385
clusterHMMs0.3200.1000.421
collapseBins2.4780.4912.969
colors0.0720.0000.072
compareMethods0.4770.0160.494
consensusSegments10.171 0.11210.283
correctGC25.283 3.30828.598
export0.0010.0000.000
filterSegments0.3390.0000.339
findCNVs4.3070.1764.484
findCNVs.strandseq5.4950.0795.575
fixedWidthBins0.1150.0040.118
getBreakpoints12.777 0.16412.942
getDistinctColors0.1120.0040.116
getQC1.0810.0071.090
getSCEcoordinates7.3540.0887.643
heatmapAneuploidies62.580 0.16762.752
heatmapGenomewide28.269 0.04328.357
heatmapGenomewideClusters31.843 0.40832.253
importBed1.1420.0041.146
karyotypeMeasures26.795 0.29427.091
loadFromFiles3.9550.0213.977
plotHeterogeneity35.211 0.16835.381
plot_pca0.9260.0040.931
refineBreakpoints53.911 0.15954.072
simulateReads44.569 3.68948.282
subsetByCNVprofile6.5020.0156.521
variableWidthBins5.3920.0095.401