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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).

CHECK results for AneuFinder on machv2

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: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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    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: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AneuFinder_1.20.0.tar.gz
StartedAt: 2021-10-14 16:12:34 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 16:27:12 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 877.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AneuFinder_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
heatmapAneuploidies       97.640  0.359  98.106
refineBreakpoints         85.811  0.670  86.599
simulateReads             67.647  2.839  70.895
heatmapGenomewideClusters 50.876  0.217  51.136
plotHeterogeneity         46.194  0.279  46.544
heatmapGenomewide         45.495  0.168  45.709
correctGC                 38.707  1.837  40.712
karyotypeMeasures         40.001  0.311  40.383
annotateBreakpoints       23.000  0.585  23.912
getBreakpoints            19.207  0.580  19.812
consensusSegments         13.782  0.054  13.842
subsetByCNVprofile         9.986  0.125  10.179
getSCEcoordinates          8.223  0.323   8.862
findCNVs.strandseq         7.650  0.284   7.944
variableWidthBins          7.034  0.139   7.190
findCNVs                   5.723  0.488   6.219
loadFromFiles              5.608  0.076   5.704
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c loghmm.cpp -o loghmm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility.cpp -o utility.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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              1
        22       -23725.416462            0.375048            0.244787              1
        23       -23725.043233            0.373229            0.307572              1
        24       -23724.671334            0.371899            0.240956              1
        25       -23724.300551            0.370783            0.275223              1
        26       -23723.930786            0.369765            0.245508              1
        27       -23723.561998            0.368789            0.262164              1
        28       -23723.194164            0.367834            0.248735              1
        29       -23722.827276            0.366888            0.256570              1
        30       -23722.461329            0.365947            0.250428              1
        31       -23722.096319            0.365010            0.254042              1
        32       -23721.732244            0.364076            0.251213              1
        33       -23721.369100            0.363144            0.252844              1
        34       -23721.006885            0.362214            0.251549              1
        35       -23720.645598            0.361287            0.252622              1
        36       -23720.285236            0.360362            0.252383              1
        37       -23719.925796            0.359440            0.253123              1
        38       -23719.567277            0.358519            0.253290              1
        39       -23719.209677            0.357600            0.254027              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        40       -23718.852994            0.356683            0.254590              1
        41       -23718.497228            0.355766            0.255400              1
        42       -23718.142378            0.354850            0.256151              1
        43       -23717.788445            0.353933            0.257145              1
        44       -23717.435431            0.353014            0.258100              1
        45       -23717.083339            0.352092            0.259094              1
        46       -23716.732173            0.351166            0.260034              1
        47       -23716.381938            0.350235            0.260935              1
        48       -23716.032640            0.349298            0.261735              1
        49       -23715.684287            0.348353            0.262424              1
        50       -23715.336886            0.347401            0.262956              1
        51       -23714.990445            0.346441            0.263312              1
        52       -23714.644972            0.345473            0.263463              1
        53       -23714.300474            0.344498            0.263396              1
        54       -23713.956958            0.343516            0.263103              1
        55       -23713.614428            0.342530            0.262584              1
        56       -23713.272887            0.341540            0.261849              1
        57       -23712.932339            0.340548            0.260917              1
        58       -23712.592783            0.339556            0.259810              1
        59       -23712.254217            0.338565            0.258559              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        60       -23711.916641            0.337576            0.257196              1
        61       -23711.580050            0.336591            0.255754              1
        62       -23711.244442            0.335609            0.254264              1
        63       -23710.909811            0.334631            0.252755              1
        64       -23710.576153            0.333657            0.251252              1
        65       -23710.243465            0.332688            0.249777              1
        66       -23709.911743            0.331722            0.248349              1
        67       -23709.580982            0.330761            0.247090              1
        68       -23709.251180            0.329802            0.245906              1
        69       -23708.922334            0.328846            0.244786              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              2
       101       -23698.895853            0.298889            0.231491              2
       102       -23698.597887            0.297966            0.231193              2
       103       -23698.300843            0.297044            0.230895              2
       104       -23698.004721            0.296122            0.230596              2
       105       -23697.709519            0.295202            0.230296              2
       106       -23697.415236            0.294282            0.229997              2
       107       -23697.121873            0.293364            0.229697              2
       108       -23696.829427            0.292446            0.229396              2
       109       -23696.537897            0.291529            0.229095              2
       110       -23696.247284            0.290613            0.228793              2
       111       -23695.957586            0.289698            0.228491              2
       112       -23695.668802            0.288784            0.228189              2
       113       -23695.380931            0.287871            0.227886              2
       114       -23695.093972            0.286959            0.227582              2
       115       -23694.807925            0.286047            0.227278              2
       116       -23694.522788            0.285137            0.226973              2
       117       -23694.238560            0.284228            0.226668              2
       118       -23693.955240            0.283320            0.226362              2
       119       -23693.672828            0.282412            0.226056              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              2
       121       -23693.110721            0.280601            0.225443              2
       122       -23692.831025            0.279696            0.225136              2
       123       -23692.552232            0.278793            0.224828              2
       124       -23692.274340            0.277891            0.224520              2
       125       -23691.997350            0.276990            0.224212              2
       126       -23691.721261            0.276090            0.223903              2
       127       -23691.446070            0.275191            0.223593              2
       128       -23691.171777            0.274293            0.223283              2
       129       -23690.898380            0.273396            0.222972              2
       130       -23690.625880            0.272501            0.222661              2
       131       -23690.354274            0.271606            0.222349              2
       132       -23690.083561            0.270713            0.222037              2
       133       -23689.813741            0.269820            0.221724              2
       134       -23689.544812            0.268929            0.221411              2
       135       -23689.276773            0.268039            0.221097              2
       136       -23689.009623            0.267150            0.220783              2
       137       -23688.743361            0.266262            0.220469              2
       138       -23688.477985            0.265376            0.220154              2
       139       -23688.213495            0.264490            0.219838              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       140       -23687.949889            0.263606            0.219522              2
       141       -23687.687165            0.262723            0.219206              2
       142       -23687.425324            0.261841            0.218889              2
       143       -23687.164363            0.260961            0.218571              2
       144       -23686.904282            0.260081            0.218253              2
       145       -23686.645079            0.259203            0.217935              2
       146       -23686.386752            0.258326            0.217616              2
       147       -23686.129301            0.257451            0.217297              2
       148       -23685.872725            0.256576            0.216977              2
       149       -23685.617022            0.255703            0.216657              2
       150       -23685.362190            0.254831            0.216336              2
       151       -23685.108229            0.253961            0.216015              2
       152       -23684.855137            0.253092            0.215694              2
       153       -23684.602914            0.252224            0.215372              2
       154       -23684.351557            0.251357            0.215049              2
       155       -23684.101065            0.250492            0.214727              2
       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              3
       204       -23672.857731            0.209846            0.198554              3
       205       -23672.648676            0.209055            0.198218              3
       206       -23672.440411            0.208266            0.197882              3
       207       -23672.232933            0.207478            0.197545              3
       208       -23672.026241            0.206692            0.197208              3
       209       -23671.820333            0.205908            0.196871              3
       210       -23671.615208            0.205125            0.196534              3
       211       -23671.410864            0.204344            0.196198              3
       212       -23671.207299            0.203565            0.195861              3
       213       -23671.004512            0.202787            0.195525              3
       214       -23670.802501            0.202011            0.195188              3
       215       -23670.601265            0.201237            0.194851              3
       216       -23670.400800            0.200464            0.194514              3
       217       -23670.201107            0.199693            0.194176              3
       218       -23670.002183            0.198924            0.193839              3
       219       -23669.804027            0.198156            0.193501              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              3
       221       -23669.410010            0.196627            0.192826              3
       222       -23669.214145            0.195864            0.192488              3
       223       -23669.019042            0.195104            0.192149              3
       224       -23668.824697            0.194345            0.191811              3
       225       -23668.631110            0.193587            0.191473              3
       226       -23668.438278            0.192832            0.191134              3
       227       -23668.246200            0.192078            0.190795              3
       228       -23668.054874            0.191326            0.190456              3
       229       -23667.864298            0.190576            0.190118              3
       230       -23667.674471            0.189827            0.189779              3
       231       -23667.485390            0.189081            0.189439              3
       232       -23667.297055            0.188336            0.189100              3
       233       -23667.109462            0.187592            0.188761              3
       234       -23666.922612            0.186851            0.188421              3
       235       -23666.736501            0.186111            0.188082              3
       236       -23666.551128            0.185373            0.187744              3
       237       -23666.366491            0.184637            0.187405              3
       238       -23666.182588            0.183902            0.187066              3
       239       -23665.999419            0.183170            0.186727              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       240       -23665.816980            0.182439            0.186388              3
       241       -23665.635270            0.181710            0.186049              3
       242       -23665.454288            0.180982            0.185710              3
       243       -23665.274031            0.180257            0.185370              3
       244       -23665.094498            0.179533            0.185031              3
       245       -23664.915686            0.178811            0.184692              3
       246       -23664.737595            0.178091            0.184352              3
       247       -23664.560223            0.177373            0.184013              3
       248       -23664.383566            0.176656            0.183674              3
       249       -23664.207625            0.175942            0.183335              3
       250       -23664.032396            0.175229            0.182996              3
       251       -23663.857879            0.174517            0.182657              3
       252       -23663.684071            0.173808            0.182318              3
       253       -23663.510970            0.173101            0.181979              3
       254       -23663.338575            0.172395            0.181641              3
       255       -23663.166884            0.171691            0.181302              3
       256       -23662.995894            0.170989            0.180963              3
       257       -23662.825605            0.170289            0.180624              3
       258       -23662.656015            0.169591            0.180285              3
       259       -23662.487121            0.168894            0.179946              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              3
       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              4
       306       -23655.300681            0.138250            0.164094              4
       307       -23655.163038            0.137643            0.163759              4
       308       -23655.026000            0.137038            0.163425              4
       309       -23654.889566            0.136434            0.163091              4
       310       -23654.753733            0.135833            0.162757              4
       311       -23654.618500            0.135233            0.162423              4
       312       -23654.483864            0.134635            0.162089              4
       313       -23654.349825            0.134040            0.161755              4
       314       -23654.216379            0.133446            0.161422              4
       315       -23654.083526            0.132854            0.161089              4
       316       -23653.951262            0.132263            0.160756              4
       317       -23653.819587            0.131675            0.160423              4
       318       -23653.688499            0.131088            0.160090              4
       319       -23653.557995            0.130504            0.159757              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       320       -23653.428074            0.129921            0.159425              4
       321       -23653.298734            0.129340            0.159092              4
       322       -23653.169973            0.128761            0.158760              4
       323       -23653.041789            0.128184            0.158428              4
       324       -23652.914180            0.127609            0.158097              4
       325       -23652.787145            0.127035            0.157765              4
       326       -23652.660681            0.126464            0.157434              4
       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           12.269889              0
        12       -23210.839848            0.922881           11.279480              0
        13       -23209.921053            0.918795            9.624877              0
        14       -23209.118734            0.802320            8.968506              0
        15       -23208.463874            0.654860            7.927086              0
        16       -23207.924958            0.538916            7.683630              0
        17       -23207.463600            0.461358            7.238144              0
        18       -23207.046263            0.417337            7.327465              0
        19       -23206.646001            0.400262            7.466156              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23206.242687            0.403315            7.882758              0
        21       -23205.828261            0.414426            8.254388              0
        22       -23205.414415            0.413846            8.474710              0
        23       -23205.032476            0.381939            8.244365              0
        24       -23204.714716            0.317760            7.544341              0
        25       -23204.473698            0.241018            6.506549              0
        26       -23204.300805            0.172894            5.379661              0
        27       -23204.178183            0.122622            4.308309              0
        28       -23204.088739            0.089444            3.383929              0
Convergence reached!
number of states = 11
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -21177.150641                 inf         5442.000000              0
         2       -20711.054012          466.096629          390.505270              0
         3       -20693.275989           17.778024           85.372131              0
         4       -20690.239855            3.036134           33.071291              0
         5       -20689.163935            1.075919           26.872093              0
         6       -20688.762950            0.400986           12.127422              0
         7       -20688.580230            0.182719            8.966009              0
         8       -20688.472739            0.107491            4.304038              0
         9       -20688.396085            0.076655            3.087959              0
Convergence reached!
number of states = 12
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -20778.885904                 inf         5442.000000              0
         2       -20214.840926          564.044978          503.589244              0
         3       -20185.942950           28.897975          137.261825              0
         4       -20179.925587            6.017363           51.421390              0
         5       -20177.170587            2.755000           36.836764              0
         6       -20175.645594            1.524994           18.722502              0
         7       -20174.658989            0.986605           13.124839              0
         8       -20173.895734            0.763255           11.327572              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              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 
 20.432   0.697  21.260 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0000.0000.001
annotateBreakpoints23.000 0.58523.912
bam2GRanges0.6070.0650.675
bed2GRanges0.9500.0430.994
binReads3.0830.1153.218
blacklist3.1190.1643.284
clusterByQuality3.2670.0683.349
clusterHMMs0.5420.0200.562
collapseBins2.6670.1402.808
colors0.0870.0020.090
compareMethods0.7820.0350.817
consensusSegments13.782 0.05413.842
correctGC38.707 1.83740.712
export0.0000.0010.000
filterSegments0.4790.0430.522
findCNVs5.7230.4886.219
findCNVs.strandseq7.6500.2847.944
fixedWidthBins0.1450.0030.147
getBreakpoints19.207 0.58019.812
getDistinctColors0.1520.0030.156
getQC1.7350.0241.764
getSCEcoordinates8.2230.3238.862
heatmapAneuploidies97.640 0.35998.106
heatmapGenomewide45.495 0.16845.709
heatmapGenomewideClusters50.876 0.21751.136
importBed1.8870.0061.894
karyotypeMeasures40.001 0.31140.383
loadFromFiles5.6080.0765.704
plotHeterogeneity46.194 0.27946.544
plot_pca1.3390.0351.378
refineBreakpoints85.811 0.67086.599
simulateReads67.647 2.83970.895
subsetByCNVprofile 9.986 0.12510.179
variableWidthBins7.0340.1397.190