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CHECK report for AneuFinder on merida2

This page was generated on 2019-04-09 13:33:01 -0400 (Tue, 09 Apr 2019).

Package 52/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.11.2
Aaron Taudt
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AneuFinder
Branch: master
Last Commit: f825933
Last Changed Date: 2019-01-04 13:18:52 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: AneuFinder
Version: 1.11.2
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_1.11.2.tar.gz
StartedAt: 2019-04-08 23:12:12 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:24:39 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 747.0 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_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AneuFinder.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.2’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
simulateReads             86.750  7.292  95.042
refineBreakpoints         67.499  1.021  71.197
correctGC                 55.449  3.844  60.779
heatmapAneuploidies       47.109  0.314  47.772
plotHeterogeneity         33.044  0.307  33.549
heatmapGenomewideClusters 31.609  0.124  32.033
karyotypeMeasures         29.892  0.263  30.394
heatmapGenomewide         26.202  0.352  26.768
annotateBreakpoints       19.117  0.847  21.953
getBreakpoints            13.246  0.824  16.176
consensusSegments         11.065  0.126  11.268
getSCEcoordinates          5.923  0.610   7.454
variableWidthBins          6.253  0.271   7.495
findCNVs.strandseq         5.490  0.536   7.051
findCNVs                   4.744  0.886   6.614
subsetByCNVprofile         5.263  0.017   5.318
loadFromFiles              5.025  0.022   5.087
* 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
  ‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/library’
* installing *source* package ‘AneuFinder’ ...
** libs
clang++ -std=gnu++11 -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c loghmm.cpp -o loghmm.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility.cpp -o utility.o
clang++ -std=gnu++11 -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/3.6/Resources/library/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
* DONE (AneuFinder)

Tests output

AneuFinder.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: cowplot
Loading required package: ggplot2

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

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              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              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              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              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              2
       262       -23661.984599            0.166816            0.178929              2
       263       -23661.818473            0.166126            0.178590              2
       264       -23661.653034            0.165439            0.178251              2
       265       -23661.488280            0.164754            0.177912              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              3
       328       -23652.409461            0.125326            0.156771              3
       329       -23652.284700            0.124760            0.156441              3
       330       -23652.160504            0.124196            0.156110              3
       331       -23652.036870            0.123634            0.155780              3
       332       -23651.913797            0.123074            0.155452              3
       333       -23651.791282            0.122515            0.155124              3
       334       -23651.669323            0.121958            0.154796              3
       335       -23651.547920            0.121404            0.154469              3
       336       -23651.427069            0.120851            0.154142              3
       337       -23651.306769            0.120300            0.153815              3
       338       -23651.187019            0.119750            0.153488              3
       339       -23651.067816            0.119203            0.153161              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       340       -23650.949159            0.118657            0.152835              3
       341       -23650.831045            0.118114            0.152509              3
       342       -23650.713473            0.117572            0.152183              3
       343       -23650.596442            0.117032            0.151857              3
       344       -23650.479948            0.116494            0.151534              3
       345       -23650.363991            0.115957            0.151210              3
       346       -23650.248568            0.115423            0.150887              3
       347       -23650.133678            0.114890            0.150564              3
       348       -23650.019319            0.114359            0.150242              3
       349       -23649.905488            0.113830            0.149919              3
       350       -23649.792185            0.113303            0.149597              3
       351       -23649.679407            0.112778            0.149275              3
       352       -23649.567153            0.112254            0.148953              3
       353       -23649.455420            0.111733            0.148632              3
       354       -23649.344207            0.111213            0.148310              3
       355       -23649.233512            0.110695            0.147989              3
       356       -23649.123334            0.110179            0.147668              3
       357       -23649.013670            0.109664            0.147348              3
       358       -23648.904518            0.109152            0.147027              3
       359       -23648.795877            0.108641            0.146707              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              3
       361       -23648.580120            0.107625            0.146067              3
       362       -23648.473000            0.107120            0.145748              3
       363       -23648.366384            0.106616            0.145429              3
       364       -23648.260270            0.106114            0.145110              3
       365       -23648.154656            0.105614            0.144791              3
       366       -23648.049539            0.105116            0.144473              3
       367       -23647.944919            0.104620            0.144154              3
       368       -23647.840794            0.104126            0.143836              3
       369       -23647.737161            0.103633            0.143519              3
       370       -23647.634019            0.103142            0.143201              3
       371       -23647.531366            0.102653            0.142884              3
       372       -23647.429201            0.102165            0.142567              3
       373       -23647.327521            0.101680            0.142251              3
       374       -23647.226325            0.101196            0.141934              3
       375       -23647.125611            0.100714            0.141618              3
       376       -23647.025378            0.100234            0.141302              3
       377       -23646.925622            0.099755            0.140986              3
Convergence reached!
number of states = 12
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24380.580428                 inf         6183.000000              0
         2       -23357.275929         1023.304498          686.821642              0
         3       -23260.421975           96.853955          172.471538              0
         4       -23232.483517           27.938458          143.506687              0
         5       -23222.142294           10.341223           76.049323              0
         6       -23217.735527            4.406767           58.626866              0
         7       -23215.521320            2.214207           35.912568              0
         8       -23214.276947            1.244373           27.484487              0
         9       -23213.395549            0.881398           18.765222              0
        10       -23212.605307            0.790242           15.594210              0
        11       -23211.762729            0.842578           12.269889              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              1
        16       -23207.924958            0.538916            7.683630              1
        17       -23207.463600            0.461358            7.238144              1
        18       -23207.046263            0.417337            7.327465              1
        19       -23206.646001            0.400262            7.466156              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23206.242687            0.403315            7.882758              1
        21       -23205.828261            0.414426            8.254388              1
        22       -23205.414415            0.413846            8.474710              1
        23       -23205.032476            0.381939            8.244365              1
        24       -23204.714716            0.317760            7.544341              1
        25       -23204.473698            0.241018            6.506549              1
        26       -23204.300805            0.172894            5.379661              1
        27       -23204.178183            0.122622            4.308309              1
        28       -23204.088739            0.089444            3.383929              1
Convergence reached!
number of states = 11
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -21177.150641                 inf         5442.000000              0
         2       -20711.054012          466.096629          390.505270              0
         3       -20693.275989           17.778024           85.372131              0
         4       -20690.239855            3.036134           33.071291              0
         5       -20689.163935            1.075919           26.872093              0
         6       -20688.762950            0.400986           12.127422              0
         7       -20688.580230            0.182719            8.966009              0
         8       -20688.472739            0.107491            4.304038              0
         9       -20688.396085            0.076655            3.087959              0
Convergence reached!
number of states = 12
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -20778.885904                 inf         5442.000000              0
         2       -20214.840926          564.044978          503.589244              0
         3       -20185.942950           28.897975          137.261825              0
         4       -20179.925587            6.017363           51.421390              0
         5       -20177.170587            2.755000           36.836764              0
         6       -20175.645594            1.524994           18.722502              0
         7       -20174.658989            0.986605           13.124839              0
         8       -20173.895734            0.763255           11.327572              0
         9       -20173.167941            0.727793            9.948167              0
        10       -20172.282987            0.884954           11.162019              0
        11       -20170.984261            1.298726           12.412190              1
        12       -20169.145246            1.839014           14.930161              1
        13       -20166.835634            2.309613           16.942694              1
        14       -20163.895031            2.940602           18.691149              1
        15       -20160.410970            3.484061           18.008358              1
        16       -20157.717749            2.693221           14.496841              1
        17       -20156.213293            1.504456           10.220281              1
        18       -20155.444668            0.768625            7.026993              1
        19       -20155.094478            0.350190            4.771865              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -20154.925350            0.169128            3.076403              1
        21       -20154.827513            0.097837            1.932927              1
Convergence reached!
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 12 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.370   0.561  18.080 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder000
annotateBreakpoints19.117 0.84721.953
bam2GRanges0.4180.0230.443
bed2GRanges1.1570.0802.116
binReads2.8620.2234.292
blacklist2.2000.0813.384
clusterByQuality2.7540.0612.851
clusterHMMs0.4850.0290.519
collapseBins2.3020.2473.532
colors0.0500.0020.054
compareMethods0.5290.0200.551
consensusSegments11.065 0.12611.268
correctGC55.449 3.84460.779
export0.0000.0000.001
filterSegments0.2840.0130.297
findCNVs4.7440.8866.614
findCNVs.strandseq5.4900.5367.051
fixedWidthBins0.0850.0060.953
getBreakpoints13.246 0.82416.176
getDistinctColors0.0310.0040.035
getQC0.8960.0150.914
getSCEcoordinates5.9230.6107.454
heatmapAneuploidies47.109 0.31447.772
heatmapGenomewide26.202 0.35226.768
heatmapGenomewideClusters31.609 0.12432.033
importBed1.7530.0571.820
karyotypeMeasures29.892 0.26330.394
loadFromFiles5.0250.0225.087
plotHeterogeneity33.044 0.30733.549
plot_pca1.1600.0311.203
refineBreakpoints67.499 1.02171.197
simulateReads86.750 7.29295.042
subsetByCNVprofile5.2630.0175.318
variableWidthBins6.2530.2717.495