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CHECK report for AneuFinder on celaya2

This page was generated on 2019-10-16 12:57:33 -0400 (Wed, 16 Oct 2019).

Package 53/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.12.1
Aaron Taudt
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/AneuFinder
Branch: RELEASE_3_9
Last Commit: e788fd0
Last Changed Date: 2019-07-20 06:41:41 -0400 (Sat, 20 Jul 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

Summary

Package: AneuFinder
Version: 1.12.1
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_1.12.1.tar.gz
StartedAt: 2019-10-16 00:29:53 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:45:56 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 963.3 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_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AneuFinder.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.1’
* 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             91.601 13.634 105.537
refineBreakpoints         99.569  1.993 103.817
correctGC                 59.830  7.794  69.314
heatmapAneuploidies       59.950  0.225  60.181
plotHeterogeneity         48.341  0.587  48.934
heatmapGenomewideClusters 39.161  0.509  39.676
karyotypeMeasures         36.748  0.476  37.225
heatmapGenomewide         35.199  0.662  35.888
annotateBreakpoints       26.388  1.855  30.510
getBreakpoints            19.857  1.659  24.568
consensusSegments         11.330  0.159  11.489
variableWidthBins          8.748  0.663  10.543
findCNVs                   7.422  1.719  10.439
findCNVs.strandseq         7.486  1.055   9.768
getSCEcoordinates          7.296  1.218   9.556
loadFromFiles              7.691  0.031   7.739
subsetByCNVprofile         7.510  0.035   7.657
* 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’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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, 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: ggplot2
Loading required package: cowplot

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_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              1
        12       -23730.007090            0.520584            4.942881              1
        13       -23729.480035            0.527055            3.803030              1
        14       -23728.932681            0.547354            2.653912              1
        15       -23728.372455            0.560226            2.141742              1
        16       -23727.839017            0.533439            1.244299              1
        17       -23727.367012            0.472005            1.109390              1
        18       -23726.947097            0.419914            0.529456              1
        19       -23726.552750            0.394348            0.602730              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23726.169459            0.383291            0.302116              1
        21       -23725.791510            0.377949            0.389827              1
        22       -23725.416462            0.375048            0.244787              1
        23       -23725.043233            0.373229            0.307572              1
        24       -23724.671334            0.371899            0.240956              1
        25       -23724.300551            0.370783            0.275223              1
        26       -23723.930786            0.369765            0.245508              1
        27       -23723.561998            0.368789            0.262164              1
        28       -23723.194164            0.367834            0.248735              1
        29       -23722.827276            0.366888            0.256570              1
        30       -23722.461329            0.365947            0.250428              1
        31       -23722.096319            0.365010            0.254042              1
        32       -23721.732244            0.364076            0.251213              1
        33       -23721.369100            0.363144            0.252844              1
        34       -23721.006885            0.362214            0.251549              1
        35       -23720.645598            0.361287            0.252622              1
        36       -23720.285236            0.360362            0.252383              1
        37       -23719.925796            0.359440            0.253123              1
        38       -23719.567277            0.358519            0.253290              1
        39       -23719.209677            0.357600            0.254027              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        40       -23718.852994            0.356683            0.254590              1
        41       -23718.497228            0.355766            0.255400              1
        42       -23718.142378            0.354850            0.256151              1
        43       -23717.788445            0.353933            0.257145              1
        44       -23717.435431            0.353014            0.258100              1
        45       -23717.083339            0.352092            0.259094              1
        46       -23716.732173            0.351166            0.260034              1
        47       -23716.381938            0.350235            0.260935              1
        48       -23716.032640            0.349298            0.261735              1
        49       -23715.684287            0.348353            0.262424              1
        50       -23715.336886            0.347401            0.262956              1
        51       -23714.990445            0.346441            0.263312              1
        52       -23714.644972            0.345473            0.263463              1
        53       -23714.300474            0.344498            0.263396              1
        54       -23713.956958            0.343516            0.263103              1
        55       -23713.614428            0.342530            0.262584              1
        56       -23713.272887            0.341540            0.261849              1
        57       -23712.932339            0.340548            0.260917              1
        58       -23712.592783            0.339556            0.259810              1
        59       -23712.254217            0.338565            0.258559              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        60       -23711.916641            0.337576            0.257196              1
        61       -23711.580050            0.336591            0.255754              1
        62       -23711.244442            0.335609            0.254264              1
        63       -23710.909811            0.334631            0.252755              1
        64       -23710.576153            0.333657            0.251252              1
        65       -23710.243465            0.332688            0.249777              1
        66       -23709.911743            0.331722            0.248349              1
        67       -23709.580982            0.330761            0.247090              1
        68       -23709.251180            0.329802            0.245906              1
        69       -23708.922334            0.328846            0.244786              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              2
        91       -23701.926408            0.308163            0.234480              2
        92       -23701.619176            0.307232            0.234179              2
        93       -23701.312874            0.306302            0.233879              2
        94       -23701.007502            0.305372            0.233580              2
        95       -23700.703059            0.304444            0.233281              2
        96       -23700.399543            0.303516            0.232982              2
        97       -23700.096954            0.302589            0.232683              2
        98       -23699.795291            0.301663            0.232384              2
        99       -23699.494554            0.300737            0.232086              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       100       -23699.194741            0.299813            0.231789              2
       101       -23698.895853            0.298889            0.231491              2
       102       -23698.597887            0.297966            0.231193              2
       103       -23698.300843            0.297044            0.230895              2
       104       -23698.004721            0.296122            0.230596              2
       105       -23697.709519            0.295202            0.230296              2
       106       -23697.415236            0.294282            0.229997              2
       107       -23697.121873            0.293364            0.229697              2
       108       -23696.829427            0.292446            0.229396              2
       109       -23696.537897            0.291529            0.229095              2
       110       -23696.247284            0.290613            0.228793              2
       111       -23695.957586            0.289698            0.228491              2
       112       -23695.668802            0.288784            0.228189              2
       113       -23695.380931            0.287871            0.227886              2
       114       -23695.093972            0.286959            0.227582              2
       115       -23694.807925            0.286047            0.227278              2
       116       -23694.522788            0.285137            0.226973              2
       117       -23694.238560            0.284228            0.226668              2
       118       -23693.955240            0.283320            0.226362              2
       119       -23693.672828            0.282412            0.226056              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              2
       121       -23693.110721            0.280601            0.225443              2
       122       -23692.831025            0.279696            0.225136              2
       123       -23692.552232            0.278793            0.224828              2
       124       -23692.274340            0.277891            0.224520              2
       125       -23691.997350            0.276990            0.224212              2
       126       -23691.721261            0.276090            0.223903              2
       127       -23691.446070            0.275191            0.223593              2
       128       -23691.171777            0.274293            0.223283              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              3
       198       -23674.128727            0.214626            0.200567              3
       199       -23673.914902            0.213825            0.200232              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              3
       201       -23673.489648            0.212228            0.199562              3
       202       -23673.278216            0.211433            0.199226              3
       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              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              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              1
        22       -23205.414415            0.413846            8.474710              1
        23       -23205.032476            0.381939            8.244365              1
        24       -23204.714716            0.317760            7.544341              1
        25       -23204.473698            0.241018            6.506549              1
        26       -23204.300805            0.172894            5.379661              1
        27       -23204.178183            0.122622            4.308309              1
        28       -23204.088739            0.089444            3.383929              1
Convergence reached!
number of states = 11
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -21177.150641                 inf         5442.000000              0
         2       -20711.054012          466.096629          390.505270              0
         3       -20693.275989           17.778024           85.372131              0
         4       -20690.239855            3.036134           33.071291              0
         5       -20689.163935            1.075919           26.872093              0
         6       -20688.762950            0.400986           12.127422              0
         7       -20688.580230            0.182719            8.966009              0
         8       -20688.472739            0.107491            4.304038              0
         9       -20688.396085            0.076655            3.087959              0
Convergence reached!
number of states = 12
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -20778.885904                 inf         5442.000000              0
         2       -20214.840926          564.044978          503.589244              0
         3       -20185.942950           28.897975          137.261825              0
         4       -20179.925587            6.017363           51.421390              0
         5       -20177.170587            2.755000           36.836764              0
         6       -20175.645594            1.524994           18.722502              0
         7       -20174.658989            0.986605           13.124839              0
         8       -20173.895734            0.763255           11.327572              0
         9       -20173.167941            0.727793            9.948167              0
        10       -20172.282987            0.884954           11.162019              0
        11       -20170.984261            1.298726           12.412190              0
        12       -20169.145246            1.839014           14.930161              0
        13       -20166.835634            2.309613           16.942694              0
        14       -20163.895031            2.940602           18.691149              0
        15       -20160.410970            3.484061           18.008358              0
        16       -20157.717749            2.693221           14.496841              0
        17       -20156.213293            1.504456           10.220281              0
        18       -20155.444668            0.768625            7.026993              0
        19       -20155.094478            0.350190            4.771865              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -20154.925350            0.169128            3.076403              0
        21       -20154.827513            0.097837            1.932927              0
Convergence reached!
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 21.414   1.303  22.668 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0010.0000.000
annotateBreakpoints26.388 1.85530.510
bam2GRanges0.5670.0420.619
bed2GRanges1.7480.1823.005
binReads2.3340.3743.779
blacklist2.8430.1924.195
clusterByQuality2.2690.1462.442
clusterHMMs0.5660.0540.621
collapseBins2.9410.5034.501
colors0.0520.0040.056
compareMethods0.7670.0620.829
consensusSegments11.330 0.15911.489
correctGC59.830 7.79469.314
export0.0000.0010.000
filterSegments0.4440.0250.470
findCNVs 7.422 1.71910.439
findCNVs.strandseq7.4861.0559.768
fixedWidthBins0.0850.0101.135
getBreakpoints19.857 1.65924.568
getDistinctColors0.0460.0080.053
getQC1.1910.0371.228
getSCEcoordinates7.2961.2189.556
heatmapAneuploidies59.950 0.22560.181
heatmapGenomewide35.199 0.66235.888
heatmapGenomewideClusters39.161 0.50939.676
importBed2.0000.1162.116
karyotypeMeasures36.748 0.47637.225
loadFromFiles7.6910.0317.739
plotHeterogeneity48.341 0.58748.934
plot_pca1.4950.0661.569
refineBreakpoints 99.569 1.993103.817
simulateReads 91.601 13.634105.537
subsetByCNVprofile7.5100.0357.657
variableWidthBins 8.748 0.66310.543