Back to Multiple platform build/check report for BioC 3.8
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AneuFinder on malbec1

This page was generated on 2019-04-16 11:51:57 -0400 (Tue, 16 Apr 2019).

Package 49/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.10.2
Aaron Taudt
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/AneuFinder
Branch: RELEASE_3_8
Last Commit: 56578ae
Last Changed Date: 2019-01-04 13:19:03 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AneuFinder
Version: 1.10.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AneuFinder_1.10.2.tar.gz
StartedAt: 2019-04-15 22:10:13 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:20:44 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 631.2 seconds
RetCode: 0
Status:  OK 
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AneuFinder_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/AneuFinder.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.10.2’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
refineBreakpoints         64.076  0.140  67.568
simulateReads             52.260  2.392  54.755
heatmapAneuploidies       45.508  0.052  45.626
correctGC                 30.680  2.592  40.573
plotHeterogeneity         30.616  0.044  30.708
karyotypeMeasures         26.052  0.036  26.161
heatmapGenomewideClusters 23.840  0.004  23.878
heatmapGenomewide         21.804  0.020  21.962
annotateBreakpoints       13.624  0.104  17.447
getBreakpoints            11.552  0.088  14.284
consensusSegments          9.996  0.008  10.027
subsetByCNVprofile         6.232  0.000   6.239
findCNVs.strandseq         5.556  0.144   7.541
variableWidthBins          5.588  0.008   6.898
getSCEcoordinates          5.360  0.000   6.769
findCNVs                   4.120  0.284   7.104
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘AneuFinder’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c loghmm.cpp -o loghmm.o
loghmm.cpp:320:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
loghmm.cpp:480:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
loghmm.cpp:518:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 ^
loghmm.cpp:583:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:400:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:694:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:732:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 ^
scalehmm.cpp:791:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(AneuFinder)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, 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              0
        43       -23717.788445            0.353933            0.257145              0
        44       -23717.435431            0.353014            0.258100              0
        45       -23717.083339            0.352092            0.259094              0
        46       -23716.732173            0.351166            0.260034              0
        47       -23716.381938            0.350235            0.260935              0
        48       -23716.032640            0.349298            0.261735              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              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              3
       188       -23676.311275            0.222719            0.203906              3
       189       -23676.089372            0.221903            0.203574              3
       190       -23675.868284            0.221088            0.203241              3
       191       -23675.648009            0.220275            0.202907              3
       192       -23675.428546            0.219463            0.202574              3
       193       -23675.209893            0.218653            0.202240              3
       194       -23674.992049            0.217844            0.201906              3
       195       -23674.775012            0.217037            0.201572              3
       196       -23674.558781            0.216232            0.201237              3
       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              4
       251       -23663.857879            0.174517            0.182657              4
       252       -23663.684071            0.173808            0.182318              4
       253       -23663.510970            0.173101            0.181979              4
       254       -23663.338575            0.172395            0.181641              4
       255       -23663.166884            0.171691            0.181302              4
       256       -23662.995894            0.170989            0.180963              4
       257       -23662.825605            0.170289            0.180624              4
       258       -23662.656015            0.169591            0.180285              4
       259       -23662.487121            0.168894            0.179946              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              4
       261       -23662.151414            0.167507            0.179268              4
       262       -23661.984599            0.166816            0.178929              4
       263       -23661.818473            0.166126            0.178590              4
       264       -23661.653034            0.165439            0.178251              4
       265       -23661.488280            0.164754            0.177912              4
       266       -23661.324210            0.164070            0.177573              4
       267       -23661.160822            0.163388            0.177234              4
       268       -23660.998114            0.162708            0.176895              4
       269       -23660.836084            0.162030            0.176556              4
       270       -23660.674730            0.161354            0.176217              4
       271       -23660.514051            0.160679            0.175879              4
       272       -23660.354044            0.160007            0.175540              4
       273       -23660.194708            0.159336            0.175202              4
       274       -23660.036041            0.158667            0.174864              4
       275       -23659.878041            0.158000            0.174526              4
       276       -23659.720706            0.157335            0.174188              4
       277       -23659.564034            0.156672            0.173851              4
       278       -23659.408024            0.156010            0.173513              4
       279       -23659.252673            0.155351            0.173175              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       280       -23659.097980            0.154693            0.172838              4
       281       -23658.943943            0.154037            0.172500              4
       282       -23658.790560            0.153383            0.172162              4
       283       -23658.637828            0.152731            0.171825              4
       284       -23658.485747            0.152081            0.171488              4
       285       -23658.334315            0.151433            0.171150              4
       286       -23658.183528            0.150786            0.170813              4
       287       -23658.033387            0.150142            0.170476              4
       288       -23657.883888            0.149499            0.170139              4
       289       -23657.735030            0.148858            0.169802              4
       290       -23657.586811            0.148219            0.169465              4
       291       -23657.439229            0.147582            0.169128              4
       292       -23657.292283            0.146947            0.168792              4
       293       -23657.145969            0.146313            0.168455              4
       294       -23657.000288            0.145682            0.168119              4
       295       -23656.855235            0.145052            0.167783              4
       296       -23656.710811            0.144424            0.167447              4
       297       -23656.567013            0.143798            0.167111              4
       298       -23656.423838            0.143174            0.166775              4
       299       -23656.281286            0.142552            0.166439              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       300       -23656.139354            0.141932            0.166104              4
       301       -23655.998040            0.141314            0.165768              4
       302       -23655.857343            0.140697            0.165433              4
       303       -23655.717260            0.140083            0.165098              4
       304       -23655.577790            0.139470            0.164763              4
       305       -23655.438931            0.138859            0.164428              4
       306       -23655.300681            0.138250            0.164094              4
       307       -23655.163038            0.137643            0.163759              4
       308       -23655.026000            0.137038            0.163425              4
       309       -23654.889566            0.136434            0.163091              4
       310       -23654.753733            0.135833            0.162757              4
       311       -23654.618500            0.135233            0.162423              4
       312       -23654.483864            0.134635            0.162089              4
       313       -23654.349825            0.134040            0.161755              4
       314       -23654.216379            0.133446            0.161422              4
       315       -23654.083526            0.132854            0.161089              4
       316       -23653.951262            0.132263            0.160756              4
       317       -23653.819587            0.131675            0.160423              4
       318       -23653.688499            0.131088            0.160090              4
       319       -23653.557995            0.130504            0.159757              4
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       320       -23653.428074            0.129921            0.159425              4
       321       -23653.298734            0.129340            0.159092              4
       322       -23653.169973            0.128761            0.158760              4
       323       -23653.041789            0.128184            0.158428              4
       324       -23652.914180            0.127609            0.158097              4
       325       -23652.787145            0.127035            0.157765              5
       326       -23652.660681            0.126464            0.157434              5
       327       -23652.534787            0.125894            0.157103              5
       328       -23652.409461            0.125326            0.156771              5
       329       -23652.284700            0.124760            0.156441              5
       330       -23652.160504            0.124196            0.156110              5
       331       -23652.036870            0.123634            0.155780              5
       332       -23651.913797            0.123074            0.155452              5
       333       -23651.791282            0.122515            0.155124              5
       334       -23651.669323            0.121958            0.154796              5
       335       -23651.547920            0.121404            0.154469              5
       336       -23651.427069            0.120851            0.154142              5
       337       -23651.306769            0.120300            0.153815              5
       338       -23651.187019            0.119750            0.153488              5
       339       -23651.067816            0.119203            0.153161              5
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       340       -23650.949159            0.118657            0.152835              5
       341       -23650.831045            0.118114            0.152509              5
       342       -23650.713473            0.117572            0.152183              5
       343       -23650.596442            0.117032            0.151857              5
       344       -23650.479948            0.116494            0.151534              5
       345       -23650.363991            0.115957            0.151210              5
       346       -23650.248568            0.115423            0.150887              5
       347       -23650.133678            0.114890            0.150564              5
       348       -23650.019319            0.114359            0.150242              5
       349       -23649.905488            0.113830            0.149919              5
       350       -23649.792185            0.113303            0.149597              5
       351       -23649.679407            0.112778            0.149275              5
       352       -23649.567153            0.112254            0.148953              5
       353       -23649.455420            0.111733            0.148632              5
       354       -23649.344207            0.111213            0.148310              5
       355       -23649.233512            0.110695            0.147989              5
       356       -23649.123334            0.110179            0.147668              5
       357       -23649.013670            0.109664            0.147348              5
       358       -23648.904518            0.109152            0.147027              5
       359       -23648.795877            0.108641            0.146707              5
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              5
       361       -23648.580120            0.107625            0.146067              5
       362       -23648.473000            0.107120            0.145748              5
       363       -23648.366384            0.106616            0.145429              5
       364       -23648.260270            0.106114            0.145110              5
       365       -23648.154656            0.105614            0.144791              5
       366       -23648.049539            0.105116            0.144473              5
       367       -23647.944919            0.104620            0.144154              5
       368       -23647.840794            0.104126            0.143836              5
       369       -23647.737161            0.103633            0.143519              5
       370       -23647.634019            0.103142            0.143201              5
       371       -23647.531366            0.102653            0.142884              5
       372       -23647.429201            0.102165            0.142567              5
       373       -23647.327521            0.101680            0.142251              5
       374       -23647.226325            0.101196            0.141934              5
       375       -23647.125611            0.100714            0.141618              5
       376       -23647.025378            0.100234            0.141302              5
       377       -23646.925622            0.099755            0.140986              5
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              1
        11       -23211.762729            0.842578           12.269888              1
        12       -23210.839848            0.922881           11.279480              1
        13       -23209.921053            0.918795            9.624877              1
        14       -23209.118734            0.802320            8.968506              1
        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              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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.380   0.324  19.802 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder000
annotateBreakpoints13.624 0.10417.447
bam2GRanges0.4880.0160.571
bed2GRanges1.6160.0403.293
binReads2.4960.0043.954
blacklist2.2120.0203.728
clusterByQuality2.4480.0282.605
clusterHMMs0.5160.0040.523
collapseBins2.1400.0243.898
colors0.0520.0000.054
compareMethods0.7560.0040.766
consensusSegments 9.996 0.00810.027
correctGC30.680 2.59240.573
export000
filterSegments0.3080.0000.306
findCNVs4.1200.2847.104
findCNVs.strandseq5.5560.1447.541
fixedWidthBins0.1160.0041.922
getBreakpoints11.552 0.08814.284
getDistinctColors0.0240.0000.023
getQC0.8080.0000.807
getSCEcoordinates5.3600.0006.769
heatmapAneuploidies45.508 0.05245.626
heatmapGenomewide21.804 0.02021.962
heatmapGenomewideClusters23.840 0.00423.878
importBed1.6760.0001.679
karyotypeMeasures26.052 0.03626.161
loadFromFiles4.6560.0084.666
plotHeterogeneity30.616 0.04430.708
plot_pca1.3480.0081.362
refineBreakpoints64.076 0.14067.568
simulateReads52.260 2.39254.755
subsetByCNVprofile6.2320.0006.239
variableWidthBins5.5880.0086.898