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This page was generated on 2023-03-20 11:05:54 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4516
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4295
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4324
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for AneuFinder on lconway


To the developers/maintainers of the AneuFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AneuFinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 50/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.26.0  (landing page)
Aaron Taudt
Snapshot Date: 2023-03-17 14:00:04 -0400 (Fri, 17 Mar 2023)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_16
git_last_commit: 7cd59a1
git_last_commit_date: 2022-11-01 11:13:19 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AneuFinder
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AneuFinder_1.26.0.tar.gz
StartedAt: 2023-03-17 18:56:22 -0400 (Fri, 17 Mar 2023)
EndedAt: 2023-03-17 19:05:12 -0400 (Fri, 17 Mar 2023)
EllapsedTime: 530.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AneuFinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AneuFinder_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/AneuFinder.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AneuFinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Aneufinder.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'bed2GRanges.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'binReads.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'blacklist.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'fixedWidthBins.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

Missing link or links in documentation object 'mergeStrandseqFiles.Rd':
  ‘[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
simulateReads             55.236  3.483  58.943
refineBreakpoints         40.697  0.878  41.676
heatmapAneuploidies       40.166  0.284  40.530
correctGC                 26.415  1.797  28.362
plotHeterogeneity         26.123  0.419  26.598
heatmapGenomewideClusters 22.841  0.187  23.067
karyotypeMeasures         20.492  0.275  20.821
heatmapGenomewide         18.885  0.248  19.183
annotateBreakpoints       12.898  0.727  13.987
getBreakpoints             8.760  0.585   9.387
consensusSegments          7.395  0.066   7.480
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c loghmm.cpp -o loghmm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility.cpp -o utility.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-AneuFinder/00new/AneuFinder/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AneuFinder)

Tests output

AneuFinder.Rcheck/tests/testthat.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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

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

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

Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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

Please visit https://github.com/ataudt/aneufinder for the latest bugfixes and features.

> 
> test_check("AneuFinder")
number of states = 11
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24789.866771                 inf         6183.000000              0
         2       -23822.331670          967.535101          601.762712              0
         3       -23761.771285           60.560384          131.281549              0
         4       -23745.235666           16.535619          119.461404              0
         5       -23738.238770            6.996896           63.831344              0
         6       -23735.137871            3.100899           48.587399              0
         7       -23733.451273            1.686598           29.803499              0
         8       -23732.421572            1.029701           21.580983              0
         9       -23731.674903            0.746669           14.186707              0
        10       -23731.069920            0.604983            9.975381              0
        11       -23730.527674            0.542246            7.021040              0
        12       -23730.007090            0.520584            4.942881              0
        13       -23729.480035            0.527055            3.803030              0
        14       -23728.932681            0.547354            2.653912              0
        15       -23728.372455            0.560226            2.141742              0
        16       -23727.839017            0.533439            1.244299              0
        17       -23727.367012            0.472005            1.109390              0
        18       -23726.947097            0.419914            0.529456              0
        19       -23726.552750            0.394348            0.602730              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23726.169459            0.383291            0.302116              0
        21       -23725.791510            0.377949            0.389827              0
        22       -23725.416462            0.375048            0.244787              0
        23       -23725.043233            0.373229            0.307572              0
        24       -23724.671334            0.371899            0.240956              0
        25       -23724.300551            0.370783            0.275223              0
        26       -23723.930786            0.369765            0.245508              0
        27       -23723.561998            0.368789            0.262164              0
        28       -23723.194164            0.367834            0.248735              0
        29       -23722.827276            0.366888            0.256570              0
        30       -23722.461329            0.365947            0.250428              0
        31       -23722.096319            0.365010            0.254042              0
        32       -23721.732244            0.364076            0.251213              0
        33       -23721.369100            0.363144            0.252844              0
        34       -23721.006885            0.362214            0.251549              0
        35       -23720.645598            0.361287            0.252622              0
        36       -23720.285236            0.360362            0.252383              0
        37       -23719.925796            0.359440            0.253123              0
        38       -23719.567277            0.358519            0.253290              0
        39       -23719.209677            0.357600            0.254027              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        40       -23718.852994            0.356683            0.254590              0
        41       -23718.497228            0.355766            0.255400              0
        42       -23718.142378            0.354850            0.256151              0
        43       -23717.788445            0.353933            0.257145              0
        44       -23717.435431            0.353014            0.258100              0
        45       -23717.083339            0.352092            0.259094              0
        46       -23716.732173            0.351166            0.260034              0
        47       -23716.381938            0.350235            0.260935              0
        48       -23716.032640            0.349298            0.261735              0
        49       -23715.684287            0.348353            0.262424              0
        50       -23715.336886            0.347401            0.262956              0
        51       -23714.990445            0.346441            0.263312              0
        52       -23714.644972            0.345473            0.263463              0
        53       -23714.300474            0.344498            0.263396              0
        54       -23713.956958            0.343516            0.263103              0
        55       -23713.614428            0.342530            0.262584              0
        56       -23713.272887            0.341540            0.261849              0
        57       -23712.932339            0.340548            0.260917              0
        58       -23712.592783            0.339556            0.259810              0
        59       -23712.254217            0.338565            0.258559              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        60       -23711.916641            0.337576            0.257196              0
        61       -23711.580050            0.336591            0.255754              0
        62       -23711.244442            0.335609            0.254264              0
        63       -23710.909811            0.334631            0.252755              0
        64       -23710.576153            0.333657            0.251252              0
        65       -23710.243465            0.332688            0.249777              0
        66       -23709.911743            0.331722            0.248349              0
        67       -23709.580982            0.330761            0.247090              0
        68       -23709.251180            0.329802            0.245906              0
        69       -23708.922334            0.328846            0.244786              0
        70       -23708.594441            0.327893            0.243757              0
        71       -23708.267498            0.326942            0.242885              0
        72       -23707.941505            0.325993            0.242069              0
        73       -23707.616459            0.325046            0.241304              0
        74       -23707.292358            0.324101            0.240590              0
        75       -23706.969202            0.323156            0.239921              0
        76       -23706.646989            0.322213            0.239394              0
        77       -23706.325719            0.321271            0.239012              0
        78       -23706.005389            0.320329            0.238641              0
        79       -23705.686000            0.319389            0.238282              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        80       -23705.367551            0.318449            0.237931              0
        81       -23705.050040            0.317511            0.237592              0
        82       -23704.733468            0.316573            0.237265              0
        83       -23704.417832            0.315635            0.236943              0
        84       -23704.103134            0.314699            0.236626              0
        85       -23703.789371            0.313763            0.236312              0
        86       -23703.476543            0.312828            0.236001              0
        87       -23703.164650            0.311893            0.235693              0
        88       -23702.853691            0.310959            0.235387              0
        89       -23702.543664            0.310026            0.235083              0
        90       -23702.234570            0.309094            0.234781              0
        91       -23701.926408            0.308163            0.234480              0
        92       -23701.619176            0.307232            0.234179              0
        93       -23701.312874            0.306302            0.233879              0
        94       -23701.007502            0.305372            0.233580              0
        95       -23700.703059            0.304444            0.233281              0
        96       -23700.399543            0.303516            0.232982              0
        97       -23700.096954            0.302589            0.232683              0
        98       -23699.795291            0.301663            0.232384              0
        99       -23699.494554            0.300737            0.232086              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       100       -23699.194741            0.299813            0.231789              0
       101       -23698.895853            0.298889            0.231491              0
       102       -23698.597887            0.297966            0.231193              0
       103       -23698.300843            0.297044            0.230895              0
       104       -23698.004721            0.296122            0.230596              0
       105       -23697.709519            0.295202            0.230296              0
       106       -23697.415236            0.294282            0.229997              0
       107       -23697.121873            0.293364            0.229697              0
       108       -23696.829427            0.292446            0.229396              0
       109       -23696.537897            0.291529            0.229095              0
       110       -23696.247284            0.290613            0.228793              0
       111       -23695.957586            0.289698            0.228491              0
       112       -23695.668802            0.288784            0.228189              0
       113       -23695.380931            0.287871            0.227886              0
       114       -23695.093972            0.286959            0.227582              0
       115       -23694.807925            0.286047            0.227278              0
       116       -23694.522788            0.285137            0.226973              0
       117       -23694.238560            0.284228            0.226668              1
       118       -23693.955240            0.283320            0.226362              1
       119       -23693.672828            0.282412            0.226056              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              1
       121       -23693.110721            0.280601            0.225443              1
       122       -23692.831025            0.279696            0.225136              1
       123       -23692.552232            0.278793            0.224828              1
       124       -23692.274340            0.277891            0.224520              1
       125       -23691.997350            0.276990            0.224212              1
       126       -23691.721261            0.276090            0.223903              1
       127       -23691.446070            0.275191            0.223593              1
       128       -23691.171777            0.274293            0.223283              1
       129       -23690.898380            0.273396            0.222972              1
       130       -23690.625880            0.272501            0.222661              1
       131       -23690.354274            0.271606            0.222349              1
       132       -23690.083561            0.270713            0.222037              1
       133       -23689.813741            0.269820            0.221724              1
       134       -23689.544812            0.268929            0.221411              1
       135       -23689.276773            0.268039            0.221097              1
       136       -23689.009623            0.267150            0.220783              1
       137       -23688.743361            0.266262            0.220469              1
       138       -23688.477985            0.265376            0.220154              1
       139       -23688.213495            0.264490            0.219838              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       140       -23687.949889            0.263606            0.219522              1
       141       -23687.687165            0.262723            0.219206              1
       142       -23687.425324            0.261841            0.218889              1
       143       -23687.164363            0.260961            0.218571              1
       144       -23686.904282            0.260081            0.218253              1
       145       -23686.645079            0.259203            0.217935              1
       146       -23686.386752            0.258326            0.217616              1
       147       -23686.129301            0.257451            0.217297              1
       148       -23685.872725            0.256576            0.216977              1
       149       -23685.617022            0.255703            0.216657              1
       150       -23685.362190            0.254831            0.216336              1
       151       -23685.108229            0.253961            0.216015              1
       152       -23684.855137            0.253092            0.215694              1
       153       -23684.602914            0.252224            0.215372              1
       154       -23684.351557            0.251357            0.215049              1
       155       -23684.101065            0.250492            0.214727              1
       156       -23683.851437            0.249628            0.214403              1
       157       -23683.602672            0.248765            0.214080              1
       158       -23683.354769            0.247904            0.213756              1
       159       -23683.107725            0.247044            0.213432              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       160       -23682.861540            0.246185            0.213107              1
       161       -23682.616213            0.245328            0.212782              1
       162       -23682.371741            0.244472            0.212456              1
       163       -23682.128124            0.243617            0.212131              1
       164       -23681.885360            0.242764            0.211806              1
       165       -23681.643448            0.241912            0.211480              1
       166       -23681.402387            0.241062            0.211154              1
       167       -23681.162174            0.240213            0.210828              1
       168       -23680.922809            0.239365            0.210502              1
       169       -23680.684291            0.238519            0.210175              1
       170       -23680.446617            0.237674            0.209848              1
       171       -23680.209786            0.236831            0.209520              1
       172       -23679.973797            0.235989            0.209192              1
       173       -23679.738649            0.235148            0.208864              1
       174       -23679.504339            0.234309            0.208536              1
       175       -23679.270868            0.233472            0.208207              1
       176       -23679.038232            0.232636            0.207878              1
       177       -23678.806431            0.231801            0.207548              1
       178       -23678.575463            0.230968            0.207219              1
       179       -23678.345326            0.230136            0.206889              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       180       -23678.116020            0.229306            0.206559              1
       181       -23677.887543            0.228478            0.206228              1
       182       -23677.659892            0.227650            0.205897              1
       183       -23677.433067            0.226825            0.205566              1
       184       -23677.207067            0.226001            0.205235              1
       185       -23676.981889            0.225178            0.204903              1
       186       -23676.757532            0.224357            0.204571              1
       187       -23676.533994            0.223537            0.204239              1
       188       -23676.311275            0.222719            0.203906              1
       189       -23676.089372            0.221903            0.203574              1
       190       -23675.868284            0.221088            0.203241              1
       191       -23675.648009            0.220275            0.202907              1
       192       -23675.428546            0.219463            0.202574              1
       193       -23675.209893            0.218653            0.202240              1
       194       -23674.992049            0.217844            0.201906              1
       195       -23674.775012            0.217037            0.201572              1
       196       -23674.558781            0.216232            0.201237              1
       197       -23674.343353            0.215428            0.200902              1
       198       -23674.128727            0.214626            0.200567              1
       199       -23673.914902            0.213825            0.200232              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              1
       201       -23673.489648            0.212228            0.199562              1
       202       -23673.278216            0.211433            0.199226              1
       203       -23673.067577            0.210638            0.198890              1
       204       -23672.857731            0.209846            0.198554              1
       205       -23672.648676            0.209055            0.198218              1
       206       -23672.440411            0.208266            0.197882              1
       207       -23672.232933            0.207478            0.197545              1
       208       -23672.026241            0.206692            0.197208              1
       209       -23671.820333            0.205908            0.196871              1
       210       -23671.615208            0.205125            0.196534              1
       211       -23671.410864            0.204344            0.196198              1
       212       -23671.207299            0.203565            0.195861              1
       213       -23671.004512            0.202787            0.195525              1
       214       -23670.802501            0.202011            0.195188              1
       215       -23670.601265            0.201237            0.194851              1
       216       -23670.400800            0.200464            0.194514              1
       217       -23670.201107            0.199693            0.194176              1
       218       -23670.002183            0.198924            0.193839              1
       219       -23669.804027            0.198156            0.193501              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              1
       221       -23669.410010            0.196627            0.192826              1
       222       -23669.214145            0.195864            0.192488              1
       223       -23669.019042            0.195104            0.192149              1
       224       -23668.824697            0.194345            0.191811              1
       225       -23668.631110            0.193587            0.191473              1
       226       -23668.438278            0.192832            0.191134              1
       227       -23668.246200            0.192078            0.190795              1
       228       -23668.054874            0.191326            0.190456              1
       229       -23667.864298            0.190576            0.190118              1
       230       -23667.674471            0.189827            0.189779              1
       231       -23667.485390            0.189081            0.189439              1
       232       -23667.297055            0.188336            0.189100              1
       233       -23667.109462            0.187592            0.188761              1
       234       -23666.922612            0.186851            0.188421              1
       235       -23666.736501            0.186111            0.188082              1
       236       -23666.551128            0.185373            0.187744              1
       237       -23666.366491            0.184637            0.187405              1
       238       -23666.182588            0.183902            0.187066              1
       239       -23665.999419            0.183170            0.186727              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       240       -23665.816980            0.182439            0.186388              1
       241       -23665.635270            0.181710            0.186049              1
       242       -23665.454288            0.180982            0.185710              1
       243       -23665.274031            0.180257            0.185370              1
       244       -23665.094498            0.179533            0.185031              1
       245       -23664.915686            0.178811            0.184692              1
       246       -23664.737595            0.178091            0.184352              1
       247       -23664.560223            0.177373            0.184013              1
       248       -23664.383566            0.176656            0.183674              1
       249       -23664.207625            0.175942            0.183335              1
       250       -23664.032396            0.175229            0.182996              1
       251       -23663.857879            0.174517            0.182657              1
       252       -23663.684071            0.173808            0.182318              1
       253       -23663.510970            0.173101            0.181979              1
       254       -23663.338575            0.172395            0.181641              1
       255       -23663.166884            0.171691            0.181302              1
       256       -23662.995894            0.170989            0.180963              1
       257       -23662.825605            0.170289            0.180624              1
       258       -23662.656015            0.169591            0.180285              1
       259       -23662.487121            0.168894            0.179946              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              1
       261       -23662.151414            0.167507            0.179268              1
       262       -23661.984599            0.166816            0.178929              1
       263       -23661.818473            0.166126            0.178590              1
       264       -23661.653034            0.165439            0.178251              1
       265       -23661.488280            0.164754            0.177912              1
       266       -23661.324210            0.164070            0.177573              1
       267       -23661.160822            0.163388            0.177234              1
       268       -23660.998114            0.162708            0.176895              1
       269       -23660.836084            0.162030            0.176556              1
       270       -23660.674730            0.161354            0.176217              1
       271       -23660.514051            0.160679            0.175879              1
       272       -23660.354044            0.160007            0.175540              1
       273       -23660.194708            0.159336            0.175202              1
       274       -23660.036041            0.158667            0.174864              1
       275       -23659.878041            0.158000            0.174526              1
       276       -23659.720706            0.157335            0.174188              1
       277       -23659.564034            0.156672            0.173851              1
       278       -23659.408024            0.156010            0.173513              1
       279       -23659.252673            0.155351            0.173175              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       280       -23659.097980            0.154693            0.172838              1
       281       -23658.943943            0.154037            0.172500              1
       282       -23658.790560            0.153383            0.172162              1
       283       -23658.637828            0.152731            0.171825              1
       284       -23658.485747            0.152081            0.171488              1
       285       -23658.334315            0.151433            0.171150              1
       286       -23658.183528            0.150786            0.170813              1
       287       -23658.033387            0.150142            0.170476              1
       288       -23657.883888            0.149499            0.170139              1
       289       -23657.735030            0.148858            0.169802              1
       290       -23657.586811            0.148219            0.169465              1
       291       -23657.439229            0.147582            0.169128              1
       292       -23657.292283            0.146947            0.168792              1
       293       -23657.145969            0.146313            0.168455              1
       294       -23657.000288            0.145682            0.168119              1
       295       -23656.855235            0.145052            0.167783              1
       296       -23656.710811            0.144424            0.167447              1
       297       -23656.567013            0.143798            0.167111              1
       298       -23656.423838            0.143174            0.166775              1
       299       -23656.281286            0.142552            0.166439              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       300       -23656.139354            0.141932            0.166104              1
       301       -23655.998040            0.141314            0.165768              1
       302       -23655.857343            0.140697            0.165433              1
       303       -23655.717260            0.140083            0.165098              2
       304       -23655.577790            0.139470            0.164763              2
       305       -23655.438931            0.138859            0.164428              2
       306       -23655.300681            0.138250            0.164094              2
       307       -23655.163038            0.137643            0.163759              2
       308       -23655.026000            0.137038            0.163425              2
       309       -23654.889566            0.136434            0.163091              2
       310       -23654.753733            0.135833            0.162757              2
       311       -23654.618500            0.135233            0.162423              2
       312       -23654.483864            0.134635            0.162089              2
       313       -23654.349825            0.134040            0.161755              2
       314       -23654.216379            0.133446            0.161422              2
       315       -23654.083526            0.132854            0.161089              2
       316       -23653.951262            0.132263            0.160756              2
       317       -23653.819587            0.131675            0.160423              2
       318       -23653.688499            0.131088            0.160090              2
       319       -23653.557995            0.130504            0.159757              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       320       -23653.428074            0.129921            0.159425              2
       321       -23653.298734            0.129340            0.159092              2
       322       -23653.169973            0.128761            0.158760              2
       323       -23653.041789            0.128184            0.158428              2
       324       -23652.914180            0.127609            0.158097              2
       325       -23652.787145            0.127035            0.157765              2
       326       -23652.660681            0.126464            0.157434              2
       327       -23652.534787            0.125894            0.157103              2
       328       -23652.409461            0.125326            0.156771              2
       329       -23652.284700            0.124760            0.156441              2
       330       -23652.160504            0.124196            0.156110              2
       331       -23652.036870            0.123634            0.155780              2
       332       -23651.913797            0.123074            0.155452              2
       333       -23651.791282            0.122515            0.155124              2
       334       -23651.669323            0.121958            0.154796              2
       335       -23651.547920            0.121404            0.154469              2
       336       -23651.427069            0.120851            0.154142              2
       337       -23651.306769            0.120300            0.153815              2
       338       -23651.187019            0.119750            0.153488              2
       339       -23651.067816            0.119203            0.153161              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       340       -23650.949159            0.118657            0.152835              2
       341       -23650.831045            0.118114            0.152509              2
       342       -23650.713473            0.117572            0.152183              2
       343       -23650.596442            0.117032            0.151857              2
       344       -23650.479948            0.116494            0.151534              2
       345       -23650.363991            0.115957            0.151210              2
       346       -23650.248568            0.115423            0.150887              2
       347       -23650.133678            0.114890            0.150564              2
       348       -23650.019319            0.114359            0.150242              2
       349       -23649.905488            0.113830            0.149919              2
       350       -23649.792185            0.113303            0.149597              2
       351       -23649.679407            0.112778            0.149275              2
       352       -23649.567153            0.112254            0.148953              2
       353       -23649.455420            0.111733            0.148632              2
       354       -23649.344207            0.111213            0.148310              2
       355       -23649.233512            0.110695            0.147989              2
       356       -23649.123334            0.110179            0.147668              2
       357       -23649.013670            0.109664            0.147348              2
       358       -23648.904518            0.109152            0.147027              2
       359       -23648.795877            0.108641            0.146707              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              2
       361       -23648.580120            0.107625            0.146067              2
       362       -23648.473000            0.107120            0.145748              2
       363       -23648.366384            0.106616            0.145429              2
       364       -23648.260270            0.106114            0.145110              2
       365       -23648.154656            0.105614            0.144791              2
       366       -23648.049539            0.105116            0.144473              2
       367       -23647.944919            0.104620            0.144154              2
       368       -23647.840794            0.104126            0.143836              2
       369       -23647.737161            0.103633            0.143519              2
       370       -23647.634019            0.103142            0.143201              2
       371       -23647.531366            0.102653            0.142884              2
       372       -23647.429201            0.102165            0.142567              2
       373       -23647.327521            0.101680            0.142251              2
       374       -23647.226325            0.101196            0.141934              2
       375       -23647.125611            0.100714            0.141618              2
       376       -23647.025378            0.100234            0.141302              2
       377       -23646.925622            0.099755            0.140986              2
Convergence reached!
number of states = 12
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24380.580428                 inf         6183.000000              0
         2       -23357.275929         1023.304498          686.821642              0
         3       -23260.421975           96.853955          172.471538              0
         4       -23232.483517           27.938458          143.506687              0
         5       -23222.142294           10.341223           76.049323              0
         6       -23217.735527            4.406767           58.626866              0
         7       -23215.521320            2.214207           35.912568              0
         8       -23214.276947            1.244373           27.484487              0
         9       -23213.395549            0.881398           18.765222              0
        10       -23212.605307            0.790242           15.594210              0
        11       -23211.762729            0.842578           12.269889              0
        12       -23210.839848            0.922881           11.279480              0
        13       -23209.921053            0.918795            9.624877              0
        14       -23209.118734            0.802320            8.968506              0
        15       -23208.463874            0.654860            7.927086              0
        16       -23207.924958            0.538916            7.683630              0
        17       -23207.463600            0.461358            7.238144              0
        18       -23207.046263            0.417337            7.327465              0
        19       -23206.646001            0.400262            7.466156              0
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        20       -23206.242687            0.403315            7.882758              0
        21       -23205.828261            0.414426            8.254388              0
        22       -23205.414415            0.413846            8.474710              0
        23       -23205.032476            0.381939            8.244365              0
        24       -23204.714716            0.317760            7.544341              0
        25       -23204.473698            0.241018            6.506549              0
        26       -23204.300805            0.172894            5.379661              0
        27       -23204.178183            0.122622            4.308309              0
        28       -23204.088739            0.089444            3.383929              0
Convergence reached!
number of states = 11
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -21177.150641                 inf         5442.000000              0
         2       -20711.054012          466.096629          390.505270              0
         3       -20693.275989           17.778024           85.372131              0
         4       -20690.239855            3.036134           33.071291              0
         5       -20689.163935            1.075919           26.872093              0
         6       -20688.762950            0.400986           12.127422              0
         7       -20688.580230            0.182719            8.966009              0
         8       -20688.472739            0.107491            4.304038              0
         9       -20688.396085            0.076655            3.087959              0
Convergence reached!
number of states = 12
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -20778.885904                 inf         5442.000000              0
         2       -20214.840926          564.044978          503.589244              0
         3       -20185.942950           28.897975          137.261825              0
         4       -20179.925587            6.017363           51.421390              0
         5       -20177.170587            2.755000           36.836764              0
         6       -20175.645594            1.524994           18.722502              0
         7       -20174.658989            0.986605           13.124839              0
         8       -20173.895734            0.763255           11.327572              0
         9       -20173.167941            0.727793            9.948167              0
        10       -20172.282987            0.884954           11.162019              0
        11       -20170.984261            1.298726           12.412190              0
        12       -20169.145246            1.839014           14.930161              0
        13       -20166.835634            2.309613           16.942694              0
        14       -20163.895031            2.940602           18.691149              0
        15       -20160.410970            3.484061           18.008358              0
        16       -20157.717749            2.693221           14.496841              0
        17       -20156.213293            1.504456           10.220281              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!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 13.651   0.451  14.118 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0000.0000.001
annotateBreakpoints12.898 0.72713.987
bam2GRanges0.2880.0500.346
bed2GRanges0.6640.0400.706
binReads2.1690.2102.386
blacklist1.5640.1281.698
clusterByQuality2.0260.0732.119
clusterHMMs0.3890.0280.420
collapseBins2.0440.1372.187
colors0.0680.0060.074
compareMethods0.4710.0310.502
consensusSegments7.3950.0667.480
correctGC26.415 1.79728.362
export0.0000.0000.001
filterSegments0.2620.0200.285
findCNVs3.0480.3933.452
findCNVs.strandseq4.3740.6105.000
fixedWidthBins0.0600.0020.062
getBreakpoints8.7600.5859.387
getDistinctColors0.1160.0020.118
getQC1.3960.0301.430
getSCEcoordinates4.3530.3514.920
heatmapAneuploidies40.166 0.28440.530
heatmapGenomewide18.885 0.24819.183
heatmapGenomewideClusters22.841 0.18723.067
importBed1.3940.0111.410
karyotypeMeasures20.492 0.27520.821
loadFromFiles4.1500.0554.226
plotHeterogeneity26.123 0.41926.598
plot_pca0.9530.0440.999
refineBreakpoints40.697 0.87841.676
simulateReads55.236 3.48358.943
subsetByCNVprofile4.4480.0434.499
variableWidthBins3.4070.1183.534