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This page was generated on 2022-06-24 12:04:28 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 51/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.24.0  (landing page)
Aaron Taudt
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_15
git_last_commit: 4c6906e
git_last_commit_date: 2022-04-26 11:30:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AneuFinder
Version: 1.24.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings AneuFinder_1.24.0.tar.gz
StartedAt: 2022-06-23 18:44:53 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 18:54:20 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 567.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AneuFinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings AneuFinder_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/AneuFinder.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.24.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
simulateReads             54.498  4.644  59.154
refineBreakpoints         46.671  0.352  47.022
heatmapAneuploidies       44.186  0.879  45.066
plotHeterogeneity         31.179  0.236  31.415
correctGC                 25.639  3.681  29.356
heatmapGenomewideClusters 23.983  0.184  24.167
karyotypeMeasures         23.016  0.174  23.190
heatmapGenomewide         22.010  0.340  22.380
annotateBreakpoints       13.919  0.700  14.807
getBreakpoints            10.310  0.176  10.486
consensusSegments          8.365  0.116   8.481
subsetByCNVprofile         6.330  0.028   6.360
getSCEcoordinates          5.206  0.304   5.701
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.



Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘AneuFinder’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  320 |  #pragma omp parallel for
      | 
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  480 |  #pragma omp parallel for
      | 
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  518 |   #pragma omp parallel for
      | 
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  583 |  #pragma omp parallel for
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  384 |  #pragma omp parallel for
      | 
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  400 |  #pragma omp parallel for
      | 
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  694 |  #pragma omp parallel for
      | 
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  732 |   #pragma omp parallel for
      | 
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  791 |  #pragma omp parallel for
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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

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, 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              1
        64       -23710.576153            0.333657            0.251252              1
        65       -23710.243465            0.332688            0.249777              1
        66       -23709.911743            0.331722            0.248349              1
        67       -23709.580982            0.330761            0.247090              1
        68       -23709.251180            0.329802            0.245906              1
        69       -23708.922334            0.328846            0.244786              1
        70       -23708.594441            0.327893            0.243757              1
        71       -23708.267498            0.326942            0.242885              1
        72       -23707.941505            0.325993            0.242069              1
        73       -23707.616459            0.325046            0.241304              1
        74       -23707.292358            0.324101            0.240590              1
        75       -23706.969202            0.323156            0.239921              1
        76       -23706.646989            0.322213            0.239394              1
        77       -23706.325719            0.321271            0.239012              1
        78       -23706.005389            0.320329            0.238641              1
        79       -23705.686000            0.319389            0.238282              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        80       -23705.367551            0.318449            0.237931              1
        81       -23705.050040            0.317511            0.237592              1
        82       -23704.733468            0.316573            0.237265              1
        83       -23704.417832            0.315635            0.236943              1
        84       -23704.103134            0.314699            0.236626              1
        85       -23703.789371            0.313763            0.236312              1
        86       -23703.476543            0.312828            0.236001              1
        87       -23703.164650            0.311893            0.235693              1
        88       -23702.853691            0.310959            0.235387              1
        89       -23702.543664            0.310026            0.235083              1
        90       -23702.234570            0.309094            0.234781              1
        91       -23701.926408            0.308163            0.234480              1
        92       -23701.619176            0.307232            0.234179              1
        93       -23701.312874            0.306302            0.233879              1
        94       -23701.007502            0.305372            0.233580              1
        95       -23700.703059            0.304444            0.233281              1
        96       -23700.399543            0.303516            0.232982              1
        97       -23700.096954            0.302589            0.232683              1
        98       -23699.795291            0.301663            0.232384              1
        99       -23699.494554            0.300737            0.232086              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       100       -23699.194741            0.299813            0.231789              1
       101       -23698.895853            0.298889            0.231491              1
       102       -23698.597887            0.297966            0.231193              1
       103       -23698.300843            0.297044            0.230895              1
       104       -23698.004721            0.296122            0.230596              1
       105       -23697.709519            0.295202            0.230296              1
       106       -23697.415236            0.294282            0.229997              1
       107       -23697.121873            0.293364            0.229697              1
       108       -23696.829427            0.292446            0.229396              1
       109       -23696.537897            0.291529            0.229095              1
       110       -23696.247284            0.290613            0.228793              1
       111       -23695.957586            0.289698            0.228491              1
       112       -23695.668802            0.288784            0.228189              1
       113       -23695.380931            0.287871            0.227886              1
       114       -23695.093972            0.286959            0.227582              1
       115       -23694.807925            0.286047            0.227278              1
       116       -23694.522788            0.285137            0.226973              1
       117       -23694.238560            0.284228            0.226668              1
       118       -23693.955240            0.283320            0.226362              1
       119       -23693.672828            0.282412            0.226056              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              1
       121       -23693.110721            0.280601            0.225443              1
       122       -23692.831025            0.279696            0.225136              1
       123       -23692.552232            0.278793            0.224828              1
       124       -23692.274340            0.277891            0.224520              1
       125       -23691.997350            0.276990            0.224212              1
       126       -23691.721261            0.276090            0.223903              1
       127       -23691.446070            0.275191            0.223593              1
       128       -23691.171777            0.274293            0.223283              1
       129       -23690.898380            0.273396            0.222972              1
       130       -23690.625880            0.272501            0.222661              1
       131       -23690.354274            0.271606            0.222349              1
       132       -23690.083561            0.270713            0.222037              1
       133       -23689.813741            0.269820            0.221724              1
       134       -23689.544812            0.268929            0.221411              1
       135       -23689.276773            0.268039            0.221097              1
       136       -23689.009623            0.267150            0.220783              1
       137       -23688.743361            0.266262            0.220469              1
       138       -23688.477985            0.265376            0.220154              1
       139       -23688.213495            0.264490            0.219838              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       140       -23687.949889            0.263606            0.219522              1
       141       -23687.687165            0.262723            0.219206              1
       142       -23687.425324            0.261841            0.218889              1
       143       -23687.164363            0.260961            0.218571              1
       144       -23686.904282            0.260081            0.218253              1
       145       -23686.645079            0.259203            0.217935              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              2
       197       -23674.343353            0.215428            0.200902              2
       198       -23674.128727            0.214626            0.200567              2
       199       -23673.914902            0.213825            0.200232              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              2
       201       -23673.489648            0.212228            0.199562              2
       202       -23673.278216            0.211433            0.199226              2
       203       -23673.067577            0.210638            0.198890              2
       204       -23672.857731            0.209846            0.198554              2
       205       -23672.648676            0.209055            0.198218              2
       206       -23672.440411            0.208266            0.197882              2
       207       -23672.232933            0.207478            0.197545              2
       208       -23672.026241            0.206692            0.197208              2
       209       -23671.820333            0.205908            0.196871              2
       210       -23671.615208            0.205125            0.196534              2
       211       -23671.410864            0.204344            0.196198              2
       212       -23671.207299            0.203565            0.195861              2
       213       -23671.004512            0.202787            0.195525              2
       214       -23670.802501            0.202011            0.195188              2
       215       -23670.601265            0.201237            0.194851              2
       216       -23670.400800            0.200464            0.194514              2
       217       -23670.201107            0.199693            0.194176              2
       218       -23670.002183            0.198924            0.193839              2
       219       -23669.804027            0.198156            0.193501              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              2
       221       -23669.410010            0.196627            0.192826              2
       222       -23669.214145            0.195864            0.192488              2
       223       -23669.019042            0.195104            0.192149              2
       224       -23668.824697            0.194345            0.191811              2
       225       -23668.631110            0.193587            0.191473              2
       226       -23668.438278            0.192832            0.191134              2
       227       -23668.246200            0.192078            0.190795              2
       228       -23668.054874            0.191326            0.190456              2
       229       -23667.864298            0.190576            0.190118              2
       230       -23667.674471            0.189827            0.189779              2
       231       -23667.485390            0.189081            0.189439              2
       232       -23667.297055            0.188336            0.189100              2
       233       -23667.109462            0.187592            0.188761              2
       234       -23666.922612            0.186851            0.188421              2
       235       -23666.736501            0.186111            0.188082              2
       236       -23666.551128            0.185373            0.187744              2
       237       -23666.366491            0.184637            0.187405              2
       238       -23666.182588            0.183902            0.187066              2
       239       -23665.999419            0.183170            0.186727              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       240       -23665.816980            0.182439            0.186388              2
       241       -23665.635270            0.181710            0.186049              2
       242       -23665.454288            0.180982            0.185710              2
       243       -23665.274031            0.180257            0.185370              2
       244       -23665.094498            0.179533            0.185031              2
       245       -23664.915686            0.178811            0.184692              2
       246       -23664.737595            0.178091            0.184352              2
       247       -23664.560223            0.177373            0.184013              2
       248       -23664.383566            0.176656            0.183674              2
       249       -23664.207625            0.175942            0.183335              2
       250       -23664.032396            0.175229            0.182996              2
       251       -23663.857879            0.174517            0.182657              2
       252       -23663.684071            0.173808            0.182318              2
       253       -23663.510970            0.173101            0.181979              2
       254       -23663.338575            0.172395            0.181641              2
       255       -23663.166884            0.171691            0.181302              2
       256       -23662.995894            0.170989            0.180963              2
       257       -23662.825605            0.170289            0.180624              2
       258       -23662.656015            0.169591            0.180285              2
       259       -23662.487121            0.168894            0.179946              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              2
       261       -23662.151414            0.167507            0.179268              2
       262       -23661.984599            0.166816            0.178929              2
       263       -23661.818473            0.166126            0.178590              2
       264       -23661.653034            0.165439            0.178251              2
       265       -23661.488280            0.164754            0.177912              2
       266       -23661.324210            0.164070            0.177573              2
       267       -23661.160822            0.163388            0.177234              2
       268       -23660.998114            0.162708            0.176895              2
       269       -23660.836084            0.162030            0.176556              2
       270       -23660.674730            0.161354            0.176217              2
       271       -23660.514051            0.160679            0.175879              2
       272       -23660.354044            0.160007            0.175540              2
       273       -23660.194708            0.159336            0.175202              2
       274       -23660.036041            0.158667            0.174864              2
       275       -23659.878041            0.158000            0.174526              2
       276       -23659.720706            0.157335            0.174188              2
       277       -23659.564034            0.156672            0.173851              2
       278       -23659.408024            0.156010            0.173513              2
       279       -23659.252673            0.155351            0.173175              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       280       -23659.097980            0.154693            0.172838              2
       281       -23658.943943            0.154037            0.172500              2
       282       -23658.790560            0.153383            0.172162              2
       283       -23658.637828            0.152731            0.171825              2
       284       -23658.485747            0.152081            0.171488              2
       285       -23658.334315            0.151433            0.171150              2
       286       -23658.183528            0.150786            0.170813              2
       287       -23658.033387            0.150142            0.170476              2
       288       -23657.883888            0.149499            0.170139              2
       289       -23657.735030            0.148858            0.169802              2
       290       -23657.586811            0.148219            0.169465              2
       291       -23657.439229            0.147582            0.169128              2
       292       -23657.292283            0.146947            0.168792              2
       293       -23657.145969            0.146313            0.168455              2
       294       -23657.000288            0.145682            0.168119              2
       295       -23656.855235            0.145052            0.167783              2
       296       -23656.710811            0.144424            0.167447              2
       297       -23656.567013            0.143798            0.167111              2
       298       -23656.423838            0.143174            0.166775              2
       299       -23656.281286            0.142552            0.166439              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       300       -23656.139354            0.141932            0.166104              2
       301       -23655.998040            0.141314            0.165768              2
       302       -23655.857343            0.140697            0.165433              2
       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              3
       341       -23650.831045            0.118114            0.152509              3
       342       -23650.713473            0.117572            0.152183              3
       343       -23650.596442            0.117032            0.151857              3
       344       -23650.479948            0.116494            0.151534              3
       345       -23650.363991            0.115957            0.151210              3
       346       -23650.248568            0.115423            0.150887              3
       347       -23650.133678            0.114890            0.150564              3
       348       -23650.019319            0.114359            0.150242              3
       349       -23649.905488            0.113830            0.149919              3
       350       -23649.792185            0.113303            0.149597              3
       351       -23649.679407            0.112778            0.149275              3
       352       -23649.567153            0.112254            0.148953              3
       353       -23649.455420            0.111733            0.148632              3
       354       -23649.344207            0.111213            0.148310              3
       355       -23649.233512            0.110695            0.147989              3
       356       -23649.123334            0.110179            0.147668              3
       357       -23649.013670            0.109664            0.147348              3
       358       -23648.904518            0.109152            0.147027              3
       359       -23648.795877            0.108641            0.146707              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              3
       361       -23648.580120            0.107625            0.146067              3
       362       -23648.473000            0.107120            0.145748              3
       363       -23648.366384            0.106616            0.145429              3
       364       -23648.260270            0.106114            0.145110              3
       365       -23648.154656            0.105614            0.144791              3
       366       -23648.049539            0.105116            0.144473              3
       367       -23647.944919            0.104620            0.144154              3
       368       -23647.840794            0.104126            0.143836              3
       369       -23647.737161            0.103633            0.143519              3
       370       -23647.634019            0.103142            0.143201              3
       371       -23647.531366            0.102653            0.142884              3
       372       -23647.429201            0.102165            0.142567              3
       373       -23647.327521            0.101680            0.142251              3
       374       -23647.226325            0.101196            0.141934              3
       375       -23647.125611            0.100714            0.141618              3
       376       -23647.025378            0.100234            0.141302              3
       377       -23646.925622            0.099755            0.140986              3
Convergence reached!
number of states = 12
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24380.580428                 inf         6183.000000              0
         2       -23357.275929         1023.304498          686.821642              0
         3       -23260.421975           96.853955          172.471538              0
         4       -23232.483517           27.938458          143.506687              0
         5       -23222.142294           10.341223           76.049323              0
         6       -23217.735527            4.406767           58.626866              0
         7       -23215.521320            2.214207           35.912568              0
         8       -23214.276947            1.244373           27.484487              0
         9       -23213.395549            0.881398           18.765222              0
        10       -23212.605307            0.790242           15.594210              0
        11       -23211.762729            0.842578           12.269888              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 
 16.143   0.647  16.778 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder0.0000.0000.001
annotateBreakpoints13.919 0.70014.807
bam2GRanges0.3700.0200.407
bed2GRanges1.5480.1641.711
binReads1.6030.0241.628
blacklist1.8450.0241.869
clusterByQuality3.2060.1373.370
clusterHMMs0.3870.0220.409
collapseBins1.6600.0441.704
colors0.0710.0040.074
compareMethods0.5600.0120.572
consensusSegments8.3650.1168.481
correctGC25.639 3.68129.356
export0.0000.0000.001
filterSegments0.3000.0120.313
findCNVs4.4660.3044.770
findCNVs.strandseq4.3640.1364.501
fixedWidthBins0.0620.0040.066
getBreakpoints10.310 0.17610.486
getDistinctColors0.1090.0030.112
getQC1.6070.0121.619
getSCEcoordinates5.2060.3045.701
heatmapAneuploidies44.186 0.87945.066
heatmapGenomewide22.01 0.3422.38
heatmapGenomewideClusters23.983 0.18424.167
importBed1.0280.0441.072
karyotypeMeasures23.016 0.17423.190
loadFromFiles4.3100.0264.336
plotHeterogeneity31.179 0.23631.415
plot_pca0.9320.0480.980
refineBreakpoints46.671 0.35247.022
simulateReads54.498 4.64459.154
subsetByCNVprofile6.3300.0286.360
variableWidthBins3.9060.0323.937