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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 64/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.32.0  (landing page)
Aaron Taudt
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_19
git_last_commit: c7a1f18
git_last_commit_date: 2024-04-30 10:49:35 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for AneuFinder on palomino3

To the developers/maintainers of the AneuFinder package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AneuFinder
Version: 1.32.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AneuFinder.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings AneuFinder_1.32.0.tar.gz
StartedAt: 2024-06-17 00:12:32 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 00:31:33 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 1141.3 seconds
RetCode: 0
Status:   OK  
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AneuFinder.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings AneuFinder_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AneuFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AneuFinder' version '1.32.0'
* 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 whether package 'AneuFinder' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for 'parallel.helper'
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/AneuFinder/libs/x64/AneuFinder.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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             192.73   7.75  201.85
correctGC                 160.51   4.34  168.59
refineBreakpoints          51.80   1.51   53.29
heatmapAneuploidies        50.45   0.56   51.04
plotHeterogeneity          30.08   0.75   30.91
heatmapGenomewideClusters  30.14   0.64   30.82
karyotypeMeasures          25.79   0.91   26.79
heatmapGenomewide          25.66   0.45   30.48
annotateBreakpoints        18.54   0.63   19.51
getBreakpoints             11.47   0.81   12.27
consensusSegments          10.20   0.11   10.36
getSCEcoordinates           5.53   0.82    6.58
subsetByCNVprofile          6.08   0.16    6.24
findCNVs.strandseq          5.24   0.64    5.83
findCNVs                    5.03   0.67    5.70
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/AneuFinder.Rcheck/00check.log'
for details.


Installation output

AneuFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL AneuFinder
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'AneuFinder' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_interface.cpp -o R_interface.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c densities.cpp -o densities.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-AneuFinder/00new/AneuFinder/libs/x64
** 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
** 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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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              1
        61       -23711.580050            0.336591            0.255754              1
        62       -23711.244442            0.335609            0.254264              1
        63       -23710.909811            0.334631            0.252755              1
        64       -23710.576153            0.333657            0.251252              1
        65       -23710.243465            0.332688            0.249777              1
        66       -23709.911743            0.331722            0.248349              1
        67       -23709.580982            0.330761            0.247090              1
        68       -23709.251180            0.329802            0.245906              1
        69       -23708.922334            0.328846            0.244786              1
        70       -23708.594441            0.327893            0.243757              1
        71       -23708.267498            0.326942            0.242885              1
        72       -23707.941505            0.325993            0.242069              1
        73       -23707.616459            0.325046            0.241304              1
        74       -23707.292358            0.324101            0.240590              1
        75       -23706.969202            0.323156            0.239921              1
        76       -23706.646989            0.322213            0.239394              1
        77       -23706.325719            0.321271            0.239012              1
        78       -23706.005389            0.320329            0.238641              1
        79       -23705.686000            0.319389            0.238282              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
        80       -23705.367551            0.318449            0.237931              1
        81       -23705.050040            0.317511            0.237592              1
        82       -23704.733468            0.316573            0.237265              1
        83       -23704.417832            0.315635            0.236943              1
        84       -23704.103134            0.314699            0.236626              1
        85       -23703.789371            0.313763            0.236312              1
        86       -23703.476543            0.312828            0.236001              1
        87       -23703.164650            0.311893            0.235693              1
        88       -23702.853691            0.310959            0.235387              1
        89       -23702.543664            0.310026            0.235083              1
        90       -23702.234570            0.309094            0.234781              1
        91       -23701.926408            0.308163            0.234480              1
        92       -23701.619176            0.307232            0.234179              1
        93       -23701.312874            0.306302            0.233879              1
        94       -23701.007502            0.305372            0.233580              1
        95       -23700.703059            0.304444            0.233281              1
        96       -23700.399543            0.303516            0.232982              1
        97       -23700.096954            0.302589            0.232683              1
        98       -23699.795291            0.301663            0.232384              1
        99       -23699.494554            0.300737            0.232086              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       100       -23699.194741            0.299813            0.231789              1
       101       -23698.895853            0.298889            0.231491              1
       102       -23698.597887            0.297966            0.231193              1
       103       -23698.300843            0.297044            0.230895              1
       104       -23698.004721            0.296122            0.230596              1
       105       -23697.709519            0.295202            0.230296              1
       106       -23697.415236            0.294282            0.229997              1
       107       -23697.121873            0.293364            0.229697              1
       108       -23696.829427            0.292446            0.229396              1
       109       -23696.537897            0.291529            0.229095              1
       110       -23696.247284            0.290613            0.228793              1
       111       -23695.957586            0.289698            0.228491              1
       112       -23695.668802            0.288784            0.228189              1
       113       -23695.380931            0.287871            0.227886              1
       114       -23695.093972            0.286959            0.227582              1
       115       -23694.807925            0.286047            0.227278              1
       116       -23694.522788            0.285137            0.226973              1
       117       -23694.238560            0.284228            0.226668              1
       118       -23693.955240            0.283320            0.226362              1
       119       -23693.672828            0.282412            0.226056              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       120       -23693.391322            0.281506            0.225749              1
       121       -23693.110721            0.280601            0.225443              1
       122       -23692.831025            0.279696            0.225136              1
       123       -23692.552232            0.278793            0.224828              1
       124       -23692.274340            0.277891            0.224520              1
       125       -23691.997350            0.276990            0.224212              1
       126       -23691.721261            0.276090            0.223903              1
       127       -23691.446070            0.275191            0.223593              1
       128       -23691.171777            0.274293            0.223283              1
       129       -23690.898380            0.273396            0.222972              1
       130       -23690.625880            0.272501            0.222661              1
       131       -23690.354274            0.271606            0.222349              1
       132       -23690.083561            0.270713            0.222037              1
       133       -23689.813741            0.269820            0.221724              1
       134       -23689.544812            0.268929            0.221411              1
       135       -23689.276773            0.268039            0.221097              1
       136       -23689.009623            0.267150            0.220783              1
       137       -23688.743361            0.266262            0.220469              1
       138       -23688.477985            0.265376            0.220154              1
       139       -23688.213495            0.264490            0.219838              1
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       140       -23687.949889            0.263606            0.219522              1
       141       -23687.687165            0.262723            0.219206              1
       142       -23687.425324            0.261841            0.218889              1
       143       -23687.164363            0.260961            0.218571              1
       144       -23686.904282            0.260081            0.218253              1
       145       -23686.645079            0.259203            0.217935              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              2
       189       -23676.089372            0.221903            0.203574              2
       190       -23675.868284            0.221088            0.203241              2
       191       -23675.648009            0.220275            0.202907              2
       192       -23675.428546            0.219463            0.202574              2
       193       -23675.209893            0.218653            0.202240              2
       194       -23674.992049            0.217844            0.201906              2
       195       -23674.775012            0.217037            0.201572              2
       196       -23674.558781            0.216232            0.201237              2
       197       -23674.343353            0.215428            0.200902              2
       198       -23674.128727            0.214626            0.200567              2
       199       -23673.914902            0.213825            0.200232              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       200       -23673.701877            0.213026            0.199897              2
       201       -23673.489648            0.212228            0.199562              2
       202       -23673.278216            0.211433            0.199226              2
       203       -23673.067577            0.210638            0.198890              2
       204       -23672.857731            0.209846            0.198554              2
       205       -23672.648676            0.209055            0.198218              2
       206       -23672.440411            0.208266            0.197882              2
       207       -23672.232933            0.207478            0.197545              2
       208       -23672.026241            0.206692            0.197208              2
       209       -23671.820333            0.205908            0.196871              2
       210       -23671.615208            0.205125            0.196534              2
       211       -23671.410864            0.204344            0.196198              2
       212       -23671.207299            0.203565            0.195861              2
       213       -23671.004512            0.202787            0.195525              2
       214       -23670.802501            0.202011            0.195188              2
       215       -23670.601265            0.201237            0.194851              2
       216       -23670.400800            0.200464            0.194514              2
       217       -23670.201107            0.199693            0.194176              2
       218       -23670.002183            0.198924            0.193839              2
       219       -23669.804027            0.198156            0.193501              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       220       -23669.606636            0.197391            0.193163              2
       221       -23669.410010            0.196627            0.192826              2
       222       -23669.214145            0.195864            0.192488              2
       223       -23669.019042            0.195104            0.192149              2
       224       -23668.824697            0.194345            0.191811              2
       225       -23668.631110            0.193587            0.191473              2
       226       -23668.438278            0.192832            0.191134              2
       227       -23668.246200            0.192078            0.190795              2
       228       -23668.054874            0.191326            0.190456              2
       229       -23667.864298            0.190576            0.190118              2
       230       -23667.674471            0.189827            0.189779              2
       231       -23667.485390            0.189081            0.189439              2
       232       -23667.297055            0.188336            0.189100              2
       233       -23667.109462            0.187592            0.188761              2
       234       -23666.922612            0.186851            0.188421              2
       235       -23666.736501            0.186111            0.188082              2
       236       -23666.551128            0.185373            0.187744              2
       237       -23666.366491            0.184637            0.187405              2
       238       -23666.182588            0.183902            0.187066              2
       239       -23665.999419            0.183170            0.186727              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       240       -23665.816980            0.182439            0.186388              2
       241       -23665.635270            0.181710            0.186049              2
       242       -23665.454288            0.180982            0.185710              2
       243       -23665.274031            0.180257            0.185370              2
       244       -23665.094498            0.179533            0.185031              2
       245       -23664.915686            0.178811            0.184692              2
       246       -23664.737595            0.178091            0.184352              2
       247       -23664.560223            0.177373            0.184013              2
       248       -23664.383566            0.176656            0.183674              2
       249       -23664.207625            0.175942            0.183335              2
       250       -23664.032396            0.175229            0.182996              2
       251       -23663.857879            0.174517            0.182657              2
       252       -23663.684071            0.173808            0.182318              2
       253       -23663.510970            0.173101            0.181979              2
       254       -23663.338575            0.172395            0.181641              2
       255       -23663.166884            0.171691            0.181302              2
       256       -23662.995894            0.170989            0.180963              2
       257       -23662.825605            0.170289            0.180624              2
       258       -23662.656015            0.169591            0.180285              2
       259       -23662.487121            0.168894            0.179946              2
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       260       -23662.318921            0.168199            0.179607              2
       261       -23662.151414            0.167507            0.179268              2
       262       -23661.984599            0.166816            0.178929              2
       263       -23661.818473            0.166126            0.178590              2
       264       -23661.653034            0.165439            0.178251              2
       265       -23661.488280            0.164754            0.177912              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              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              3
       359       -23648.795877            0.108641            0.146707              3
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
       360       -23648.687745            0.108132            0.146387              3
       361       -23648.580120            0.107625            0.146067              3
       362       -23648.473000            0.107120            0.145748              3
       363       -23648.366384            0.106616            0.145429              3
       364       -23648.260270            0.106114            0.145110              3
       365       -23648.154656            0.105614            0.144791              3
       366       -23648.049539            0.105116            0.144473              3
       367       -23647.944919            0.104620            0.144154              3
       368       -23647.840794            0.104126            0.143836              3
       369       -23647.737161            0.103633            0.143519              3
       370       -23647.634019            0.103142            0.143201              3
       371       -23647.531366            0.102653            0.142884              3
       372       -23647.429201            0.102165            0.142567              3
       373       -23647.327521            0.101680            0.142251              3
       374       -23647.226325            0.101196            0.141934              3
       375       -23647.125611            0.100714            0.141618              3
       376       -23647.025378            0.100234            0.141302              3
       377       -23646.925622            0.099755            0.140986              3
Convergence reached!
number of states = 12
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
 Iteration              log(P)             dlog(P)   Diff in posterior    Time in sec
         0                -inf                   -                   -              0
         1       -24380.580428                 inf         6183.000000              0
         2       -23357.275929         1023.304498          686.821642              0
         3       -23260.421975           96.853955          172.471538              0
         4       -23232.483517           27.938458          143.506687              0
         5       -23222.142294           10.341223           76.049323              0
         6       -23217.735527            4.406767           58.626866              0
         7       -23215.521320            2.214207           35.912568              0
         8       -23214.276947            1.244373           27.484487              0
         9       -23213.395549            0.881398           18.765222              0
        10       -23212.605307            0.790242           15.594210              0
        11       -23211.762729            0.842578           12.269889              0
        12       -23210.839848            0.922881           11.279480              0
        13       -23209.921053            0.918795            9.624877              0
        14       -23209.118734            0.802320            8.968506              0
        15       -23208.463874            0.654860            7.927086              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 
  16.53    8.89   26.14 

Example timings

AneuFinder.Rcheck/AneuFinder-Ex.timings

nameusersystemelapsed
Aneufinder000
annotateBreakpoints18.54 0.6319.51
bam2GRanges0.300.010.57
bed2GRanges0.840.070.91
binReads1.730.141.91
blacklist1.680.231.92
clusterByQuality3.000.204.83
clusterHMMs0.530.070.62
collapseBins2.810.122.94
colors0.080.000.07
compareMethods0.580.110.69
consensusSegments10.20 0.1110.36
correctGC160.51 4.34168.59
export000
filterSegments0.380.020.42
findCNVs5.030.675.70
findCNVs.strandseq5.240.645.83
fixedWidthBins0.070.030.11
getBreakpoints11.47 0.8112.27
getDistinctColors0.190.000.19
getQC2.000.052.04
getSCEcoordinates5.530.826.58
heatmapAneuploidies50.45 0.5651.04
heatmapGenomewide25.66 0.4530.48
heatmapGenomewideClusters30.14 0.6430.82
importBed1.700.031.75
karyotypeMeasures25.79 0.9126.79
loadFromFiles3.620.113.75
plotHeterogeneity30.08 0.7530.91
plot_pca1.140.111.26
refineBreakpoints51.80 1.5153.29
simulateReads192.73 7.75201.85
subsetByCNVprofile6.080.166.24
variableWidthBins4.300.204.51