Aaron Taudt
| Snapshot Date: 2025-01-21 13:40 -0500 (Tue, 21 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/AneuFinder |
| git_branch: devel |
| git_last_commit: 42b7837 |
| git_last_commit_date: 2024-10-29 10:08:55 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-22 11:41 -0500 (Wed, 22 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4779 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4503 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4468 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4423 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4407 |
| 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 65/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AneuFinder 1.35.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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. |
| Package: AneuFinder |
| Version: 1.35.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AneuFinder.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings AneuFinder_1.35.0.tar.gz |
| StartedAt: 2025-01-21 22:34:10 -0500 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 22:51:19 -0500 (Tue, 21 Jan 2025) |
| EllapsedTime: 1028.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AneuFinder.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AneuFinder.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings AneuFinder_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 '1.35.0'
* 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) 13.3.0'
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Aneufinder.Rd: GRanges-class
DNAcopy.findCNVs.Rd: GRanges-class
HMM.findCNVs.Rd: GRanges-class, GRangesList
aneuBiHMM.Rd: GRanges-class
aneuHMM.Rd: GRanges-class
annotateBreakpoints.Rd: GRanges-class
bam2GRanges.Rd: GRanges-class
bed2GRanges.Rd: GRanges-class
bi.edivisive.findCNVs.Rd: e.divisive, GRanges-class
biDNAcopy.findCNVs.Rd: GRanges-class
biHMM.findCNVs.Rd: GRanges-class, GRangesList
binReads.Rd: GRanges-class, GenomicRanges, GRangesList
binned.data.Rd: GRanges-class
blacklist.Rd: GRanges-class
clusterByQuality.Rd: mclust
clusterHMMs.Rd: GRanges-class
edivisive.findCNVs.Rd: e.divisive, GRanges-class
estimateComplexity.Rd: GRanges-class
export.Rd: GRanges-class
filterSegments.Rd: GRanges-class
findCNVs.Rd: GRanges-class
findCNVs.strandseq.Rd: GRanges-class
findHotspots.Rd: GRanges-class
fixedWidthBins.Rd: GRanges-class, GRangesList
getBreakpoints.Rd: GRanges-class
getQC.Rd: GRanges-class
getSCEcoordinates.Rd: GRanges-class
heatmapGenomewide.Rd: GRanges-class
hotspotter.Rd: GRanges-class
hotspotter.variable.Rd: GRanges-class
importBed.Rd: GRanges-class
karyotypeMeasures.Rd: GRanges-class
loadFromFiles.Rd: GRanges-class, GRangesList
mergeStrandseqFiles.Rd: GRanges-class
plot.GRanges.Rd: GRanges-class
plot.GRangesList.Rd: GRangesList
plotHeterogeneity.Rd: GRanges-class
plot_pca.Rd: GRanges-class
refineBreakpoints.Rd: GRanges-class
subsetByCNVprofile.Rd: GRanges-class
transCoord.Rd: GRanges-class
variableWidthBins.Rd: GRanges-class, GRangesList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 'E:/biocbuild/bbs-3.21-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 218.00 6.37 224.84
correctGC 174.42 3.60 178.52
refineBreakpoints 58.33 1.28 59.68
heatmapAneuploidies 54.49 0.47 54.95
plotHeterogeneity 35.64 0.75 36.39
heatmapGenomewideClusters 29.48 0.34 37.55
karyotypeMeasures 28.03 0.61 30.31
heatmapGenomewide 25.89 0.36 28.53
annotateBreakpoints 17.96 0.53 19.02
getBreakpoints 13.61 0.70 14.34
consensusSegments 10.25 0.14 10.39
getSCEcoordinates 7.37 0.44 8.10
subsetByCNVprofile 6.72 0.10 6.81
findCNVs.strandseq 5.54 0.46 5.98
findCNVs 4.94 0.51 5.45
variableWidthBins 5.04 0.18 5.24
* 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: 3 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck/00check.log'
for details.
AneuFinder.Rcheck/00install.out
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL AneuFinder
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'AneuFinder' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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)
AneuFinder.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 1
44 -23717.435431 0.353014 0.258100 1
45 -23717.083339 0.352092 0.259094 1
46 -23716.732173 0.351166 0.260034 1
47 -23716.381938 0.350235 0.260935 1
48 -23716.032640 0.349298 0.261735 1
49 -23715.684287 0.348353 0.262424 1
50 -23715.336886 0.347401 0.262956 1
51 -23714.990445 0.346441 0.263312 1
52 -23714.644972 0.345473 0.263463 1
53 -23714.300474 0.344498 0.263396 1
54 -23713.956958 0.343516 0.263103 1
55 -23713.614428 0.342530 0.262584 1
56 -23713.272887 0.341540 0.261849 1
57 -23712.932339 0.340548 0.260917 1
58 -23712.592783 0.339556 0.259810 1
59 -23712.254217 0.338565 0.258559 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
60 -23711.916641 0.337576 0.257196 1
61 -23711.580050 0.336591 0.255754 1
62 -23711.244442 0.335609 0.254264 1
63 -23710.909811 0.334631 0.252755 1
64 -23710.576153 0.333657 0.251252 1
65 -23710.243465 0.332688 0.249777 1
66 -23709.911743 0.331722 0.248349 1
67 -23709.580982 0.330761 0.247090 1
68 -23709.251180 0.329802 0.245906 1
69 -23708.922334 0.328846 0.244786 1
70 -23708.594441 0.327893 0.243757 1
71 -23708.267498 0.326942 0.242885 1
72 -23707.941505 0.325993 0.242069 1
73 -23707.616459 0.325046 0.241304 1
74 -23707.292358 0.324101 0.240590 1
75 -23706.969202 0.323156 0.239921 1
76 -23706.646989 0.322213 0.239394 1
77 -23706.325719 0.321271 0.239012 1
78 -23706.005389 0.320329 0.238641 1
79 -23705.686000 0.319389 0.238282 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
80 -23705.367551 0.318449 0.237931 1
81 -23705.050040 0.317511 0.237592 1
82 -23704.733468 0.316573 0.237265 1
83 -23704.417832 0.315635 0.236943 1
84 -23704.103134 0.314699 0.236626 1
85 -23703.789371 0.313763 0.236312 1
86 -23703.476543 0.312828 0.236001 1
87 -23703.164650 0.311893 0.235693 1
88 -23702.853691 0.310959 0.235387 1
89 -23702.543664 0.310026 0.235083 1
90 -23702.234570 0.309094 0.234781 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 2
163 -23682.128124 0.243617 0.212131 2
164 -23681.885360 0.242764 0.211806 2
165 -23681.643448 0.241912 0.211480 2
166 -23681.402387 0.241062 0.211154 2
167 -23681.162174 0.240213 0.210828 2
168 -23680.922809 0.239365 0.210502 2
169 -23680.684291 0.238519 0.210175 2
170 -23680.446617 0.237674 0.209848 2
171 -23680.209786 0.236831 0.209520 2
172 -23679.973797 0.235989 0.209192 2
173 -23679.738649 0.235148 0.208864 2
174 -23679.504339 0.234309 0.208536 2
175 -23679.270868 0.233472 0.208207 2
176 -23679.038232 0.232636 0.207878 2
177 -23678.806431 0.231801 0.207548 2
178 -23678.575463 0.230968 0.207219 2
179 -23678.345326 0.230136 0.206889 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
180 -23678.116020 0.229306 0.206559 2
181 -23677.887543 0.228478 0.206228 2
182 -23677.659892 0.227650 0.205897 2
183 -23677.433067 0.226825 0.205566 2
184 -23677.207067 0.226001 0.205235 2
185 -23676.981889 0.225178 0.204903 2
186 -23676.757532 0.224357 0.204571 2
187 -23676.533994 0.223537 0.204239 2
188 -23676.311275 0.222719 0.203906 2
189 -23676.089372 0.221903 0.203574 2
190 -23675.868284 0.221088 0.203241 2
191 -23675.648009 0.220275 0.202907 2
192 -23675.428546 0.219463 0.202574 2
193 -23675.209893 0.218653 0.202240 2
194 -23674.992049 0.217844 0.201906 2
195 -23674.775012 0.217037 0.201572 2
196 -23674.558781 0.216232 0.201237 2
197 -23674.343353 0.215428 0.200902 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 3
296 -23656.710811 0.144424 0.167447 3
297 -23656.567013 0.143798 0.167111 3
298 -23656.423838 0.143174 0.166775 3
299 -23656.281286 0.142552 0.166439 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
300 -23656.139354 0.141932 0.166104 3
301 -23655.998040 0.141314 0.165768 3
302 -23655.857343 0.140697 0.165433 3
303 -23655.717260 0.140083 0.165098 3
304 -23655.577790 0.139470 0.164763 3
305 -23655.438931 0.138859 0.164428 3
306 -23655.300681 0.138250 0.164094 3
307 -23655.163038 0.137643 0.163759 3
308 -23655.026000 0.137038 0.163425 3
309 -23654.889566 0.136434 0.163091 3
310 -23654.753733 0.135833 0.162757 3
311 -23654.618500 0.135233 0.162423 3
312 -23654.483864 0.134635 0.162089 3
313 -23654.349825 0.134040 0.161755 3
314 -23654.216379 0.133446 0.161422 3
315 -23654.083526 0.132854 0.161089 3
316 -23653.951262 0.132263 0.160756 3
317 -23653.819587 0.131675 0.160423 3
318 -23653.688499 0.131088 0.160090 3
319 -23653.557995 0.130504 0.159757 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
320 -23653.428074 0.129921 0.159425 3
321 -23653.298734 0.129340 0.159092 3
322 -23653.169973 0.128761 0.158760 3
323 -23653.041789 0.128184 0.158428 3
324 -23652.914180 0.127609 0.158097 3
325 -23652.787145 0.127035 0.157765 3
326 -23652.660681 0.126464 0.157434 3
327 -23652.534787 0.125894 0.157103 3
328 -23652.409461 0.125326 0.156771 3
329 -23652.284700 0.124760 0.156441 3
330 -23652.160504 0.124196 0.156110 3
331 -23652.036870 0.123634 0.155780 3
332 -23651.913797 0.123074 0.155452 3
333 -23651.791282 0.122515 0.155124 3
334 -23651.669323 0.121958 0.154796 3
335 -23651.547920 0.121404 0.154469 3
336 -23651.427069 0.120851 0.154142 3
337 -23651.306769 0.120300 0.153815 3
338 -23651.187019 0.119750 0.153488 3
339 -23651.067816 0.119203 0.153161 3
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 12.269889 1
12 -23210.839848 0.922881 11.279480 1
13 -23209.921053 0.918795 9.624877 1
14 -23209.118734 0.802320 8.968506 1
15 -23208.463874 0.654860 7.927086 1
16 -23207.924958 0.538916 7.683630 1
17 -23207.463600 0.461358 7.238144 1
18 -23207.046263 0.417337 7.327465 1
19 -23206.646001 0.400262 7.466156 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
20 -23206.242687 0.403315 7.882758 1
21 -23205.828261 0.414426 8.254388 1
22 -23205.414415 0.413846 8.474710 1
23 -23205.032476 0.381939 8.244365 1
24 -23204.714716 0.317760 7.544341 1
25 -23204.473698 0.241018 6.506549 1
26 -23204.300805 0.172894 5.379661 1
27 -23204.178183 0.122622 4.308309 1
28 -23204.088739 0.089444 3.383929 1
Convergence reached!
number of states = 11
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
Iteration log(P) dlog(P) Diff in posterior Time in sec
0 -inf - - 0
1 -21177.150641 inf 5442.000000 0
2 -20711.054012 466.096629 390.505270 0
3 -20693.275989 17.778024 85.372131 0
4 -20690.239855 3.036134 33.071291 0
5 -20689.163935 1.075919 26.872093 0
6 -20688.762950 0.400986 12.127422 0
7 -20688.580230 0.182719 8.966009 0
8 -20688.472739 0.107491 4.304038 0
9 -20688.396085 0.076655 3.087959 0
Convergence reached!
number of states = 12
number of bins = 5442
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 63.9717, data variance = 1059.32
Iteration log(P) dlog(P) Diff in posterior Time in sec
0 -inf - - 0
1 -20778.885904 inf 5442.000000 0
2 -20214.840926 564.044978 503.589244 0
3 -20185.942950 28.897975 137.261825 0
4 -20179.925587 6.017363 51.421390 0
5 -20177.170587 2.755000 36.836764 0
6 -20175.645594 1.524994 18.722502 0
7 -20174.658989 0.986605 13.124839 0
8 -20173.895734 0.763255 11.327572 0
9 -20173.167941 0.727793 9.948167 0
10 -20172.282987 0.884954 11.162019 0
11 -20170.984261 1.298726 12.412190 0
12 -20169.145246 1.839014 14.930161 0
13 -20166.835634 2.309613 16.942694 0
14 -20163.895031 2.940602 18.691149 0
15 -20160.410970 3.484061 18.008358 0
16 -20157.717749 2.693221 14.496841 0
17 -20156.213293 1.504456 10.220281 0
18 -20155.444668 0.768625 7.026993 0
19 -20155.094478 0.350190 4.771865 0
Iteration log(P) dlog(P) Diff in posterior Time in sec
20 -20154.925350 0.169128 3.076403 0
21 -20154.827513 0.097837 1.932927 0
Convergence reached!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
>
> proc.time()
user system elapsed
17.79 0.84 19.01
AneuFinder.Rcheck/AneuFinder-Ex.timings
| name | user | system | elapsed | |
| Aneufinder | 0 | 0 | 0 | |
| annotateBreakpoints | 17.96 | 0.53 | 19.02 | |
| bam2GRanges | 0.42 | 0.02 | 0.47 | |
| bed2GRanges | 1.95 | 0.04 | 2.00 | |
| binReads | 2.25 | 0.07 | 2.31 | |
| blacklist | 2.31 | 0.06 | 2.37 | |
| clusterByQuality | 3.32 | 0.05 | 4.55 | |
| clusterHMMs | 0.61 | 0.03 | 0.64 | |
| collapseBins | 2.20 | 0.18 | 2.39 | |
| colors | 0.06 | 0.02 | 0.08 | |
| compareMethods | 0.64 | 0.14 | 0.78 | |
| consensusSegments | 10.25 | 0.14 | 10.39 | |
| correctGC | 174.42 | 3.60 | 178.52 | |
| export | 0 | 0 | 0 | |
| filterSegments | 0.24 | 0.06 | 0.30 | |
| findCNVs | 4.94 | 0.51 | 5.45 | |
| findCNVs.strandseq | 5.54 | 0.46 | 5.98 | |
| fixedWidthBins | 0.08 | 0.00 | 0.08 | |
| getBreakpoints | 13.61 | 0.70 | 14.34 | |
| getDistinctColors | 0.19 | 0.00 | 0.19 | |
| getQC | 2.12 | 0.03 | 2.16 | |
| getSCEcoordinates | 7.37 | 0.44 | 8.10 | |
| heatmapAneuploidies | 54.49 | 0.47 | 54.95 | |
| heatmapGenomewide | 25.89 | 0.36 | 28.53 | |
| heatmapGenomewideClusters | 29.48 | 0.34 | 37.55 | |
| importBed | 1.60 | 0.03 | 1.66 | |
| karyotypeMeasures | 28.03 | 0.61 | 30.31 | |
| loadFromFiles | 4.15 | 0.03 | 4.19 | |
| plotHeterogeneity | 35.64 | 0.75 | 36.39 | |
| plot_pca | 1.13 | 0.10 | 1.21 | |
| refineBreakpoints | 58.33 | 1.28 | 59.68 | |
| simulateReads | 218.00 | 6.37 | 224.84 | |
| subsetByCNVprofile | 6.72 | 0.10 | 6.81 | |
| variableWidthBins | 5.04 | 0.18 | 5.24 | |