Aaron Taudt
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/AneuFinder |
| Branch: master |
| Last Commit: f825933 |
| Last Changed Date: 2019-01-04 13:18:52 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:33:01 -0400 (Tue, 09 Apr 2019).
| Package 52/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AneuFinder 1.11.2 Aaron Taudt
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: AneuFinder |
| Version: 1.11.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AneuFinder_1.11.2.tar.gz |
| StartedAt: 2019-04-08 23:12:12 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:24:39 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 747.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AneuFinder.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AneuFinder_1.11.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AneuFinder.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.11.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AneuFinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simulateReads 86.750 7.292 95.042
refineBreakpoints 67.499 1.021 71.197
correctGC 55.449 3.844 60.779
heatmapAneuploidies 47.109 0.314 47.772
plotHeterogeneity 33.044 0.307 33.549
heatmapGenomewideClusters 31.609 0.124 32.033
karyotypeMeasures 29.892 0.263 30.394
heatmapGenomewide 26.202 0.352 26.768
annotateBreakpoints 19.117 0.847 21.953
getBreakpoints 13.246 0.824 16.176
consensusSegments 11.065 0.126 11.268
getSCEcoordinates 5.923 0.610 7.454
variableWidthBins 6.253 0.271 7.495
findCNVs.strandseq 5.490 0.536 7.051
findCNVs 4.744 0.886 6.614
subsetByCNVprofile 5.263 0.017 5.318
loadFromFiles 5.025 0.022 5.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.
AneuFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AneuFinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘AneuFinder’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_interface.cpp -o R_interface.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c densities.cpp -o densities.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c loghmm.cpp -o loghmm.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c utility.cpp -o utility.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/AneuFinder/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (AneuFinder)
AneuFinder.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(AneuFinder)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: cowplot
Loading required package: ggplot2
Attaching package: 'cowplot'
The following object is masked from 'package:ggplot2':
ggsave
Loading required package: AneuFinderData
Please visit https://github.com/ataudt/aneufinder for the latest bugfixes and features.
>
> test_check("AneuFinder")
number of states = 11
number of bins = 6183
maximum number of iterations = 1000
maximum running time = none
epsilon = 0.1
data mean = 58.8193, data variance = 486.587
Iteration log(P) dlog(P) Diff in posterior Time in sec
0 -inf - - 0
1 -24789.866771 inf 6183.000000 0
2 -23822.331670 967.535101 601.762712 0
3 -23761.771285 60.560384 131.281549 0
4 -23745.235666 16.535619 119.461404 0
5 -23738.238770 6.996896 63.831344 0
6 -23735.137871 3.100899 48.587399 0
7 -23733.451273 1.686598 29.803499 0
8 -23732.421572 1.029701 21.580983 0
9 -23731.674903 0.746669 14.186707 0
10 -23731.069920 0.604983 9.975381 0
11 -23730.527674 0.542246 7.021040 0
12 -23730.007090 0.520584 4.942881 0
13 -23729.480035 0.527055 3.803030 0
14 -23728.932681 0.547354 2.653912 0
15 -23728.372455 0.560226 2.141742 0
16 -23727.839017 0.533439 1.244299 0
17 -23727.367012 0.472005 1.109390 0
18 -23726.947097 0.419914 0.529456 0
19 -23726.552750 0.394348 0.602730 0
Iteration log(P) dlog(P) Diff in posterior Time in sec
20 -23726.169459 0.383291 0.302116 0
21 -23725.791510 0.377949 0.389827 0
22 -23725.416462 0.375048 0.244787 0
23 -23725.043233 0.373229 0.307572 0
24 -23724.671334 0.371899 0.240956 0
25 -23724.300551 0.370783 0.275223 0
26 -23723.930786 0.369765 0.245508 0
27 -23723.561998 0.368789 0.262164 0
28 -23723.194164 0.367834 0.248735 0
29 -23722.827276 0.366888 0.256570 0
30 -23722.461329 0.365947 0.250428 0
31 -23722.096319 0.365010 0.254042 0
32 -23721.732244 0.364076 0.251213 0
33 -23721.369100 0.363144 0.252844 0
34 -23721.006885 0.362214 0.251549 0
35 -23720.645598 0.361287 0.252622 0
36 -23720.285236 0.360362 0.252383 0
37 -23719.925796 0.359440 0.253123 0
38 -23719.567277 0.358519 0.253290 0
39 -23719.209677 0.357600 0.254027 0
Iteration log(P) dlog(P) Diff in posterior Time in sec
40 -23718.852994 0.356683 0.254590 0
41 -23718.497228 0.355766 0.255400 0
42 -23718.142378 0.354850 0.256151 1
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 2
146 -23686.386752 0.258326 0.217616 2
147 -23686.129301 0.257451 0.217297 2
148 -23685.872725 0.256576 0.216977 2
149 -23685.617022 0.255703 0.216657 2
150 -23685.362190 0.254831 0.216336 2
151 -23685.108229 0.253961 0.216015 2
152 -23684.855137 0.253092 0.215694 2
153 -23684.602914 0.252224 0.215372 2
154 -23684.351557 0.251357 0.215049 2
155 -23684.101065 0.250492 0.214727 2
156 -23683.851437 0.249628 0.214403 2
157 -23683.602672 0.248765 0.214080 2
158 -23683.354769 0.247904 0.213756 2
159 -23683.107725 0.247044 0.213432 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
160 -23682.861540 0.246185 0.213107 2
161 -23682.616213 0.245328 0.212782 2
162 -23682.371741 0.244472 0.212456 2
163 -23682.128124 0.243617 0.212131 2
164 -23681.885360 0.242764 0.211806 2
165 -23681.643448 0.241912 0.211480 2
166 -23681.402387 0.241062 0.211154 2
167 -23681.162174 0.240213 0.210828 2
168 -23680.922809 0.239365 0.210502 2
169 -23680.684291 0.238519 0.210175 2
170 -23680.446617 0.237674 0.209848 2
171 -23680.209786 0.236831 0.209520 2
172 -23679.973797 0.235989 0.209192 2
173 -23679.738649 0.235148 0.208864 2
174 -23679.504339 0.234309 0.208536 2
175 -23679.270868 0.233472 0.208207 2
176 -23679.038232 0.232636 0.207878 2
177 -23678.806431 0.231801 0.207548 2
178 -23678.575463 0.230968 0.207219 2
179 -23678.345326 0.230136 0.206889 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
180 -23678.116020 0.229306 0.206559 2
181 -23677.887543 0.228478 0.206228 2
182 -23677.659892 0.227650 0.205897 2
183 -23677.433067 0.226825 0.205566 2
184 -23677.207067 0.226001 0.205235 2
185 -23676.981889 0.225178 0.204903 2
186 -23676.757532 0.224357 0.204571 2
187 -23676.533994 0.223537 0.204239 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 3
266 -23661.324210 0.164070 0.177573 3
267 -23661.160822 0.163388 0.177234 3
268 -23660.998114 0.162708 0.176895 3
269 -23660.836084 0.162030 0.176556 3
270 -23660.674730 0.161354 0.176217 3
271 -23660.514051 0.160679 0.175879 3
272 -23660.354044 0.160007 0.175540 3
273 -23660.194708 0.159336 0.175202 3
274 -23660.036041 0.158667 0.174864 3
275 -23659.878041 0.158000 0.174526 3
276 -23659.720706 0.157335 0.174188 3
277 -23659.564034 0.156672 0.173851 3
278 -23659.408024 0.156010 0.173513 3
279 -23659.252673 0.155351 0.173175 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
280 -23659.097980 0.154693 0.172838 3
281 -23658.943943 0.154037 0.172500 3
282 -23658.790560 0.153383 0.172162 3
283 -23658.637828 0.152731 0.171825 3
284 -23658.485747 0.152081 0.171488 3
285 -23658.334315 0.151433 0.171150 3
286 -23658.183528 0.150786 0.170813 3
287 -23658.033387 0.150142 0.170476 3
288 -23657.883888 0.149499 0.170139 3
289 -23657.735030 0.148858 0.169802 3
290 -23657.586811 0.148219 0.169465 3
291 -23657.439229 0.147582 0.169128 3
292 -23657.292283 0.146947 0.168792 3
293 -23657.145969 0.146313 0.168455 3
294 -23657.000288 0.145682 0.168119 3
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 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 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 1
12 -20169.145246 1.839014 14.930161 1
13 -20166.835634 2.309613 16.942694 1
14 -20163.895031 2.940602 18.691149 1
15 -20160.410970 3.484061 18.008358 1
16 -20157.717749 2.693221 14.496841 1
17 -20156.213293 1.504456 10.220281 1
18 -20155.444668 0.768625 7.026993 1
19 -20155.094478 0.350190 4.771865 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
20 -20154.925350 0.169128 3.076403 1
21 -20154.827513 0.097837 1.932927 1
Convergence reached!
══ testthat results ═══════════════════════════════════════════════════════════
OK: 12 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
17.370 0.561 18.080
AneuFinder.Rcheck/AneuFinder-Ex.timings
| name | user | system | elapsed | |
| Aneufinder | 0 | 0 | 0 | |
| annotateBreakpoints | 19.117 | 0.847 | 21.953 | |
| bam2GRanges | 0.418 | 0.023 | 0.443 | |
| bed2GRanges | 1.157 | 0.080 | 2.116 | |
| binReads | 2.862 | 0.223 | 4.292 | |
| blacklist | 2.200 | 0.081 | 3.384 | |
| clusterByQuality | 2.754 | 0.061 | 2.851 | |
| clusterHMMs | 0.485 | 0.029 | 0.519 | |
| collapseBins | 2.302 | 0.247 | 3.532 | |
| colors | 0.050 | 0.002 | 0.054 | |
| compareMethods | 0.529 | 0.020 | 0.551 | |
| consensusSegments | 11.065 | 0.126 | 11.268 | |
| correctGC | 55.449 | 3.844 | 60.779 | |
| export | 0.000 | 0.000 | 0.001 | |
| filterSegments | 0.284 | 0.013 | 0.297 | |
| findCNVs | 4.744 | 0.886 | 6.614 | |
| findCNVs.strandseq | 5.490 | 0.536 | 7.051 | |
| fixedWidthBins | 0.085 | 0.006 | 0.953 | |
| getBreakpoints | 13.246 | 0.824 | 16.176 | |
| getDistinctColors | 0.031 | 0.004 | 0.035 | |
| getQC | 0.896 | 0.015 | 0.914 | |
| getSCEcoordinates | 5.923 | 0.610 | 7.454 | |
| heatmapAneuploidies | 47.109 | 0.314 | 47.772 | |
| heatmapGenomewide | 26.202 | 0.352 | 26.768 | |
| heatmapGenomewideClusters | 31.609 | 0.124 | 32.033 | |
| importBed | 1.753 | 0.057 | 1.820 | |
| karyotypeMeasures | 29.892 | 0.263 | 30.394 | |
| loadFromFiles | 5.025 | 0.022 | 5.087 | |
| plotHeterogeneity | 33.044 | 0.307 | 33.549 | |
| plot_pca | 1.160 | 0.031 | 1.203 | |
| refineBreakpoints | 67.499 | 1.021 | 71.197 | |
| simulateReads | 86.750 | 7.292 | 95.042 | |
| subsetByCNVprofile | 5.263 | 0.017 | 5.318 | |
| variableWidthBins | 6.253 | 0.271 | 7.495 | |