Aaron Taudt
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/AneuFinder |
| Branch: RELEASE_3_9 |
| Last Commit: e788fd0 |
| Last Changed Date: 2019-07-20 06:41:41 -0400 (Sat, 20 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:57:33 -0400 (Wed, 16 Oct 2019).
| Package 53/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AneuFinder 1.12.1 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 | |
| Package: AneuFinder |
| Version: 1.12.1 |
| 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_1.12.1.tar.gz |
| StartedAt: 2019-10-16 00:29:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:45:56 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 963.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AneuFinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AneuFinder.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.1’
* 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 91.601 13.634 105.537
refineBreakpoints 99.569 1.993 103.817
correctGC 59.830 7.794 69.314
heatmapAneuploidies 59.950 0.225 60.181
plotHeterogeneity 48.341 0.587 48.934
heatmapGenomewideClusters 39.161 0.509 39.676
karyotypeMeasures 36.748 0.476 37.225
heatmapGenomewide 35.199 0.662 35.888
annotateBreakpoints 26.388 1.855 30.510
getBreakpoints 19.857 1.659 24.568
consensusSegments 11.330 0.159 11.489
variableWidthBins 8.748 0.663 10.543
findCNVs 7.422 1.719 10.439
findCNVs.strandseq 7.486 1.055 9.768
getSCEcoordinates 7.296 1.218 9.556
loadFromFiles 7.691 0.031 7.739
subsetByCNVprofile 7.510 0.035 7.657
* 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’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/00LOCK-AneuFinder/00new/AneuFinder/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AneuFinder)
AneuFinder.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, 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: ggplot2
Loading required package: cowplot
********************************************************
Note: As of version 1.0.0, cowplot does not change the
default ggplot2 theme anymore. To recover the previous
behavior, execute:
theme_set(theme_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 1
12 -23730.007090 0.520584 4.942881 1
13 -23729.480035 0.527055 3.803030 1
14 -23728.932681 0.547354 2.653912 1
15 -23728.372455 0.560226 2.141742 1
16 -23727.839017 0.533439 1.244299 1
17 -23727.367012 0.472005 1.109390 1
18 -23726.947097 0.419914 0.529456 1
19 -23726.552750 0.394348 0.602730 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
20 -23726.169459 0.383291 0.302116 1
21 -23725.791510 0.377949 0.389827 1
22 -23725.416462 0.375048 0.244787 1
23 -23725.043233 0.373229 0.307572 1
24 -23724.671334 0.371899 0.240956 1
25 -23724.300551 0.370783 0.275223 1
26 -23723.930786 0.369765 0.245508 1
27 -23723.561998 0.368789 0.262164 1
28 -23723.194164 0.367834 0.248735 1
29 -23722.827276 0.366888 0.256570 1
30 -23722.461329 0.365947 0.250428 1
31 -23722.096319 0.365010 0.254042 1
32 -23721.732244 0.364076 0.251213 1
33 -23721.369100 0.363144 0.252844 1
34 -23721.006885 0.362214 0.251549 1
35 -23720.645598 0.361287 0.252622 1
36 -23720.285236 0.360362 0.252383 1
37 -23719.925796 0.359440 0.253123 1
38 -23719.567277 0.358519 0.253290 1
39 -23719.209677 0.357600 0.254027 1
Iteration log(P) dlog(P) Diff in posterior Time in sec
40 -23718.852994 0.356683 0.254590 1
41 -23718.497228 0.355766 0.255400 1
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 2
91 -23701.926408 0.308163 0.234480 2
92 -23701.619176 0.307232 0.234179 2
93 -23701.312874 0.306302 0.233879 2
94 -23701.007502 0.305372 0.233580 2
95 -23700.703059 0.304444 0.233281 2
96 -23700.399543 0.303516 0.232982 2
97 -23700.096954 0.302589 0.232683 2
98 -23699.795291 0.301663 0.232384 2
99 -23699.494554 0.300737 0.232086 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
100 -23699.194741 0.299813 0.231789 2
101 -23698.895853 0.298889 0.231491 2
102 -23698.597887 0.297966 0.231193 2
103 -23698.300843 0.297044 0.230895 2
104 -23698.004721 0.296122 0.230596 2
105 -23697.709519 0.295202 0.230296 2
106 -23697.415236 0.294282 0.229997 2
107 -23697.121873 0.293364 0.229697 2
108 -23696.829427 0.292446 0.229396 2
109 -23696.537897 0.291529 0.229095 2
110 -23696.247284 0.290613 0.228793 2
111 -23695.957586 0.289698 0.228491 2
112 -23695.668802 0.288784 0.228189 2
113 -23695.380931 0.287871 0.227886 2
114 -23695.093972 0.286959 0.227582 2
115 -23694.807925 0.286047 0.227278 2
116 -23694.522788 0.285137 0.226973 2
117 -23694.238560 0.284228 0.226668 2
118 -23693.955240 0.283320 0.226362 2
119 -23693.672828 0.282412 0.226056 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
120 -23693.391322 0.281506 0.225749 2
121 -23693.110721 0.280601 0.225443 2
122 -23692.831025 0.279696 0.225136 2
123 -23692.552232 0.278793 0.224828 2
124 -23692.274340 0.277891 0.224520 2
125 -23691.997350 0.276990 0.224212 2
126 -23691.721261 0.276090 0.223903 2
127 -23691.446070 0.275191 0.223593 2
128 -23691.171777 0.274293 0.223283 2
129 -23690.898380 0.273396 0.222972 2
130 -23690.625880 0.272501 0.222661 2
131 -23690.354274 0.271606 0.222349 2
132 -23690.083561 0.270713 0.222037 2
133 -23689.813741 0.269820 0.221724 2
134 -23689.544812 0.268929 0.221411 2
135 -23689.276773 0.268039 0.221097 2
136 -23689.009623 0.267150 0.220783 2
137 -23688.743361 0.266262 0.220469 2
138 -23688.477985 0.265376 0.220154 2
139 -23688.213495 0.264490 0.219838 2
Iteration log(P) dlog(P) Diff in posterior Time in sec
140 -23687.949889 0.263606 0.219522 2
141 -23687.687165 0.262723 0.219206 2
142 -23687.425324 0.261841 0.218889 2
143 -23687.164363 0.260961 0.218571 2
144 -23686.904282 0.260081 0.218253 2
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 3
198 -23674.128727 0.214626 0.200567 3
199 -23673.914902 0.213825 0.200232 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
200 -23673.701877 0.213026 0.199897 3
201 -23673.489648 0.212228 0.199562 3
202 -23673.278216 0.211433 0.199226 3
203 -23673.067577 0.210638 0.198890 3
204 -23672.857731 0.209846 0.198554 3
205 -23672.648676 0.209055 0.198218 3
206 -23672.440411 0.208266 0.197882 3
207 -23672.232933 0.207478 0.197545 3
208 -23672.026241 0.206692 0.197208 3
209 -23671.820333 0.205908 0.196871 3
210 -23671.615208 0.205125 0.196534 3
211 -23671.410864 0.204344 0.196198 3
212 -23671.207299 0.203565 0.195861 3
213 -23671.004512 0.202787 0.195525 3
214 -23670.802501 0.202011 0.195188 3
215 -23670.601265 0.201237 0.194851 3
216 -23670.400800 0.200464 0.194514 3
217 -23670.201107 0.199693 0.194176 3
218 -23670.002183 0.198924 0.193839 3
219 -23669.804027 0.198156 0.193501 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
220 -23669.606636 0.197391 0.193163 3
221 -23669.410010 0.196627 0.192826 3
222 -23669.214145 0.195864 0.192488 3
223 -23669.019042 0.195104 0.192149 3
224 -23668.824697 0.194345 0.191811 3
225 -23668.631110 0.193587 0.191473 3
226 -23668.438278 0.192832 0.191134 3
227 -23668.246200 0.192078 0.190795 3
228 -23668.054874 0.191326 0.190456 3
229 -23667.864298 0.190576 0.190118 3
230 -23667.674471 0.189827 0.189779 3
231 -23667.485390 0.189081 0.189439 3
232 -23667.297055 0.188336 0.189100 3
233 -23667.109462 0.187592 0.188761 3
234 -23666.922612 0.186851 0.188421 3
235 -23666.736501 0.186111 0.188082 3
236 -23666.551128 0.185373 0.187744 3
237 -23666.366491 0.184637 0.187405 3
238 -23666.182588 0.183902 0.187066 3
239 -23665.999419 0.183170 0.186727 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
240 -23665.816980 0.182439 0.186388 3
241 -23665.635270 0.181710 0.186049 3
242 -23665.454288 0.180982 0.185710 3
243 -23665.274031 0.180257 0.185370 3
244 -23665.094498 0.179533 0.185031 3
245 -23664.915686 0.178811 0.184692 3
246 -23664.737595 0.178091 0.184352 3
247 -23664.560223 0.177373 0.184013 3
248 -23664.383566 0.176656 0.183674 3
249 -23664.207625 0.175942 0.183335 3
250 -23664.032396 0.175229 0.182996 3
251 -23663.857879 0.174517 0.182657 3
252 -23663.684071 0.173808 0.182318 3
253 -23663.510970 0.173101 0.181979 3
254 -23663.338575 0.172395 0.181641 3
255 -23663.166884 0.171691 0.181302 3
256 -23662.995894 0.170989 0.180963 3
257 -23662.825605 0.170289 0.180624 3
258 -23662.656015 0.169591 0.180285 3
259 -23662.487121 0.168894 0.179946 3
Iteration log(P) dlog(P) Diff in posterior Time in sec
260 -23662.318921 0.168199 0.179607 3
261 -23662.151414 0.167507 0.179268 3
262 -23661.984599 0.166816 0.178929 3
263 -23661.818473 0.166126 0.178590 3
264 -23661.653034 0.165439 0.178251 3
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 4
Iteration log(P) dlog(P) Diff in posterior Time in sec
320 -23653.428074 0.129921 0.159425 4
321 -23653.298734 0.129340 0.159092 4
322 -23653.169973 0.128761 0.158760 4
323 -23653.041789 0.128184 0.158428 4
324 -23652.914180 0.127609 0.158097 4
325 -23652.787145 0.127035 0.157765 4
326 -23652.660681 0.126464 0.157434 4
327 -23652.534787 0.125894 0.157103 4
328 -23652.409461 0.125326 0.156771 4
329 -23652.284700 0.124760 0.156441 4
330 -23652.160504 0.124196 0.156110 4
331 -23652.036870 0.123634 0.155780 4
332 -23651.913797 0.123074 0.155452 4
333 -23651.791282 0.122515 0.155124 4
334 -23651.669323 0.121958 0.154796 4
335 -23651.547920 0.121404 0.154469 4
336 -23651.427069 0.120851 0.154142 4
337 -23651.306769 0.120300 0.153815 4
338 -23651.187019 0.119750 0.153488 4
339 -23651.067816 0.119203 0.153161 4
Iteration log(P) dlog(P) Diff in posterior Time in sec
340 -23650.949159 0.118657 0.152835 4
341 -23650.831045 0.118114 0.152509 4
342 -23650.713473 0.117572 0.152183 4
343 -23650.596442 0.117032 0.151857 4
344 -23650.479948 0.116494 0.151534 4
345 -23650.363991 0.115957 0.151210 4
346 -23650.248568 0.115423 0.150887 4
347 -23650.133678 0.114890 0.150564 4
348 -23650.019319 0.114359 0.150242 4
349 -23649.905488 0.113830 0.149919 4
350 -23649.792185 0.113303 0.149597 4
351 -23649.679407 0.112778 0.149275 4
352 -23649.567153 0.112254 0.148953 4
353 -23649.455420 0.111733 0.148632 4
354 -23649.344207 0.111213 0.148310 4
355 -23649.233512 0.110695 0.147989 4
356 -23649.123334 0.110179 0.147668 4
357 -23649.013670 0.109664 0.147348 4
358 -23648.904518 0.109152 0.147027 4
359 -23648.795877 0.108641 0.146707 4
Iteration log(P) dlog(P) Diff in posterior Time in sec
360 -23648.687745 0.108132 0.146387 4
361 -23648.580120 0.107625 0.146067 4
362 -23648.473000 0.107120 0.145748 4
363 -23648.366384 0.106616 0.145429 4
364 -23648.260270 0.106114 0.145110 4
365 -23648.154656 0.105614 0.144791 4
366 -23648.049539 0.105116 0.144473 4
367 -23647.944919 0.104620 0.144154 4
368 -23647.840794 0.104126 0.143836 4
369 -23647.737161 0.103633 0.143519 4
370 -23647.634019 0.103142 0.143201 4
371 -23647.531366 0.102653 0.142884 4
372 -23647.429201 0.102165 0.142567 4
373 -23647.327521 0.101680 0.142251 4
374 -23647.226325 0.101196 0.141934 4
375 -23647.125611 0.100714 0.141618 4
376 -23647.025378 0.100234 0.141302 4
377 -23646.925622 0.099755 0.140986 4
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 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!
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
21.414 1.303 22.668
AneuFinder.Rcheck/AneuFinder-Ex.timings
| name | user | system | elapsed | |
| Aneufinder | 0.001 | 0.000 | 0.000 | |
| annotateBreakpoints | 26.388 | 1.855 | 30.510 | |
| bam2GRanges | 0.567 | 0.042 | 0.619 | |
| bed2GRanges | 1.748 | 0.182 | 3.005 | |
| binReads | 2.334 | 0.374 | 3.779 | |
| blacklist | 2.843 | 0.192 | 4.195 | |
| clusterByQuality | 2.269 | 0.146 | 2.442 | |
| clusterHMMs | 0.566 | 0.054 | 0.621 | |
| collapseBins | 2.941 | 0.503 | 4.501 | |
| colors | 0.052 | 0.004 | 0.056 | |
| compareMethods | 0.767 | 0.062 | 0.829 | |
| consensusSegments | 11.330 | 0.159 | 11.489 | |
| correctGC | 59.830 | 7.794 | 69.314 | |
| export | 0.000 | 0.001 | 0.000 | |
| filterSegments | 0.444 | 0.025 | 0.470 | |
| findCNVs | 7.422 | 1.719 | 10.439 | |
| findCNVs.strandseq | 7.486 | 1.055 | 9.768 | |
| fixedWidthBins | 0.085 | 0.010 | 1.135 | |
| getBreakpoints | 19.857 | 1.659 | 24.568 | |
| getDistinctColors | 0.046 | 0.008 | 0.053 | |
| getQC | 1.191 | 0.037 | 1.228 | |
| getSCEcoordinates | 7.296 | 1.218 | 9.556 | |
| heatmapAneuploidies | 59.950 | 0.225 | 60.181 | |
| heatmapGenomewide | 35.199 | 0.662 | 35.888 | |
| heatmapGenomewideClusters | 39.161 | 0.509 | 39.676 | |
| importBed | 2.000 | 0.116 | 2.116 | |
| karyotypeMeasures | 36.748 | 0.476 | 37.225 | |
| loadFromFiles | 7.691 | 0.031 | 7.739 | |
| plotHeterogeneity | 48.341 | 0.587 | 48.934 | |
| plot_pca | 1.495 | 0.066 | 1.569 | |
| refineBreakpoints | 99.569 | 1.993 | 103.817 | |
| simulateReads | 91.601 | 13.634 | 105.537 | |
| subsetByCNVprofile | 7.510 | 0.035 | 7.657 | |
| variableWidthBins | 8.748 | 0.663 | 10.543 | |