Aaron Taudt
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/chromstaR |
| Branch: RELEASE_3_6 |
| Last Commit: b76d634 |
| Last Changed Date: 2017-10-30 12:41:19 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:09 -0400 (Thu, 12 Apr 2018).
| Package 231/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromstaR 1.4.0 Aaron Taudt
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: chromstaR |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.4.0.tar.gz |
| StartedAt: 2018-04-12 01:42:08 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:49:58 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 469.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromstaR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chromstaR’ 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 loading without being on the library search path ... 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
Chromstar: 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
combineMultivariates 19.928 1.633 22.529
enrichment_analysis 14.499 0.730 19.160
readCustomBedFile 11.100 0.166 11.565
callPeaksMultivariate 10.246 0.608 11.111
Chromstar 9.486 0.307 52.785
callPeaksReplicates 7.694 0.603 8.453
transitionFrequencies 7.415 0.509 69.717
unis2pseudomulti 6.038 0.439 6.601
combinatorialStates 4.767 0.385 5.273
plotExpression 2.755 0.116 6.093
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/00check.log’
for details.
chromstaR.Rcheck/00install.out
* installing *source* package ‘chromstaR’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_interface.cpp -o R_interface.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c densities.cpp -o densities.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c utility.cpp -o utility.o clang++ -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 chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/chromstaR/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (chromstaR)
chromstaR.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(chromstaR)
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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: ggplot2
Loading required package: chromstaRData
Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.
>
> test_check("chromstaR")
HMM: number of states = 3
HMM: number of bins = 125194
HMM: maximum number of iterations = 5000
HMM: maximum running time = none
HMM: epsilon = 1
HMM: data mean = 4.06434, data variance = 10.7002
Iteration log(P) dlog(P) Diff in state 2 Time in sec
0 -inf - - 0
1 -221107.608192 inf 4898 0
2 -202927.094167 18180.514025 17717 0
3 -200120.881709 2806.212458 5825 0
4 -199468.394347 652.487362 888 0
5 -199127.131702 341.262646 1058 0
6 -198860.279250 266.852451 603 0
7 -198629.337990 230.941260 795 1
8 -198419.546135 209.791855 735 1
9 -198220.599452 198.946683 705 1
10 -198025.863024 194.736428 601 1
11 -197831.634581 194.228443 629 1
12 -197636.953896 194.680685 605 1
13 -197443.159115 193.794781 551 1
14 -197253.226838 189.932277 526 1
15 -197070.870496 182.356342 462 1
16 -196899.581897 171.288599 504 1
17 -196741.879226 157.702671 518 1
18 -196598.968651 142.910575 455 1
19 -196470.829967 128.138683 414 1
Iteration log(P) dlog(P) Diff in state 2 Time in sec
20 -196356.547470 114.282498 478 1
21 -196254.666304 101.881166 436 1
22 -196163.460342 91.205962 408 1
23 -196081.121315 82.339027 403 1
24 -196005.917090 75.204225 380 1
25 -195936.332041 69.585049 347 1
26 -195871.165174 65.166867 353 1
27 -195809.562263 61.602912 366 1
28 -195750.988447 58.573815 382 1
29 -195695.169980 55.818467 418 1
30 -195642.025316 53.144664 382 1
31 -195591.590246 50.435070 358 1
32 -195543.944190 47.646056 358 1
33 -195499.151606 44.792584 307 1
34 -195457.227470 41.924136 285 1
35 -195418.125988 39.101483 257 1
36 -195381.745667 36.380321 216 1
37 -195347.942282 33.803385 244 1
38 -195316.543289 31.398993 165 1
39 -195287.360604 29.182684 168 1
Iteration log(P) dlog(P) Diff in state 2 Time in sec
40 -195260.200914 27.159691 142 1
41 -195234.873581 25.327333 163 1
42 -195211.196441 23.677140 134 1
43 -195188.999774 22.196666 94 1
44 -195168.128759 20.871016 84 1
45 -195148.444676 19.684082 121 1
46 -195129.825149 18.619528 115 1
47 -195112.163631 17.661518 104 2
48 -195095.368371 16.795260 82 2
49 -195079.361021 16.007349 79 2
50 -195064.075048 15.285974 65 2
51 -195049.454066 14.620982 101 2
52 -195035.450211 14.003855 64 2
53 -195022.022611 13.427600 54 2
54 -195009.136022 12.886589 73 2
55 -194996.759650 12.376372 66 2
56 -194984.866167 11.893483 56 2
57 -194973.430930 11.435238 54 2
58 -194962.431364 10.999566 53 2
59 -194951.846510 10.584854 33 2
Iteration log(P) dlog(P) Diff in state 2 Time in sec
60 -194941.656694 10.189816 50 2
61 -194931.843299 9.813395 48 2
62 -194922.388613 9.454686 35 2
63 -194913.275737 9.112876 32 2
64 -194904.488524 8.787213 31 2
65 -194896.011551 8.476973 38 2
66 -194887.830099 8.181453 23 2
67 -194879.930141 7.899958 26 2
68 -194872.298334 7.631807 28 2
69 -194864.922010 7.376324 22 2
70 -194857.789160 7.132850 25 2
71 -194850.888420 6.900740 28 2
72 -194844.209049 6.679371 28 2
73 -194837.740907 6.468142 28 2
74 -194831.474431 6.266476 37 2
75 -194825.400605 6.073826 25 2
76 -194819.510934 5.889672 30 2
77 -194813.797412 5.713521 20 2
78 -194808.252500 5.544913 17 2
79 -194802.869088 5.383412 13 2
Iteration log(P) dlog(P) Diff in state 2 Time in sec
80 -194797.640477 5.228611 16 2
81 -194792.560346 5.080131 12 2
82 -194787.622729 4.937617 11 2
83 -194782.821992 4.800737 17 2
84 -194778.152810 4.669182 15 2
85 -194773.610144 4.542666 17 2
86 -194769.189224 4.420919 21 2
87 -194764.885531 4.303693 19 2
88 -194760.694777 4.190754 17 3
89 -194756.612893 4.081885 13 3
90 -194752.636009 3.976883 12 3
91 -194748.760450 3.875560 16 3
92 -194744.982713 3.777737 12 3
93 -194741.299463 3.683250 12 3
94 -194737.707521 3.591943 9 3
95 -194734.203851 3.503670 9 3
96 -194730.785554 3.418296 15 3
97 -194727.449862 3.335692 9 3
98 -194724.194125 3.255737 9 3
99 -194721.015807 3.178318 14 3
Iteration log(P) dlog(P) Diff in state 2 Time in sec
100 -194717.912479 3.103328 5 3
101 -194714.881814 3.030665 14 3
102 -194711.921579 2.960234 12 3
103 -194709.029634 2.891945 11 3
104 -194706.203921 2.825713 12 3
105 -194703.442465 2.761456 8 3
106 -194700.743366 2.699098 10 3
107 -194698.104800 2.638567 9 3
108 -194695.525008 2.579792 10 3
109 -194693.002300 2.522708 9 3
110 -194690.535048 2.467253 8 3
111 -194688.121681 2.413366 10 3
112 -194685.760689 2.360993 19 3
113 -194683.450612 2.310077 7 3
114 -194681.190044 2.260568 5 3
115 -194678.977628 2.212416 12 3
116 -194676.812054 2.165574 14 3
117 -194674.692057 2.119998 10 3
118 -194672.616414 2.075643 9 3
119 -194670.583945 2.032469 15 3
Iteration log(P) dlog(P) Diff in state 2 Time in sec
120 -194668.593508 1.990437 8 3
121 -194666.644000 1.949508 12 3
122 -194664.734354 1.909646 8 3
123 -194662.863537 1.870817 14 3
124 -194661.030550 1.832987 11 3
125 -194659.234427 1.796124 14 3
126 -194657.474230 1.760197 12 3
127 -194655.749053 1.725177 13 3
128 -194654.058017 1.691035 12 3
129 -194652.400273 1.657745 9 3
130 -194650.774994 1.625279 13 4
131 -194649.181381 1.593613 16 4
132 -194647.618659 1.562722 4 4
133 -194646.086077 1.532582 11 4
134 -194644.582905 1.503172 10 4
135 -194643.108436 1.474469 9 4
136 -194641.661983 1.446453 6 4
137 -194640.242879 1.419103 8 4
138 -194638.850479 1.392400 7 4
139 -194637.484154 1.366325 12 4
Iteration log(P) dlog(P) Diff in state 2 Time in sec
140 -194636.143294 1.340860 7 4
141 -194634.827307 1.315987 8 4
142 -194633.535617 1.291690 7 4
143 -194632.267664 1.267952 2 4
144 -194631.022907 1.244758 6 4
145 -194629.800816 1.222091 10 4
146 -194628.600877 1.199939 7 4
147 -194627.422592 1.178285 9 4
148 -194626.265475 1.157117 6 4
149 -194625.129053 1.136422 5 4
150 -194624.012868 1.116185 8 4
151 -194622.916472 1.096396 4 4
152 -194621.839430 1.077042 7 4
153 -194620.781320 1.058111 10 4
154 -194619.741728 1.039592 10 4
155 -194618.720255 1.021474 8 4
156 -194617.716509 1.003746 9 4
157 -194616.730110 0.986399 12 4
HMM: Convergence reached!
HMM: Recoding posteriors ...
══ testthat results ═══════════════════════════════════════════════════════════
OK: 44 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
17.367 0.531 18.234
chromstaR.Rcheck/chromstaR-Ex.timings
| name | user | system | elapsed | |
| Chromstar | 9.486 | 0.307 | 52.785 | |
| binReads | 0.612 | 0.027 | 0.675 | |
| callPeaksMultivariate | 10.246 | 0.608 | 11.111 | |
| callPeaksReplicates | 7.694 | 0.603 | 8.453 | |
| callPeaksUnivariate | 2.374 | 0.174 | 2.589 | |
| changeFDR | 3.541 | 0.226 | 3.834 | |
| changePostCutoff | 3.094 | 0.258 | 3.400 | |
| collapseBins | 0.790 | 0.034 | 0.837 | |
| combinatorialStates | 4.767 | 0.385 | 5.273 | |
| combineMultivariates | 19.928 | 1.633 | 22.529 | |
| combined_model | 0.114 | 0.023 | 0.138 | |
| conversion | 0.000 | 0.000 | 0.001 | |
| enrichment_analysis | 14.499 | 0.730 | 19.160 | |
| experiment.table | 0.005 | 0.001 | 0.007 | |
| exportFiles | 0.797 | 0.028 | 0.865 | |
| exportGRangesAsBedFile | 0.925 | 0.056 | 1.002 | |
| fixedWidthBins | 0.076 | 0.003 | 0.082 | |
| genes_rn4 | 0.133 | 0.006 | 0.140 | |
| genomicFrequencies | 0.144 | 0.015 | 0.161 | |
| getCombinations | 0.209 | 0.013 | 0.229 | |
| getDistinctColors | 0.031 | 0.003 | 0.034 | |
| getStateColors | 0.021 | 0.001 | 0.022 | |
| heatmapCombinations | 0.491 | 0.011 | 0.523 | |
| heatmapCountCorrelation | 0.355 | 0.010 | 0.378 | |
| heatmapTransitionProbs | 0.330 | 0.009 | 0.350 | |
| loadHmmsFromFiles | 1.500 | 0.149 | 1.672 | |
| multiHMM | 0.121 | 0.013 | 0.134 | |
| multivariate_model | 0.135 | 0.012 | 0.150 | |
| plotExpression | 2.755 | 0.116 | 6.093 | |
| plotHistogram | 1.968 | 0.194 | 2.202 | |
| readBamFileAsGRanges | 1.295 | 0.093 | 1.421 | |
| readBedFileAsGRanges | 4.002 | 0.185 | 4.314 | |
| readCustomBedFile | 11.100 | 0.166 | 11.565 | |
| removeCondition | 0.857 | 0.101 | 0.969 | |
| state.brewer | 0.017 | 0.001 | 0.018 | |
| stateBrewer | 0.046 | 0.002 | 0.048 | |
| transitionFrequencies | 7.415 | 0.509 | 69.717 | |
| unis2pseudomulti | 6.038 | 0.439 | 6.601 | |
| variableWidthBins | 3.375 | 0.380 | 3.831 | |