Aaron Taudt
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/chromstaR |
| Branch: RELEASE_3_10 |
| Last Commit: b37e9bf |
| Last Changed Date: 2019-10-29 13:09:48 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:43:50 -0400 (Wed, 15 Apr 2020).
| Package 287/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromstaR 1.12.0 Aaron Taudt
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: chromstaR |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromstaR_1.12.0.tar.gz |
| StartedAt: 2020-04-15 01:10:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:18:45 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 483.7 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 --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromstaR_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/chromstaR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 4.5Mb
* 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
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 ... 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
combineMultivariates 25.831 1.903 27.944
enrichment_analysis 15.298 0.982 19.343
callPeaksMultivariate 11.877 0.688 12.671
plotGenomeBrowser 12.051 0.105 12.283
unis2pseudomulti 10.640 0.589 11.341
callPeaksReplicates 10.555 0.674 11.312
changePostCutoff 9.771 0.677 10.545
readCustomBedFile 9.473 0.167 9.729
Chromstar 7.388 0.424 53.799
combinatorialStates 7.216 0.516 7.787
changeMaxPostCutoff 6.601 0.490 7.149
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/chromstaR.Rcheck/00check.log’
for details.
chromstaR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromstaR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘chromstaR’ ... ** 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 -fopenmp -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 -fopenmp -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 -fopenmp -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 -fopenmp -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 -fopenmp -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 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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-chromstaR/00new/chromstaR/libs ** R ** data ** 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 (chromstaR)
chromstaR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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: chromstaRData
Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.
>
> test_check("chromstaR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
20.973 0.976 22.116
chromstaR.Rcheck/chromstaR-Ex.timings
| name | user | system | elapsed | |
| Chromstar | 7.388 | 0.424 | 53.799 | |
| binReads | 0.711 | 0.045 | 0.763 | |
| callPeaksMultivariate | 11.877 | 0.688 | 12.671 | |
| callPeaksReplicates | 10.555 | 0.674 | 11.312 | |
| callPeaksUnivariate | 2.546 | 0.193 | 2.758 | |
| changeMaxPostCutoff | 6.601 | 0.490 | 7.149 | |
| changePostCutoff | 9.771 | 0.677 | 10.545 | |
| collapseBins | 0.899 | 0.055 | 0.965 | |
| combinatorialStates | 7.216 | 0.516 | 7.787 | |
| combineMultivariates | 25.831 | 1.903 | 27.944 | |
| conversion | 0.000 | 0.000 | 0.001 | |
| enrichment_analysis | 15.298 | 0.982 | 19.343 | |
| experiment.table | 0.005 | 0.002 | 0.007 | |
| exportFiles | 1.678 | 0.059 | 1.757 | |
| exportGRangesAsBedFile | 1.374 | 0.068 | 1.460 | |
| fixedWidthBins | 0.115 | 0.004 | 0.119 | |
| genes_rn4 | 0.159 | 0.007 | 0.168 | |
| genomicFrequencies | 0.325 | 0.036 | 0.363 | |
| getCombinations | 0.306 | 0.020 | 0.328 | |
| getDistinctColors | 0.037 | 0.004 | 0.041 | |
| getStateColors | 0.019 | 0.001 | 0.020 | |
| heatmapCombinations | 0.591 | 0.020 | 0.617 | |
| heatmapCountCorrelation | 0.484 | 0.019 | 0.511 | |
| heatmapTransitionProbs | 0.500 | 0.017 | 0.519 | |
| loadHmmsFromFiles | 2.215 | 0.179 | 2.410 | |
| model.combined | 0.948 | 0.051 | 1.004 | |
| model.multivariate | 0.262 | 0.020 | 0.285 | |
| model.univariate | 0.090 | 0.013 | 0.103 | |
| multiHMM | 0.275 | 0.016 | 0.295 | |
| plotExpression | 2.050 | 0.074 | 3.548 | |
| plotGenomeBrowser | 12.051 | 0.105 | 12.283 | |
| plotHistogram | 3.092 | 0.215 | 3.324 | |
| readBamFileAsGRanges | 0.878 | 0.080 | 0.960 | |
| readBedFileAsGRanges | 1.937 | 0.128 | 2.102 | |
| readCustomBedFile | 9.473 | 0.167 | 9.729 | |
| removeCondition | 2.155 | 0.147 | 2.321 | |
| state.brewer | 0.017 | 0.000 | 0.016 | |
| stateBrewer | 0.054 | 0.002 | 0.056 | |
| transitionFrequencies | 0.420 | 0.046 | 0.468 | |
| unis2pseudomulti | 10.640 | 0.589 | 11.341 | |
| variableWidthBins | 2.321 | 0.309 | 2.656 | |