Aaron Taudt
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/chromstaR |
| git_branch: RELEASE_3_19 |
| git_last_commit: d0560fd |
| git_last_commit_date: 2024-04-30 10:51:52 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:31 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 349/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromstaR 1.30.0 (landing page) Aaron Taudt
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the chromstaR package: - 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: chromstaR |
| Version: 1.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromstaR_1.30.0.tar.gz |
| StartedAt: 2024-05-06 20:22:56 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 20:25:29 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 153.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromstaR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromstaR_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/chromstaR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.30.0’
* 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
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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
Chromstar: multiple local function definitions for ‘parallel.helper’
with different formal arguments
* checking Rd files ... NOTE
checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces
66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
| ^
checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces
66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
| ^
checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces
60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
| ^
checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces
60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
| ^
checkRd: (-1) plotGenomeBrowser.Rd:28-68: Lost braces
28 | plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol='black', peakcols=NULL, style='peaks', peakTrackHeight=5) {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:36-41: Lost braces
36 | if (style == 'peaks') {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:41-45: Lost braces
41 | } else if (style == 'density') {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:45-47: Lost braces
45 | } else {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:50-65: Lost braces
50 | if (!is.null(peaklist)) {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:51-53: Lost braces
51 | if (is.null(peakcols)) {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:54-64: Lost braces
54 | for (i1 in 1:length(peaklist)) {
| ^
checkRd: (-1) plotGenomeBrowser.Rd:57-60: Lost braces
57 | if (length(peaks) > 0) {
| ^
* 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s
user system elapsed
combineMultivariates 8.001 0.286 8.316
enrichment_analysis 4.671 0.232 7.709
Chromstar 2.444 0.093 15.699
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/chromstaR.Rcheck/00check.log’
for details.
chromstaR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chromstaR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘chromstaR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_interface.cpp -o R_interface.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densities.cpp -o densities.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.cpp -o init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility.cpp -o utility.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, 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':
expand.grid, I, unname
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
>
> proc.time()
user system elapsed
6.927 0.177 7.100
chromstaR.Rcheck/chromstaR-Ex.timings
| name | user | system | elapsed | |
| Chromstar | 2.444 | 0.093 | 15.699 | |
| binReads | 0.198 | 0.013 | 0.215 | |
| callPeaksMultivariate | 3.767 | 0.113 | 3.883 | |
| callPeaksReplicates | 3.554 | 0.105 | 3.661 | |
| callPeaksUnivariate | 0.631 | 0.028 | 0.660 | |
| changeMaxPostCutoff | 1.484 | 0.055 | 1.540 | |
| changePostCutoff | 2.000 | 0.098 | 2.103 | |
| collapseBins | 0.191 | 0.004 | 0.195 | |
| combinatorialStates | 2.263 | 0.085 | 2.349 | |
| combineMultivariates | 8.001 | 0.286 | 8.316 | |
| conversion | 0 | 0 | 0 | |
| enrichment_analysis | 4.671 | 0.232 | 7.709 | |
| experiment.table | 0.001 | 0.001 | 0.002 | |
| exportFiles | 0.382 | 0.006 | 0.389 | |
| exportGRangesAsBedFile | 0.290 | 0.010 | 0.299 | |
| fixedWidthBins | 0.019 | 0.001 | 0.020 | |
| genes_rn4 | 0.049 | 0.001 | 0.049 | |
| genomicFrequencies | 0.103 | 0.003 | 0.106 | |
| getCombinations | 0.112 | 0.001 | 0.114 | |
| getDistinctColors | 0.006 | 0.000 | 0.007 | |
| getStateColors | 0.004 | 0.000 | 0.005 | |
| heatmapCombinations | 0.191 | 0.003 | 0.194 | |
| heatmapCountCorrelation | 0.135 | 0.004 | 0.141 | |
| heatmapTransitionProbs | 0.140 | 0.004 | 0.144 | |
| loadHmmsFromFiles | 0.647 | 0.030 | 0.679 | |
| model.combined | 0.131 | 0.003 | 0.134 | |
| model.multivariate | 0.105 | 0.003 | 0.108 | |
| model.univariate | 0.038 | 0.001 | 0.039 | |
| multiHMM | 0.091 | 0.002 | 0.093 | |
| plotExpression | 0.963 | 0.064 | 2.493 | |
| plotGenomeBrowser | 2.277 | 0.045 | 2.323 | |
| plotHistogram | 0.952 | 0.045 | 0.998 | |
| readBamFileAsGRanges | 0.230 | 0.008 | 0.239 | |
| readBedFileAsGRanges | 0.548 | 0.020 | 0.570 | |
| readCustomBedFile | 2.018 | 0.041 | 2.059 | |
| removeCondition | 0.855 | 0.022 | 0.877 | |
| state.brewer | 0.003 | 0.000 | 0.003 | |
| stateBrewer | 0.008 | 0.001 | 0.009 | |
| transitionFrequencies | 0.144 | 0.004 | 0.148 | |
| unis2pseudomulti | 3.007 | 0.115 | 3.125 | |
| variableWidthBins | 0.662 | 0.066 | 0.728 | |