Back to Multiple platform build/check report for BioC 3.19:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 349/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.30.0  (landing page)
Aaron Taudt
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for chromstaR on nebbiolo1

To the developers/maintainers of the chromstaR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromstaR.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: chromstaR
Version: 1.30.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings chromstaR_1.30.0.tar.gz
StartedAt: 2024-06-19 21:36:26 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:47:07 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 641.4 seconds
RetCode: 0
Status:   OK  
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings chromstaR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/chromstaR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  5.6Mb
  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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
combineMultivariates  19.179  0.332  19.516
enrichment_analysis   12.166  0.676  16.153
callPeaksMultivariate  9.457  0.468   9.927
callPeaksReplicates    8.614  0.348   8.963
unis2pseudomulti       7.086  0.217   7.303
plotGenomeBrowser      6.675  0.348   7.028
Chromstar              5.812  0.605  38.967
combinatorialStates    5.624  0.148   5.772
changePostCutoff       5.310  0.164   5.473
plotExpression         3.916  0.468  15.073
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/chromstaR.Rcheck/00check.log’
for details.


Installation output

chromstaR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c R_interface.cpp -o R_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c densities.cpp -o densities.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

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: x86_64-pc-linux-gnu

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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, 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':

    I, expand.grid, 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 
 17.998   0.833  18.820 

Example timings

chromstaR.Rcheck/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 5.812 0.60538.967
binReads0.5390.0360.578
callPeaksMultivariate9.4570.4689.927
callPeaksReplicates8.6140.3488.963
callPeaksUnivariate1.6670.0361.703
changeMaxPostCutoff3.7420.1323.874
changePostCutoff5.3100.1645.473
collapseBins0.4890.0000.489
combinatorialStates5.6240.1485.772
combineMultivariates19.179 0.33219.516
conversion0.0000.0000.001
enrichment_analysis12.166 0.67616.153
experiment.table0.0010.0020.004
exportFiles1.0370.0421.079
exportGRangesAsBedFile0.7780.0200.797
fixedWidthBins0.0610.0000.061
genes_rn40.1020.0030.105
genomicFrequencies0.2050.0160.222
getCombinations0.2320.0120.243
getDistinctColors0.0160.0000.016
getStateColors0.0130.0000.012
heatmapCombinations0.4570.0440.501
heatmapCountCorrelation0.3270.0390.366
heatmapTransitionProbs0.3260.0120.338
loadHmmsFromFiles1.530.041.57
model.combined0.2540.0070.260
model.multivariate0.210.000.21
model.univariate0.0820.0000.083
multiHMM0.2110.0200.231
plotExpression 3.916 0.46815.073
plotGenomeBrowser6.6750.3487.028
plotHistogram1.9340.0802.013
readBamFileAsGRanges0.6600.0240.685
readBedFileAsGRanges2.2370.1962.434
readCustomBedFile3.4910.0963.588
removeCondition1.9600.1162.076
state.brewer0.0080.0000.008
stateBrewer0.0260.0000.026
transitionFrequencies0.2720.0340.306
unis2pseudomulti7.0860.2177.303
variableWidthBins1.6210.0441.665