Multiple platform build/check report for BioC 3.20 - CHECK results for consensusSeekeR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for consensusSeekeR on nebbiolo2

To the developers/maintainers of the consensusSeekeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consensusSeekeR.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: consensusSeekeR

Version: 1.34.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings consensusSeekeR_1.34.0.tar.gz

StartedAt: 2024-12-19 21:55:55 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 22:04:18 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 503.3 seconds

RetCode: 0

Status: OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings consensusSeekeR_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘consensusSeekeR’ 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 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) A549_CTCF_MYJ_NarrowPeaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYJ_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_CTCF_MYJ_NarrowPeaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYJ_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYJ_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_CTCF_MYJ_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYN_NarrowPeaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYN_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_CTCF_MYN_NarrowPeaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYN_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYN_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_CTCF_MYN_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOSL2_01_NarrowPeaks_partial.Rd:73-74: Lost braces
    73 | \item \code{\link{A549_FOSL2_01_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_FOSL2_01_NarrowPeaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOSL2_01_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_FOSL2_01_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_FOSL2_01_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOXA1_01_NarrowPeaks_partial.Rd:71-72: Lost braces
    71 | \item \code{\link{A549_FOXA1_01_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_FOXA1_01_NarrowPeaks_partial.Rd:73-74: Lost braces
    73 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOXA1_01_Peaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{A549_FOXA1_01_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_FOXA1_01_Peaks_partial.Rd:77-78: Lost braces
    77 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFQ_NarrowPeaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFQ_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFQ_NarrowPeaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFQ_Peaks_partial.Rd:89-90: Lost braces
    89 | \item \code{\link{A549_NR3C1_CFQ_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFQ_Peaks_partial.Rd:91-92: Lost braces
    91 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFR_NarrowPeaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFR_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFR_NarrowPeaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFR_Peaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFR_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFR_Peaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFS_NarrowPeaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{A549_NR3C1_CFS_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFS_NarrowPeaks_partial.Rd:77-78: Lost braces
    77 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFS_Peaks_partial.Rd:79-80: Lost braces
    79 | \item \code{\link{A549_NR3C1_CFS_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFS_Peaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{NOrMAL_nucleosome_ranges}} { the associate
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_positions.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_ranges.Rd:80-81: Lost braces
    80 | \item \code{\link{NOrMAL_nucleosome_positions}} { the associate
       |                                                 ^
checkRd: (-1) NOrMAL_nucleosome_ranges.Rd:82-83: Lost braces
    82 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NucPosSimulator_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{NucPosSimulator_nucleosome_ranges}} { the associate
       |                                                       ^
checkRd: (-1) NucPosSimulator_nucleosome_positions.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NucPosSimulator_nucleosome_ranges.Rd:80-81: Lost braces
    80 | \item \code{\link{NucPosSimulator_nucleosome_positions}} { the associate
       |                                                          ^
checkRd: (-1) NucPosSimulator_nucleosome_ranges.Rd:82-83: Lost braces
    82 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) PING_nucleosome_positions.Rd:79-80: Lost braces
    79 | \item \code{\link{PING_nucleosome_ranges}} { the associate
       |                                            ^
checkRd: (-1) PING_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) PING_nucleosome_ranges.Rd:81-82: Lost braces
    81 | \item \code{\link{PING_nucleosome_positions}} { the associate
       |                                               ^
checkRd: (-1) PING_nucleosome_ranges.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) consensusSeekeR-package.Rd:18-19: Lost braces
    18 | \item \code{\link{readNarrowPeakFile}} {for extracting regions and peaks
       |                                        ^
checkRd: (-1) consensusSeekeR-package.Rd:20-21: Lost braces
    20 | \item \code{\link{findConsensusPeakRegions}} { for extracting regions
       |                                              ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.

Installation output

consensusSeekeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL consensusSeekeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘consensusSeekeR’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (consensusSeekeR)

Tests output

consensusSeekeR.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> ## Run all tests present in the package
> BiocGenerics:::testPackage("consensusSeekeR")

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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname



RUNIT TEST PROTOCOL -- Thu Dec 19 22:02:56 2024 
*********************************************** 
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensusSeekeR RUnit Tests - 56 test functions, 0 errors, 0 failures
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.389   0.485  12.860

Example timings

consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings

name	user	system	elapsed
A549_CTCF_MYJ_NarrowPeaks_partial	0.660	0.097	0.758
A549_CTCF_MYJ_Peaks_partial	0.278	0.002	0.280
A549_CTCF_MYN_NarrowPeaks_partial	0.257	0.002	0.260
A549_CTCF_MYN_Peaks_partial	0.319	0.001	0.320
A549_FOSL2_01_NarrowPeaks_partial	0.241	0.001	0.242
A549_FOSL2_01_Peaks_partial	0.301	0.002	0.304
A549_FOXA1_01_NarrowPeaks_partial	0.307	0.000	0.307
A549_FOXA1_01_Peaks_partial	0.420	0.002	0.422
A549_NR3C1_CFQ_NarrowPeaks_partial	0.259	0.002	0.261
A549_NR3C1_CFQ_Peaks_partial	0.328	0.001	0.329
A549_NR3C1_CFR_NarrowPeaks_partial	0.256	0.001	0.257
A549_NR3C1_CFR_Peaks_partial	0.248	0.005	0.253
A549_NR3C1_CFS_NarrowPeaks_partial	0.637	0.001	0.638
A549_NR3C1_CFS_Peaks_partial	0.636	0.000	0.637
NOrMAL_nucleosome_positions	0.486	0.003	0.490
NOrMAL_nucleosome_ranges	0.492	0.004	0.497
NucPosSimulator_nucleosome_positions	0.487	0.018	0.506
NucPosSimulator_nucleosome_ranges	0.557	0.008	0.566
PING_nucleosome_positions	0.313	0.001	0.315
PING_nucleosome_ranges	0.281	0.003	0.284
findConsensusPeakRegions	0.574	0.003	0.577
findConsensusPeakRegionsValidation	0.064	0.001	0.065
readNarrowPeakFile	0.065	0.002	0.069