Astrid Deschênes
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/consensusSeekeR |
| git_branch: devel |
| git_last_commit: d8c3500 |
| git_last_commit_date: 2024-02-22 19:59:06 -0400 (Thu, 22 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:39:05 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 428/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| consensusSeekeR 1.31.2 (landing page) Astrid Deschênes
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: consensusSeekeR |
| Version: 1.31.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings consensusSeekeR_1.31.2.tar.gz |
| StartedAt: 2024-03-27 20:24:16 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 20:29:03 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 286.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: consensusSeekeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings consensusSeekeR_1.31.2.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/consensusSeekeR.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.31.2’
* package encoding: UTF-8
* 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 ‘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 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 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-3.19-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.
consensusSeekeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL consensusSeekeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
consensusSeekeR.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.
> ## 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, 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 -- Wed Mar 27 20:28:50 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
17.210 0.721 18.050
consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings
| name | user | system | elapsed | |
| A549_CTCF_MYJ_NarrowPeaks_partial | 1.030 | 0.059 | 1.100 | |
| A549_CTCF_MYJ_Peaks_partial | 0.355 | 0.027 | 0.385 | |
| A549_CTCF_MYN_NarrowPeaks_partial | 0.376 | 0.048 | 0.428 | |
| A549_CTCF_MYN_Peaks_partial | 0.502 | 0.013 | 0.521 | |
| A549_FOSL2_01_NarrowPeaks_partial | 0.294 | 0.009 | 0.305 | |
| A549_FOSL2_01_Peaks_partial | 0.429 | 0.012 | 0.446 | |
| A549_FOXA1_01_NarrowPeaks_partial | 1.090 | 0.026 | 1.122 | |
| A549_FOXA1_01_Peaks_partial | 0.505 | 0.018 | 0.527 | |
| A549_NR3C1_CFQ_NarrowPeaks_partial | 0.329 | 0.022 | 0.354 | |
| A549_NR3C1_CFQ_Peaks_partial | 0.389 | 0.011 | 0.400 | |
| A549_NR3C1_CFR_NarrowPeaks_partial | 0.337 | 0.009 | 0.347 | |
| A549_NR3C1_CFR_Peaks_partial | 0.354 | 0.009 | 0.364 | |
| A549_NR3C1_CFS_NarrowPeaks_partial | 0.870 | 0.014 | 0.891 | |
| A549_NR3C1_CFS_Peaks_partial | 0.905 | 0.014 | 0.926 | |
| NOrMAL_nucleosome_positions | 0.709 | 0.015 | 0.729 | |
| NOrMAL_nucleosome_ranges | 0.715 | 0.017 | 0.737 | |
| NucPosSimulator_nucleosome_positions | 0.729 | 0.016 | 0.750 | |
| NucPosSimulator_nucleosome_ranges | 0.705 | 0.017 | 0.727 | |
| PING_nucleosome_positions | 0.466 | 0.014 | 0.483 | |
| PING_nucleosome_ranges | 0.402 | 0.014 | 0.418 | |
| findConsensusPeakRegions | 0.836 | 0.014 | 0.854 | |
| findConsensusPeakRegionsValidation | 0.099 | 0.007 | 0.107 | |
| readNarrowPeakFile | 0.093 | 0.003 | 0.097 | |