Astrid Deschênes
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/consensusSeekeR |
| git_branch: devel |
| git_last_commit: b3d93cc |
| git_last_commit_date: 2024-04-30 10:46:48 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 421/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| consensusSeekeR 1.33.0 (landing page) Astrid Deschênes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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: 1.33.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings consensusSeekeR_1.33.0.tar.gz |
| StartedAt: 2024-07-15 22:57:37 -0400 (Mon, 15 Jul 2024) |
| EndedAt: 2024-07-15 23:01:31 -0400 (Mon, 15 Jul 2024) |
| EllapsedTime: 234.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: consensusSeekeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings consensusSeekeR_1.33.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'consensusSeekeR/DESCRIPTION' ... OK
* this is package 'consensusSeekeR' version '1.33.0'
* 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 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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck/00check.log'
for details.
consensusSeekeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL consensusSeekeR ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
RUNIT TEST PROTOCOL -- Mon Jul 15 23:01:19 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
13.82 0.56 14.40
consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings
| name | user | system | elapsed | |
| A549_CTCF_MYJ_NarrowPeaks_partial | 0.69 | 0.03 | 0.72 | |
| A549_CTCF_MYJ_Peaks_partial | 0.26 | 0.06 | 0.33 | |
| A549_CTCF_MYN_NarrowPeaks_partial | 0.25 | 0.08 | 0.33 | |
| A549_CTCF_MYN_Peaks_partial | 0.30 | 0.03 | 0.33 | |
| A549_FOSL2_01_NarrowPeaks_partial | 0.22 | 0.03 | 0.25 | |
| A549_FOSL2_01_Peaks_partial | 0.45 | 0.00 | 0.45 | |
| A549_FOXA1_01_NarrowPeaks_partial | 0.89 | 0.02 | 0.91 | |
| A549_FOXA1_01_Peaks_partial | 0.44 | 0.00 | 0.43 | |
| A549_NR3C1_CFQ_NarrowPeaks_partial | 0.25 | 0.03 | 0.29 | |
| A549_NR3C1_CFQ_Peaks_partial | 0.28 | 0.06 | 0.34 | |
| A549_NR3C1_CFR_NarrowPeaks_partial | 0.25 | 0.02 | 0.28 | |
| A549_NR3C1_CFR_Peaks_partial | 0.24 | 0.03 | 0.27 | |
| A549_NR3C1_CFS_NarrowPeaks_partial | 0.60 | 0.01 | 0.63 | |
| A549_NR3C1_CFS_Peaks_partial | 0.60 | 0.02 | 0.63 | |
| NOrMAL_nucleosome_positions | 0.46 | 0.04 | 0.50 | |
| NOrMAL_nucleosome_ranges | 0.48 | 0.05 | 0.53 | |
| NucPosSimulator_nucleosome_positions | 0.42 | 0.06 | 0.48 | |
| NucPosSimulator_nucleosome_ranges | 1.66 | 0.05 | 1.74 | |
| PING_nucleosome_positions | 0.30 | 0.05 | 0.34 | |
| PING_nucleosome_ranges | 0.25 | 0.03 | 0.28 | |
| findConsensusPeakRegions | 0.51 | 0.01 | 0.53 | |
| findConsensusPeakRegionsValidation | 0.08 | 0.03 | 0.11 | |
| readNarrowPeakFile | 0.06 | 0.00 | 0.07 | |