Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 429/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
consensusSeekeR 1.34.0 (landing page) Astrid Deschênes
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2024-11-19 20:51:50 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 20:59:00 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 429.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: consensusSeekeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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-3.20-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 version 4.4.1 (2024-06-14) -- "Race for Your Life" 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, 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 -- Tue Nov 19 20:58:50 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 12.552 0.525 13.120
consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings
name | user | system | elapsed | |
A549_CTCF_MYJ_NarrowPeaks_partial | 0.637 | 0.045 | 0.683 | |
A549_CTCF_MYJ_Peaks_partial | 0.253 | 0.009 | 0.263 | |
A549_CTCF_MYN_NarrowPeaks_partial | 0.264 | 0.037 | 0.302 | |
A549_CTCF_MYN_Peaks_partial | 0.379 | 0.008 | 0.388 | |
A549_FOSL2_01_NarrowPeaks_partial | 0.234 | 0.005 | 0.239 | |
A549_FOSL2_01_Peaks_partial | 0.299 | 0.005 | 0.305 | |
A549_FOXA1_01_NarrowPeaks_partial | 0.899 | 0.027 | 0.942 | |
A549_FOXA1_01_Peaks_partial | 0.390 | 0.010 | 0.402 | |
A549_NR3C1_CFQ_NarrowPeaks_partial | 0.254 | 0.014 | 0.269 | |
A549_NR3C1_CFQ_Peaks_partial | 0.301 | 0.010 | 0.313 | |
A549_NR3C1_CFR_NarrowPeaks_partial | 0.240 | 0.006 | 0.246 | |
A549_NR3C1_CFR_Peaks_partial | 0.253 | 0.006 | 0.260 | |
A549_NR3C1_CFS_NarrowPeaks_partial | 0.588 | 0.007 | 0.597 | |
A549_NR3C1_CFS_Peaks_partial | 0.581 | 0.006 | 0.589 | |
NOrMAL_nucleosome_positions | 0.449 | 0.007 | 0.457 | |
NOrMAL_nucleosome_ranges | 0.463 | 0.009 | 0.473 | |
NucPosSimulator_nucleosome_positions | 0.463 | 0.009 | 0.474 | |
NucPosSimulator_nucleosome_ranges | 0.464 | 0.010 | 0.475 | |
PING_nucleosome_positions | 0.302 | 0.009 | 0.311 | |
PING_nucleosome_ranges | 0.250 | 0.007 | 0.257 | |
findConsensusPeakRegions | 0.575 | 0.007 | 0.585 | |
findConsensusPeakRegionsValidation | 0.059 | 0.005 | 0.065 | |
readNarrowPeakFile | 0.066 | 0.002 | 0.070 | |