Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:41:06 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1934/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SELEX 1.36.0 (landing page) Harmen J. Bussemaker
| 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 | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SELEX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SELEX.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: SELEX |
Version: 1.36.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SELEX_1.36.0.tar.gz |
StartedAt: 2024-05-04 11:53:56 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 11:55:52 -0000 (Sat, 04 May 2024) |
EllapsedTime: 115.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SELEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SELEX_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SELEX.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SELEX/DESCRIPTION’ ... OK * this is package ‘SELEX’ version ‘1.36.0’ * 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 ‘SELEX’ 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) SELEX.Rd:114: Lost braces 114 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) SELEX.Rd:114: Lost braces 114 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) SELEX.Rd:118: Lost braces 118 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) SELEX.Rd:118: Lost braces 118 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) SELEX.Rd:118: Lost braces 118 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) SELEX.Rd:118: Lost braces 118 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.affinities.Rd:33: Lost braces 33 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.affinities.Rd:33: Lost braces 33 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.affinities.Rd:37: Lost braces 37 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.affinities.Rd:37: Lost braces 37 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.affinities.Rd:37: Lost braces 37 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.affinities.Rd:37: Lost braces 37 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.counts.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.counts.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.counts.Rd:42: Lost braces 42 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.counts.Rd:42: Lost braces 42 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.counts.Rd:42: Lost braces 42 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.counts.Rd:42: Lost braces 42 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.infogain.Rd:27: Lost braces 27 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.infogain.Rd:27: Lost braces 27 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.infogain.Rd:31: Lost braces 31 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.infogain.Rd:31: Lost braces 31 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.infogain.Rd:31: Lost braces 31 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.infogain.Rd:31: Lost braces 31 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mm.Rd:60: Lost braces 60 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.mm.Rd:60: Lost braces 60 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.mm.Rd:64: Lost braces 64 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mm.Rd:64: Lost braces 64 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mm.Rd:64: Lost braces 64 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mm.Rd:64: Lost braces 64 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mmProb.Rd:39: Lost braces 39 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.mmProb.Rd:39: Lost braces 39 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.mmProb.Rd:43: Lost braces 43 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mmProb.Rd:43: Lost braces 43 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mmProb.Rd:43: Lost braces 43 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.mmProb.Rd:43: Lost braces 43 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.run.Rd:34: Lost braces 34 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.run.Rd:34: Lost braces 34 | \href{http://www.ncbi.nlm.nih.gov/pubmed/22153072}{{C}ofactor binding evokes latent differences in {D}{N}{A} binding specificity between {H}ox proteins.} | ^ checkRd: (-1) selex.run.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.run.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.run.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ checkRd: (-1) selex.run.Rd:38: Lost braces 38 | \href{http://www.ncbi.nlm.nih.gov/pubmed/25151169}{{S}{E}{L}{E}{X}-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.} | ^ * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SELEX 17.391 0.988 6.929 selex.seqfilter 7.645 0.419 2.506 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/SELEX.Rcheck/00check.log’ for details.
SELEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SELEX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘SELEX’ ... ** using staged installation ** R ** 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 (SELEX)
SELEX.Rcheck/SELEX-Ex.timings
name | user | system | elapsed | |
SELEX | 17.391 | 0.988 | 6.929 | |
selex.affinities | 1.013 | 0.029 | 0.410 | |
selex.config | 0.108 | 0.012 | 0.036 | |
selex.countSummary | 0.999 | 0.013 | 0.341 | |
selex.counts | 1.371 | 0.036 | 0.605 | |
selex.defineSample | 0.070 | 0.005 | 0.044 | |
selex.exampledata | 0.081 | 0.004 | 0.033 | |
selex.fastqPSFM | 0.661 | 0.008 | 0.376 | |
selex.getAttributes | 0.231 | 0.016 | 0.066 | |
selex.getRound0 | 0.443 | 0.007 | 0.112 | |
selex.getSeqfilter | 0.119 | 0.007 | 0.034 | |
selex.infogain | 1.641 | 0.033 | 0.508 | |
selex.infogainSummary | 0.843 | 0.029 | 0.266 | |
selex.jvmStatus | 0.104 | 0.004 | 0.037 | |
selex.kmax | 1.111 | 0.096 | 0.526 | |
selex.kmerPSFM | 0.368 | 0.016 | 0.208 | |
selex.loadAnnotation | 0.236 | 0.000 | 0.102 | |
selex.mm | 0.638 | 0.008 | 0.251 | |
selex.mmProb | 0.412 | 0.017 | 0.235 | |
selex.mmSummary | 0.291 | 0.008 | 0.232 | |
selex.revcomp | 0.710 | 0.051 | 0.433 | |
selex.run | 1.479 | 0.068 | 0.518 | |
selex.sample | 0.227 | 0.004 | 0.080 | |
selex.samplePSFM | 0.413 | 0.004 | 0.199 | |
selex.sampleSummary | 0.132 | 0.008 | 0.074 | |
selex.saveAnnotation | 0.036 | 0.008 | 0.042 | |
selex.seqfilter | 7.645 | 0.419 | 2.506 | |
selex.setwd | 0.057 | 0.003 | 0.021 | |
selex.split | 0.627 | 0.012 | 0.178 | |
selex.summary | 0.867 | 0.033 | 0.556 | |