Harmen J. Bussemaker
| Snapshot Date: 2025-08-17 13:45 -0400 (Sun, 17 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SELEX |
| git_branch: devel |
| git_last_commit: 3c68102 |
| git_last_commit_date: 2025-04-15 10:38:11 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-18 12:08 -0400 (Mon, 18 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1936/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SELEX 1.41.0 (landing page) Harmen J. Bussemaker
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.41.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SELEX_1.41.0.tar.gz |
| StartedAt: 2025-08-15 10:56:47 -0000 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 10:59:19 -0000 (Fri, 15 Aug 2025) |
| EllapsedTime: 152.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SELEX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SELEX_1.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SELEX.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.41.0’
* 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 18.267 0.927 14.808
selex.seqfilter 8.350 0.223 4.599
* 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-3.22-bioc/meat/SELEX.Rcheck/00check.log’
for details.
SELEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SELEX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘SELEX’ ... ** this is package ‘SELEX’ version ‘1.41.0’ ** 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 | 18.267 | 0.927 | 14.808 | |
| selex.affinities | 0.784 | 0.030 | 0.477 | |
| selex.config | 0.088 | 0.009 | 0.058 | |
| selex.countSummary | 0.972 | 0.020 | 0.484 | |
| selex.counts | 1.071 | 0.019 | 0.843 | |
| selex.defineSample | 0.070 | 0.000 | 0.095 | |
| selex.exampledata | 0.038 | 0.005 | 0.029 | |
| selex.fastqPSFM | 0.405 | 0.013 | 0.278 | |
| selex.getAttributes | 0.103 | 0.008 | 0.060 | |
| selex.getRound0 | 0.295 | 0.004 | 0.105 | |
| selex.getSeqfilter | 0.055 | 0.000 | 0.043 | |
| selex.infogain | 1.870 | 0.021 | 0.575 | |
| selex.infogainSummary | 0.840 | 0.011 | 0.354 | |
| selex.jvmStatus | 0.206 | 0.004 | 0.091 | |
| selex.kmax | 0.865 | 0.132 | 0.741 | |
| selex.kmerPSFM | 0.301 | 0.026 | 0.230 | |
| selex.loadAnnotation | 0.183 | 0.004 | 0.102 | |
| selex.mm | 0.678 | 0.007 | 0.297 | |
| selex.mmProb | 0.529 | 0.015 | 0.212 | |
| selex.mmSummary | 0.670 | 0.004 | 0.453 | |
| selex.revcomp | 0.983 | 0.001 | 0.688 | |
| selex.run | 1.264 | 0.022 | 0.522 | |
| selex.sample | 0.209 | 0.008 | 0.085 | |
| selex.samplePSFM | 0.518 | 0.007 | 0.194 | |
| selex.sampleSummary | 0.247 | 0.012 | 0.086 | |
| selex.saveAnnotation | 0.137 | 0.000 | 0.042 | |
| selex.seqfilter | 8.350 | 0.223 | 4.599 | |
| selex.setwd | 0.075 | 0.000 | 0.054 | |
| selex.split | 0.466 | 0.007 | 0.198 | |
| selex.summary | 1.366 | 0.044 | 0.645 | |