Harmen J. Bussemaker
| Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SELEX |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1337acf |
| git_last_commit_date: 2024-10-29 09:58:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-23 12:09 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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 1920/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SELEX 1.38.0 (landing page) Harmen J. Bussemaker
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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. |
| Package: SELEX |
| Version: 1.38.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SELEX_1.38.0.tar.gz |
| StartedAt: 2025-01-21 10:07:37 -0500 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 10:11:13 -0500 (Tue, 21 Jan 2025) |
| EllapsedTime: 216.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SELEX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SELEX_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SELEX.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.38.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SELEX 30.576 3.445 13.718
selex.seqfilter 16.002 1.721 5.730
* 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/SELEX.Rcheck/00check.log’
for details.
SELEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SELEX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 30.576 | 3.445 | 13.718 | |
| selex.affinities | 2.376 | 0.070 | 0.795 | |
| selex.config | 0.302 | 0.009 | 0.093 | |
| selex.countSummary | 1.436 | 0.073 | 0.738 | |
| selex.counts | 2.764 | 0.088 | 1.114 | |
| selex.defineSample | 0.367 | 0.021 | 0.122 | |
| selex.exampledata | 0.241 | 0.014 | 0.074 | |
| selex.fastqPSFM | 3.013 | 0.087 | 0.893 | |
| selex.getAttributes | 0.615 | 0.022 | 0.160 | |
| selex.getRound0 | 0.820 | 0.031 | 0.235 | |
| selex.getSeqfilter | 0.268 | 0.007 | 0.073 | |
| selex.infogain | 2.516 | 0.128 | 1.045 | |
| selex.infogainSummary | 1.876 | 0.071 | 0.566 | |
| selex.jvmStatus | 0.231 | 0.008 | 0.084 | |
| selex.kmax | 1.249 | 0.435 | 1.355 | |
| selex.kmerPSFM | 0.537 | 0.089 | 0.399 | |
| selex.loadAnnotation | 0.555 | 0.028 | 0.200 | |
| selex.mm | 0.948 | 0.044 | 0.458 | |
| selex.mmProb | 1.006 | 0.049 | 0.458 | |
| selex.mmSummary | 0.584 | 0.045 | 0.471 | |
| selex.revcomp | 1.151 | 0.060 | 0.751 | |
| selex.run | 2.906 | 0.145 | 1.108 | |
| selex.sample | 0.465 | 0.021 | 0.180 | |
| selex.samplePSFM | 1.282 | 0.050 | 0.418 | |
| selex.sampleSummary | 0.498 | 0.027 | 0.169 | |
| selex.saveAnnotation | 0.157 | 0.018 | 0.083 | |
| selex.seqfilter | 16.002 | 1.721 | 5.730 | |
| selex.setwd | 0.085 | 0.003 | 0.042 | |
| selex.split | 0.683 | 0.032 | 0.326 | |
| selex.summary | 1.193 | 0.103 | 1.087 | |