Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 | ![]() | ||||||||
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: 1.36.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SELEX_1.36.0.tar.gz |
StartedAt: 2024-06-13 03:29:34 -0400 (Thu, 13 Jun 2024) |
EndedAt: 2024-06-13 03:31:17 -0400 (Thu, 13 Jun 2024) |
EllapsedTime: 103.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SELEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 22.197 1.525 6.285 selex.seqfilter 8.613 0.310 2.256 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * 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/bbs-3.19-bioc/R/bin/R CMD INSTALL SELEX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 | 22.197 | 1.525 | 6.285 | |
selex.affinities | 0.776 | 0.017 | 0.278 | |
selex.config | 0.135 | 0.007 | 0.032 | |
selex.countSummary | 0.969 | 0.036 | 0.275 | |
selex.counts | 1.430 | 0.075 | 0.491 | |
selex.defineSample | 0.109 | 0.004 | 0.033 | |
selex.exampledata | 0.086 | 0.004 | 0.025 | |
selex.fastqPSFM | 0.498 | 0.033 | 0.297 | |
selex.getAttributes | 0.266 | 0.035 | 0.069 | |
selex.getRound0 | 0.202 | 0.000 | 0.091 | |
selex.getSeqfilter | 0.084 | 0.008 | 0.024 | |
selex.infogain | 1.397 | 0.045 | 0.370 | |
selex.infogainSummary | 0.906 | 0.011 | 0.203 | |
selex.jvmStatus | 0.102 | 0.001 | 0.027 | |
selex.kmax | 1.248 | 0.179 | 0.550 | |
selex.kmerPSFM | 0.411 | 0.044 | 0.146 | |
selex.loadAnnotation | 0.340 | 0.012 | 0.069 | |
selex.mm | 0.566 | 0.000 | 0.161 | |
selex.mmProb | 0.691 | 0.080 | 0.176 | |
selex.mmSummary | 0.275 | 0.008 | 0.153 | |
selex.revcomp | 0.634 | 0.004 | 0.273 | |
selex.run | 0.859 | 0.012 | 0.352 | |
selex.sample | 0.121 | 0.004 | 0.054 | |
selex.samplePSFM | 0.333 | 0.004 | 0.164 | |
selex.sampleSummary | 0.097 | 0.004 | 0.049 | |
selex.saveAnnotation | 0.020 | 0.008 | 0.029 | |
selex.seqfilter | 8.613 | 0.310 | 2.256 | |
selex.setwd | 0.041 | 0.000 | 0.015 | |
selex.split | 0.339 | 0.003 | 0.114 | |
selex.summary | 0.723 | 0.032 | 0.400 | |