Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1934/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.36.0  (landing page)
Harmen J. Bussemaker
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/SELEX
git_branch: RELEASE_3_19
git_last_commit: ee8e854
git_last_commit_date: 2024-04-30 10:41:48 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SELEX on nebbiolo1

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.

raw results


Summary

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: 2024-06-10 03:19:29 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:21:11 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 102.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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           22.45  2.101   6.764
selex.seqfilter  7.94  0.505   2.284
* 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.


Installation output

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)

Tests output


Example timings

SELEX.Rcheck/SELEX-Ex.timings

nameusersystemelapsed
SELEX22.450 2.101 6.764
selex.affinities1.0250.0390.294
selex.config0.1060.0000.025
selex.countSummary0.7650.0250.246
selex.counts0.9530.0310.387
selex.defineSample0.0610.0000.029
selex.exampledata0.0680.0000.022
selex.fastqPSFM0.6940.0240.311
selex.getAttributes0.2270.0070.051
selex.getRound00.2770.0050.076
selex.getSeqfilter0.0930.0070.025
selex.infogain1.2780.0690.381
selex.infogainSummary0.7870.0320.188
selex.jvmStatus0.0660.0030.026
selex.kmax1.1860.1910.548
selex.kmerPSFM0.3850.0280.153
selex.loadAnnotation0.2220.0000.072
selex.mm0.5020.0080.164
selex.mmProb0.4470.0750.172
selex.mmSummary0.2670.0080.168
selex.revcomp0.7870.0110.334
selex.run1.0980.0230.357
selex.sample0.1400.0040.052
selex.samplePSFM0.4570.0160.175
selex.sampleSummary0.1480.0120.052
selex.saveAnnotation0.0560.0080.031
selex.seqfilter7.9400.5052.284
selex.setwd0.0520.0000.013
selex.split0.3910.0030.112
selex.summary0.7020.0480.378