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This page was generated on 2022-01-21 13:07:05 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for SELEX on tokay2


To the developers/maintainers of the SELEX package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1757/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.26.0  (landing page)
Harmen J. Bussemaker
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/SELEX
git_branch: RELEASE_3_14
git_last_commit: cd751a9
git_last_commit_date: 2021-10-26 12:18:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SELEX
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:SELEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SELEX_1.26.0.tar.gz
StartedAt: 2022-01-21 02:38:44 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:40:44 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 120.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:SELEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SELEX_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SELEX.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SELEX/DESCRIPTION' ... OK
* this is package 'SELEX' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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 R 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 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 ... OK
* 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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SELEX           33.33   4.64   12.92
selex.seqfilter 16.46   1.92    4.95
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SELEX.Rcheck/00check.log'
for details.



Installation output

SELEX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch SELEX
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'SELEX' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SELEX'
    finding HTML links ... done
    SELEX                                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/R/library/00LOCK-SELEX/00new/SELEX/help/selex.html
    selex.affinities                        html  
    selex.config                            html  
    selex.countSummary                      html  
    selex.counts                            html  
    selex.defineSample                      html  
    selex.exampledata                       html  
    selex.fastqPSFM                         html  
    selex.getAttributes                     html  
    selex.getRound0                         html  
    selex.getSeqfilter                      html  
    selex.infogain                          html  
    selex.infogainSummary                   html  
    selex.jvmStatus                         html  
    selex.kmax                              html  
    selex.kmerPSFM                          html  
    selex.loadAnnotation                    html  
    selex.mm                                html  
    selex.mmProb                            html  
    selex.mmSummary                         html  
    selex.revcomp                           html  
    selex.run                               html  
    selex.sample                            html  
    selex.samplePSFM                        html  
    selex.sampleSummary                     html  
    selex.saveAnnotation                    html  
    selex.seqfilter                         html  
    selex.setwd                             html  
    selex.split                             html  
    selex.summary                           html  
** 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)
Making 'packages.html' ... done

Tests output


Example timings

SELEX.Rcheck/SELEX-Ex.timings

nameusersystemelapsed
SELEX33.33 4.6412.92
selex.affinities0.750.030.44
selex.config0.200.000.03
selex.countSummary1.490.000.39
selex.counts1.530.050.68
selex.defineSample0.200.020.04
selex.exampledata0.090.020.03
selex.fastqPSFM0.750.030.41
selex.getAttributes0.300.000.09
selex.getRound00.440.030.14
selex.getSeqfilter0.170.000.03
selex.infogain2.060.080.50
selex.infogainSummary0.960.030.27
selex.jvmStatus0.040.010.03
selex.kmax2.100.601.11
selex.kmerPSFM0.450.080.30
selex.loadAnnotation0.270.010.10
selex.mm0.600.000.27
selex.mmProb0.490.000.19
selex.mmSummary0.610.000.26
selex.revcomp0.850.030.44
selex.run1.400.050.45
selex.sample0.160.000.08
selex.samplePSFM0.730.030.22
selex.sampleSummary0.380.020.11
selex.saveAnnotation0.120.000.06
selex.seqfilter16.46 1.92 4.95
selex.setwd0.050.000.01
selex.split0.720.040.24
selex.summary1.590.030.61