Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:05:39 -0400 (Fri, 15 Oct 2021).

CHECK results for deltaCaptureC on nebbiolo1

To the developers/maintainers of the deltaCaptureC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deltaCaptureC.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 473/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaCaptureC 1.6.0  (landing page)
Michael Shapiro
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/deltaCaptureC
git_branch: RELEASE_3_13
git_last_commit: 1bc5aff
git_last_commit_date: 2021-05-19 12:45:56 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: deltaCaptureC
Version: 1.6.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:deltaCaptureC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings deltaCaptureC_1.6.0.tar.gz
StartedAt: 2021-10-14 09:32:32 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:37:36 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 304.4 seconds
RetCode: 0
Status:   OK  
CheckDir: deltaCaptureC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:deltaCaptureC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings deltaCaptureC_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/deltaCaptureC.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deltaCaptureC/DESCRIPTION’ ... OK
* this is package ‘deltaCaptureC’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘deltaCaptureC’ 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 ... NOTE
getDeltaSE: warning in SummarizedExperiment(assay = list(delta =
  delta), colData = colData): partial argument match of 'assay' to
  'assays'
plotSignificantRegions: no visible binding for global variable ‘ctr’
plotSignificantRegions: no visible binding for global variable ‘delta’
plotSignificantRegions: no visible binding for global variable
  ‘significance’
Undefined global functions or variables:
  ctr delta significance
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
binSummarizedExperiment 114.289  0.803 115.897
getOverlapWeights        13.292  0.000  13.295
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/deltaCaptureC.Rcheck/00check.log’
for details.



Installation output

deltaCaptureC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL deltaCaptureC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘deltaCaptureC’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (deltaCaptureC)

Tests output


Example timings

deltaCaptureC.Rcheck/deltaCaptureC-Ex.timings

nameusersystemelapsed
binSummarizedExperiment114.289 0.803115.897
downshiftDFtoMatrix0.0020.0000.002
generatePermutation0.0180.0000.018
getDeltaSE0.3830.0040.388
getLopsidedness0.1080.0000.107
getMeanNormalizedCountsSE0.2460.0000.246
getNormalizedCountsSE0.1790.0000.179
getOverlapWeights13.292 0.00013.295
getPValueCutoff0.0010.0000.000
getRunTotals0.1370.0000.137
getSizeFactorsDF0.0020.0000.002
getSizeFactorsSE0.0230.0000.023
plotSignificantRegions0.0250.0000.025
rebinToMultiple0.7200.0000.721