Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:26 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 deltaCaptureC on palomino5


To the developers/maintainers of the deltaCaptureC package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 497/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deltaCaptureC 1.13.0  (landing page)
Michael Shapiro
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/deltaCaptureC
git_branch: master
git_last_commit: 882fe39
git_last_commit_date: 2022-11-01 11:20:27 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: deltaCaptureC
Version: 1.13.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deltaCaptureC.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings deltaCaptureC_1.13.0.tar.gz
StartedAt: 2022-12-28 23:07:59 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 23:11:43 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 224.0 seconds
RetCode: 0
Status:   OK  
CheckDir: deltaCaptureC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deltaCaptureC.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings deltaCaptureC_1.13.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/deltaCaptureC.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'deltaCaptureC/DESCRIPTION' ... OK
* this is package 'deltaCaptureC' version '1.13.0'
* 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 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 ... NOTE
Namespace in Imports field not imported from: 'tictoc'
  All declared Imports should be used.
* 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 59.03   0.61   59.68
getOverlapWeights        6.89   0.05    6.93
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/deltaCaptureC.Rcheck/00check.log'
for details.



Installation output

deltaCaptureC.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL deltaCaptureC
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'deltaCaptureC' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (deltaCaptureC)

Tests output


Example timings

deltaCaptureC.Rcheck/deltaCaptureC-Ex.timings

nameusersystemelapsed
binSummarizedExperiment59.03 0.6159.68
downshiftDFtoMatrix000
generatePermutation0.020.000.01
getDeltaSE0.20.00.2
getLopsidedness0.060.000.07
getMeanNormalizedCountsSE0.110.000.11
getNormalizedCountsSE0.110.000.11
getOverlapWeights6.890.056.93
getPValueCutoff000
getRunTotals0.080.000.08
getSizeFactorsDF0.020.000.02
getSizeFactorsSE000
plotSignificantRegions0.040.000.04
rebinToMultiple0.330.000.33