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This page was generated on 2023-01-31 11:06:57 -0500 (Tue, 31 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 stepNorm on nebbiolo2


To the developers/maintainers of the stepNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/stepNorm.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1978/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.70.0  (landing page)
Yuanyuan Xiao
Snapshot Date: 2023-01-30 14:00:05 -0500 (Mon, 30 Jan 2023)
git_url: https://git.bioconductor.org/packages/stepNorm
git_branch: RELEASE_3_16
git_last_commit: 1b73255
git_last_commit_date: 2022-11-01 10:38:09 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: stepNorm
Version: 1.70.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:stepNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings stepNorm_1.70.0.tar.gz
StartedAt: 2023-01-31 00:14:55 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 00:15:58 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 63.0 seconds
RetCode: 0
Status:   OK  
CheckDir: stepNorm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:stepNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings stepNorm_1.70.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/stepNorm.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘stepNorm/DESCRIPTION’ ... OK
* this is package ‘stepNorm’ version ‘1.70.0’
* 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 ‘stepNorm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘methods’
A package should be listed in only one of these fields.
* 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
loess2Dfit: warning in loess.control(trace.hat = "approximate",
  iteration = 5, surface = "direct"): partial argument match of
  'iteration' to 'iterations'
loessfit: warning in loess.control(trace.hat = "approximate", iteration
  = 5, surface = "direct"): partial argument match of 'iteration' to
  'iterations'
* 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
stepWithinNorm 17.385  0.028  17.414
fitWithin      15.251  0.012  15.263
fit2DWithin     6.933  0.080   7.013
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/stepNorm.Rcheck/00check.log’
for details.



Installation output

stepNorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL stepNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘stepNorm’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (stepNorm)

Tests output


Example timings

stepNorm.Rcheck/stepNorm-Ex.timings

nameusersystemelapsed
calcAIC0.1010.0200.122
calcBIC0.0620.0080.070
fit2DWithin6.9330.0807.013
fitWithin15.251 0.01215.263
maCompPlate20.0070.0000.007
makeStepList0.0510.0000.051
marrayFitClass0.0620.0000.062
seqWithinNorm0.1890.0080.198
stepWithinNorm17.385 0.02817.414
withinNorm0.0450.0000.045