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CHECK report for nnNorm on malbec2

This page was generated on 2020-10-17 11:55:16 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE nnNorm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1196/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nnNorm 2.52.0
Adi Laurentiu Tarca
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/nnNorm
Branch: RELEASE_3_11
Last Commit: d676bf1
Last Changed Date: 2020-04-27 14:10:14 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nnNorm
Version: 2.52.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nnNorm.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nnNorm_2.52.0.tar.gz
StartedAt: 2020-10-17 03:41:08 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:42:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 102.2 seconds
RetCode: 0
Status:  OK 
CheckDir: nnNorm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nnNorm.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nnNorm_2.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/nnNorm.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nnNorm/DESCRIPTION’ ... OK
* this is package ‘nnNorm’ version ‘2.52.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘methods’
* 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 ‘nnNorm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’
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
detectSpatialBias: no visible global function definition for ‘as’
maNormNN: no visible global function definition for ‘as’
maNormNN: no visible global function definition for ‘slot<-’
Undefined global functions or variables:
  as slot<-
Consider adding
  importFrom("methods", "as", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
maNormNN          39.653  0.008  39.663
compNorm          19.892  0.032  19.943
detectSpatialBias 13.044  0.003  13.049
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/nnNorm.Rcheck/00check.log’
for details.



Installation output

nnNorm.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL nnNorm
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘nnNorm’ ...
** 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 (nnNorm)

Tests output


Example timings

nnNorm.Rcheck/nnNorm-Ex.timings

nameusersystemelapsed
compNorm19.892 0.03219.943
detectSpatialBias13.044 0.00313.049
maNormNN39.653 0.00839.663