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CHECK report for SNAGEE on malbec2

This page was generated on 2020-10-17 11:55:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SNAGEE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1688/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNAGEE 1.28.0
David Venet
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SNAGEE
Branch: RELEASE_3_11
Last Commit: 976da90
Last Changed Date: 2020-04-27 14:32:02 -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  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNAGEE
Version: 1.28.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SNAGEE.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SNAGEE_1.28.0.tar.gz
StartedAt: 2020-10-17 05:38:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:39:24 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 35.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SNAGEE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SNAGEE.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SNAGEE_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SNAGEE.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 ‘SNAGEE/DESCRIPTION’ ... OK
* this is package ‘SNAGEE’ version ‘1.28.0’
* 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 ‘SNAGEE’ 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
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
qualSample: no visible global function definition for ‘sd’
qualSample: no visible global function definition for ‘cor’
qualSample: no visible global function definition for ‘mclapply’
qualSample: no visible global function definition for ‘median’
qualSample: no visible global function definition for ‘mad’
qualStudy: no visible global function definition for ‘cor’
qualStudy: no visible global function definition for ‘sd’
toSnageeFormat: no visible global function definition for ‘is’
toSnageeFormat: no visible global function definition for ‘annotation’
toSnageeFormat: no visible global function definition for ‘exprs’
toSnageeFormat: no visible global function definition for
  ‘selectMethod’
toSnageeFormat: no visible global function definition for ‘medpolish’
Undefined global functions or variables:
  annotation cor exprs is mad mclapply median medpolish sd selectMethod
Consider adding
  importFrom("methods", "is", "selectMethod")
  importFrom("stats", "cor", "mad", "median", "medpolish", "sd")
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
SNAGEE-package 8.523  0.700   9.283
qualSample     6.275  0.032   6.307
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/SNAGEE.Rcheck/00check.log’
for details.



Installation output

SNAGEE.Rcheck/00install.out

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

Tests output


Example timings

SNAGEE.Rcheck/SNAGEE-Ex.timings

nameusersystemelapsed
SNAGEE-package8.5230.7009.283
qualSample6.2750.0326.307
qualStudy1.5760.0041.580
toSnageeFormat1.6270.0041.630