Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:30 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 frma on palomino3


To the developers/maintainers of the frma package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/frma.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 707/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frma 1.48.0  (landing page)
Matthew N. McCall
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/frma
git_branch: RELEASE_3_15
git_last_commit: 3c39bcf
git_last_commit_date: 2022-04-26 11:04:03 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: frma
Version: 1.48.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:frma.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings frma_1.48.0.tar.gz
StartedAt: 2022-10-19 00:22:06 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 00:26:06 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 240.1 seconds
RetCode: 0
Status:   OK  
CheckDir: frma.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:frma.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings frma_1.48.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/frma.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'frma/DESCRIPTION' ... OK
* this is package 'frma' version '1.48.0'
* 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 whether package 'frma' 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:
  'Biobase'
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
GNUSE: no visible binding for global variable 'median'
GNUSE: no visible binding for global variable 'quantile'
GNUSE: no visible global function definition for 'boxplot'
barcode: no visible global function definition for 'pnorm'
batchFit: no visible global function definition for 'median'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot<-'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot'
randomeffects<-,frmaExpressionSet: no visible global function
  definition for 'validObject'
residuals<-,frmaExpressionSet: no visible global function definition
  for 'validObject'
se.exprs<-,ExpressionSet: no visible global function definition for
  'validObject'
se.exprs<-,frmaExpressionSet: no visible global function definition for
  'validObject'
weights<-,frmaExpressionSet: no visible global function definition for
  'validObject'
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
GNUSE   17.50   1.70   19.44
frma    12.06   1.02   13.08
barcode 11.83   0.89   12.74
* 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-3.15-bioc/meat/frma.Rcheck/00check.log'
for details.



Installation output

frma.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL frma
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'frma' ...
** 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 (frma)

Tests output


Example timings

frma.Rcheck/frma-Ex.timings

nameusersystemelapsed
GNUSE17.50 1.7019.44
barcode11.83 0.8912.74
frma12.06 1.0213.08
frmaExpressionSet-class0.10.00.1