Back to Multiple platform build/check report for BioC 3.11
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for ITALICS on malbec2

This page was generated on 2020-10-17 11:55:00 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ITALICS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 905/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ITALICS 2.48.0
Guillem Rigaill
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ITALICS
Branch: RELEASE_3_11
Last Commit: 7bf7334
Last Changed Date: 2020-04-27 14:17:41 -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: ITALICS
Version: 2.48.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ITALICS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ITALICS_2.48.0.tar.gz
StartedAt: 2020-10-17 02:31:10 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:34:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 172.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ITALICS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ITALICS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ITALICS_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ITALICS.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 ‘ITALICS/DESCRIPTION’ ... OK
* this is package ‘ITALICS’ version ‘2.48.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ITALICS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affxparser’ ‘GLAD’ ‘oligo’
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 ... NOTE
Packages in Depends field not imported from:
  ‘ITALICSData’ ‘pd.mapping50k.xba240’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
trainITALICS: warning in list.files(dir, full.name = TRUE): partial
  argument match of 'full.name' to 'full.names'
* checking Rd files ... NOTE
prepare_Rd: GLAD.GLAD.Rd:33: Dropping empty section \keyword
prepare_Rd: ITALICSNew.Rd:82: Dropping empty section \keyword
prepare_Rd: ITALICSTrain.Rd:43: Dropping empty section \keyword
prepare_Rd: Model.GetConfDat.Rd:23: Dropping empty section \keyword
prepare_Rd: Model.GetCorrection.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetEffet.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetModel.Rd:21: Dropping empty section \keyword
prepare_Rd: Model.GetResidu.Rd:18: Dropping empty section \keyword
prepare_Rd: New.AddInfo.Rd:24: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:31: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:25: Dropping empty section \examples
prepare_Rd: New.fromSnpToQuartet.Rd:25: Dropping empty section \keyword
prepare_Rd: New.getQuartet.Rd:27: Dropping empty section \keyword
prepare_Rd: New.getSnpInfo.Rd:25: Dropping empty section \keyword
prepare_Rd: New.readQuartetCopyNb.Rd:23: Dropping empty section \keyword
* 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
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/ITALICS.Rcheck/00check.log’
for details.



Installation output

ITALICS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ITALICS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ITALICS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package keeps a record of temporary installation path
* DONE (ITALICS)

Tests output


Example timings

ITALICS.Rcheck/ITALICS-Ex.timings

nameusersystemelapsed
ITALICSNew000