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This page was generated on 2023-04-12 11:05:08 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 ITALICS on nebbiolo2


To the developers/maintainers of the ITALICS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ITALICS.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 1010/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ITALICS 2.58.0  (landing page)
Guillem Rigaill
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ITALICS
git_branch: RELEASE_3_16
git_last_commit: 331d965
git_last_commit_date: 2022-11-01 11:03:59 -0400 (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: ITALICS
Version: 2.58.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ITALICS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ITALICS_2.58.0.tar.gz
StartedAt: 2023-04-10 21:31:12 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:34:46 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 214.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ITALICS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ITALICS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ITALICS_2.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/ITALICS.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ITALICS/DESCRIPTION’ ... OK
* this is package ‘ITALICS’ version ‘2.58.0’
* 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 loading without being on the library search path ... 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 ...
  ‘ITALICS.Rnw’ using ‘latin1’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/ITALICS.Rcheck/00check.log’
for details.



Installation output

ITALICS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ITALICS
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘ITALICS’ ...
** 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 (ITALICS)

Tests output


Example timings

ITALICS.Rcheck/ITALICS-Ex.timings

nameusersystemelapsed
ITALICSNew000