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This page was generated on 2023-06-06 11:00:40 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for RefPlus on kunpeng2


To the developers/maintainers of the RefPlus package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RefPlus.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1651/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefPlus 1.71.0  (landing page)
Kai-Ming Chang
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/RefPlus
git_branch: devel
git_last_commit: 0ca226b
git_last_commit_date: 2023-04-25 13:44:38 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: RefPlus
Version: 1.71.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings RefPlus_1.71.0.tar.gz
StartedAt: 2023-06-06 05:07:13 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 05:10:34 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 201.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RefPlus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings RefPlus_1.71.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘RefPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefPlus’ version ‘1.71.0’
* 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 ‘RefPlus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘affyPLM’
  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
rma.para: no visible global function definition for ‘rmaPLM’
rma.para: no visible global function definition for ‘coefs.probe’
rma.para: no visible global function definition for ‘coefs’
Undefined global functions or variables:
  coefs coefs.probe rmaPLM
* checking Rd files ... NOTE
prepare_Rd: colMedians.Rd:19: Dropping empty section \references
prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples
* 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
RefPlus-package 79.131  4.161  88.506
rmaplus          8.161  0.091   8.273
rma.para         5.391  0.120   5.523
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RefPlus.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/RefPlus.Rcheck/00check.log’
for details.



Installation output

RefPlus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL RefPlus
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘RefPlus’ ...
** 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 (RefPlus)

Tests output


Example timings

RefPlus.Rcheck/RefPlus-Ex.timings

nameusersystemelapsed
RefPlus-package79.131 4.16188.506
colMedians0.0000.0000.001
normalize.quantiles20.0010.0000.001
rma.para5.3910.1205.523
rmaplus8.1610.0918.273