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CHECK report for HDCytoData on malbec2

This page was generated on 2021-01-04 15:59:06 -0500 (Mon, 04 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HDCytoData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 164/385HostnameOS / ArchINSTALLBUILDCHECK
HDCytoData 1.11.0
Lukas M. Weber
Snapshot Date: 2021-01-04 09:00:11 -0500 (Mon, 04 Jan 2021)
URL: https://git.bioconductor.org/packages/HDCytoData
Branch: master
Last Commit: 58d130f
Last Changed Date: 2020-10-27 10:26:33 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: HDCytoData
Version: 1.11.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HDCytoData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HDCytoData_1.11.0.tar.gz
StartedAt: 2021-01-04 12:11:08 -0500 (Mon, 04 Jan 2021)
EndedAt: 2021-01-04 12:16:28 -0500 (Mon, 04 Jan 2021)
EllapsedTime: 320.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HDCytoData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HDCytoData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HDCytoData_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HDCytoData.Rcheck’
* using R Under development (unstable) (2020-11-14 r79432)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDCytoData/DESCRIPTION’ ... OK
* this is package ‘HDCytoData’ version ‘1.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDCytoData’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Samusik_all_SE            13.726  0.487  16.728
Bodenmiller_BCR_XL_SE      9.464  0.280  13.274
Levine_32dim_SE            8.368  0.144  13.002
Weber_AML_sim_main_5pc_SE  7.854  0.200  11.303
Mosmann_rare_SE            7.602  0.144   9.464
Krieg_Anti_PD_1_SE         7.026  0.124   8.679
Levine_13dim_SE            6.978  0.096   8.424
Samusik_01_SE              6.811  0.128   8.637
Weber_BCR_XL_sim_main_SE   6.677  0.056   8.328
Nilsson_rare_SE            6.393  0.080   8.063
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HDCytoData.Rcheck/00check.log’
for details.



Installation output

HDCytoData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HDCytoData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘HDCytoData’ ...
** 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
snapshotDate(): 2020-12-22
** testing if installed package can be loaded from final location
snapshotDate(): 2020-12-22
** testing if installed package keeps a record of temporary installation path
* DONE (HDCytoData)

Tests output


Example timings

HDCytoData.Rcheck/HDCytoData-Ex.timings

nameusersystemelapsed
Bodenmiller_BCR_XL_SE 9.464 0.28013.274
Krieg_Anti_PD_1_SE7.0260.1248.679
Levine_13dim_SE6.9780.0968.424
Levine_32dim_SE 8.368 0.14413.002
Mosmann_rare_SE7.6020.1449.464
Nilsson_rare_SE6.3930.0808.063
Samusik_01_SE6.8110.1288.637
Samusik_all_SE13.726 0.48716.728
Weber_AML_sim_main_5pc_SE 7.854 0.20011.303
Weber_BCR_XL_sim_main_SE6.6770.0568.328