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CHECK report for SCATEData on malbec2

This page was generated on 2021-01-14 15:59:05 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SCATEData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 321/385HostnameOS / ArchINSTALLBUILDCHECK
SCATEData 1.1.0
Wenpin Hou
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/SCATEData
Branch: master
Last Commit: 21918ad
Last Changed Date: 2020-10-27 10:32:09 -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: SCATEData
Version: 1.1.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SCATEData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SCATEData_1.1.0.tar.gz
StartedAt: 2021-01-14 12:47:05 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:51:20 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 255.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SCATEData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SCATEData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SCATEData_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/SCATEData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCATEData/DESCRIPTION’ ... OK
* this is package ‘SCATEData’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘SCATEData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 190.0Mb
  sub-directories of 1Mb or more:
    extdata  189.9Mb
* 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 ... NOTE
prepare_Rd: hg19.rds.Rd:18-19: Dropping empty section \usage
prepare_Rd: mm10.rds.Rd:18-19: Dropping empty section \usage
* 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
hg19.rds 10.599  0.200  11.559
mm10.rds  7.121  0.232   7.408
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/SCATEData.Rcheck/00check.log’
for details.



Installation output

SCATEData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SCATEData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘SCATEData’ ...
** 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(): 2021-01-14
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-14
** testing if installed package keeps a record of temporary installation path
* DONE (SCATEData)

Tests output


Example timings

SCATEData.Rcheck/SCATEData-Ex.timings

nameusersystemelapsed
GSM1596831.bam0.0690.0000.128
GSM1596840.bam0.1080.0000.155
GSM1596874.bam0.0680.0000.252
GSM1596881.bam0.0590.0000.093
GSM1596940.bam0.0220.0030.047
GSM1596942.bam0.0610.0080.401
GSM1596944.bam0.1040.0080.484
GSM1596961.bam0.1760.0080.398
GSM1597041.bam0.1060.0010.389
GSM1597096.bam0.0750.0040.176
SRR1779746.bam0.1010.0040.139
SRR1779805.bam0.1870.0030.427
SRR1779856.bam0.0280.0000.044
SRR1779874.bam0.2150.0070.509
SRR1779956.bam0.1350.0000.135
SRR1779959.bam0.0880.0040.092
SRR1779973.bam0.080.000.48
SRR1780018.bam0.0380.0000.221
SRR1780020.bam0.0680.0040.341
SRR1780054.bam0.1720.0040.176
hg19.rds10.599 0.20011.559
mm10.rds7.1210.2327.408