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This page was generated on 2021-07-23 15:05:50 -0400 (Fri, 23 Jul 2021).

CHECK results for RNASeqR on nebbiolo1

To the developers/maintainers of the RNASeqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNASeqR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1612/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNASeqR 1.10.0  (landing page)
Kuan-Hao Chao
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/RNASeqR
Branch: RELEASE_3_13
Last Commit: c89d5c1
Last Changed Date: 2021-05-19 12:38:39 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RNASeqR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RNASeqR_1.10.0.tar.gz
StartedAt: 2021-07-22 11:20:21 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 11:26:24 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 363.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RNASeqR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RNASeqR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RNASeqR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNASeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNASeqR’ version ‘1.10.0’
* 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:
  .BBSoptions
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 ‘RNASeqR’ 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 ... NOTE
AlignmentPlot: no visible binding for global variable ‘value’
Update_Fastq_gz: no visible binding for global variable
  ‘sample.pattern’
Undefined global functions or variables:
  sample.pattern value
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/RNASeqR.Rcheck/00check.log’
for details.



Installation output

RNASeqR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RNASeqR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘RNASeqR’ ...
** using staged installation
** R
** data
** 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 (RNASeqR)

Tests output


Example timings

RNASeqR.Rcheck/RNASeqR-Ex.timings

nameusersystemelapsed
All_Steps_Interface0.0040.0000.003
All_Steps_Interface_CMD0.0010.0000.001
CheckToolAll0.0020.0000.001
RNASeqDifferentialAnalysis0.0010.0000.001
RNASeqDifferentialAnalysis_CMD0.0010.0000.001
RNASeqEnvironmentSet0.0010.0000.001
RNASeqEnvironmentSet_CMD0.0010.0000.001
RNASeqGoKegg0.0010.0000.001
RNASeqGoKegg_CMD0.0010.0000.001
RNASeqQualityAssessment0.0000.0010.001
RNASeqQualityAssessment_CMD0.0000.0010.001
RNASeqRParam-class0.0010.0000.002
RNASeqRParam-constructor0.4330.0550.494
RNASeqRParam_Bam-class0.0320.0040.036
RNASeqRParam_Bam-constructor0.0070.0030.010
RNASeqRParam_Sam-class0.0340.0000.034
RNASeqRParam_Sam-constructor0.0090.0000.010
RNASeqReadProcess0.0040.0040.008
RNASeqReadProcess_CMD0.0080.0000.008
Update_Fastq_gz0.0070.0000.008
yeast0.0110.0000.011