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This page was generated on 2022-01-19 11:06:46 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 RnaSeqSampleSize on nebbiolo1


To the developers/maintainers of the RnaSeqSampleSize package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnaSeqSampleSize.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 1631/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnaSeqSampleSize 2.5.1  (landing page)
Shilin Zhao Developer
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/RnaSeqSampleSize
git_branch: master
git_last_commit: 3898c19
git_last_commit_date: 2021-12-03 15:25:22 -0500 (Fri, 03 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'biomaRt' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RnaSeqSampleSize
Version: 2.5.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RnaSeqSampleSize_2.5.1.tar.gz
StartedAt: 2022-01-18 20:47:53 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 20:53:06 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 313.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RnaSeqSampleSize.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RnaSeqSampleSize_2.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RnaSeqSampleSize.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnaSeqSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RnaSeqSampleSize’ version ‘2.5.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnaSeqSampleSize’ 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
analyze_dataset: no visible binding for global variable ‘logFC’
analyze_dataset: no visible binding for global variable
  ‘DispersionInTreatmentVsControl’
analyze_dataset: no visible binding for global variable
  ‘DispersionInControlOnly’
plot_gene_counts_range: no visible binding for global variable ‘name’
plot_gene_counts_range: no visible binding for global variable ‘value’
plot_mappedReads_percent: no visible binding for global variable
  ‘Reads’
plot_mappedReads_percent: no visible binding for global variable
  ‘Category’
plot_mappedReads_percent: no visible binding for global variable
  ‘Tissue’
plot_mappedReads_percent: no visible binding for global variable
  ‘MappedReadsPercent’
Undefined global functions or variables:
  Category DispersionInControlOnly DispersionInTreatmentVsControl
  MappedReadsPercent Reads Tissue logFC name 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
est_power_curve          7.970  0.180   8.151
sample_size_distribution 7.564  0.039   7.605
convertIdOneToOne        2.043  0.029  13.559
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RnaSeqSampleSize.Rcheck/00check.log’
for details.



Installation output

RnaSeqSampleSize.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RnaSeqSampleSize
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘RnaSeqSampleSize’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RnaSeqSampleSize.c -o RnaSeqSampleSize.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bd0.c -o bd0.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cumsumBorder.cpp -o cumsumBorder.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stirlerr.c -o stirlerr.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o RnaSeqSampleSize.so RcppExports.o RnaSeqSampleSize.o bd0.o cumsumBorder.o stirlerr.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RnaSeqSampleSize/00new/RnaSeqSampleSize/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RnaSeqSampleSize)

Tests output

RnaSeqSampleSize.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RnaSeqSampleSize)
Loading required package: ggplot2
Loading required package: RnaSeqSampleSizeData
Loading required package: edgeR
Loading required package: limma
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("RnaSeqSampleSize")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 16.565   1.048  17.601 

Example timings

RnaSeqSampleSize.Rcheck/RnaSeqSampleSize-Ex.timings

nameusersystemelapsed
analyze_dataset0.0010.0000.000
convertIdOneToOne 2.043 0.02913.559
est_count_dispersion0.1820.0000.182
est_power2.6140.0522.667
est_power_curve7.9700.1808.151
est_power_distribution3.5371.0844.625
optimize_parameter4.5390.0234.563
plot_gene_counts_range000
plot_mappedReads_percent000
plot_power_curve0.2480.0000.249
sample_size0.3710.0000.371
sample_size_distribution7.5640.0397.605