Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:33 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 POWSC on machv2


To the developers/maintainers of the POWSC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/POWSC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1443/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POWSC 1.2.0  (landing page)
Kenong Su
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/POWSC
git_branch: RELEASE_3_14
git_last_commit: c5947c0
git_last_commit_date: 2021-10-26 13:09:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: POWSC
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:POWSC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings POWSC_1.2.0.tar.gz
StartedAt: 2022-04-12 16:53:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:00:09 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 405.6 seconds
RetCode: 0
Status:   OK  
CheckDir: POWSC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:POWSC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings POWSC_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/POWSC.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POWSC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘POWSC’ version ‘1.2.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘POWSC’ 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
Est2Phase: no visible global function definition for ‘is’
Est2Phase: no visible global function definition for ‘dpois’
Est2Phase: no visible global function definition for ‘qpois’
GenerateCountMatrix: no visible global function definition for ‘rbinom’
RobustPoi0: no visible global function definition for ‘lm’
Simulate2SCE: no visible global function definition for ‘runif’
Simulate2SCE: no visible global function definition for ‘rnorm’
SimulateMultiSCEs: no visible global function definition for
  ‘rmultinom’
dLNP2: no visible global function definition for ‘pnorm’
dZinf.pois: no visible global function definition for ‘dpois’
eset2Phase: no visible global function definition for ‘dpois’
eset2Phase: no visible global function definition for ‘qpois’
eset2Phase: no visible global function definition for ‘loess’
eset2Phase: no visible binding for global variable ‘span’
eset2Phase : <anonymous>: no visible global function definition for
  ‘loess’
eset2Phase: no visible global function definition for ‘new’
my.mad: no visible global function definition for ‘median’
plot_POWSC: no visible binding for global variable ‘Strata’
plot_POWSC: no visible binding for global variable ‘Power’
plot_POWSC: no visible binding for global variable ‘Reps’
rLNP: no visible global function definition for ‘rnorm’
rLNP: no visible global function definition for ‘rpois’
runMAST: no visible global function definition for ‘p.adjust’
runMAST: no visible global function definition for ‘complete.cases’
runSC2P: no visible global function definition for ‘p.adjust’
runSC2P: no visible global function definition for ‘<-<-’
rzip: no visible global function definition for ‘rbinom’
rzip: no visible global function definition for ‘rpois’
shrink.mu: no visible global function definition for ‘weighted.mean’
toEset: no visible global function definition for ‘new’
twoPhaseDE: no visible global function definition for ‘median’
twoPhaseDE0 : <anonymous>: no visible global function definition for
  ‘pchisq’
twoPhaseDE0: no visible global function definition for ‘qt’
Undefined global functions or variables:
  <-<- Power Reps Strata complete.cases dpois is lm loess median new
  p.adjust pchisq pnorm qpois qt rbinom rmultinom rnorm rpois runif
  span weighted.mean
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "complete.cases", "dpois", "lm", "loess", "median",
             "p.adjust", "pchisq", "pnorm", "qpois", "qt", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_POWSC    19.186  0.445  19.644
runPOWSC      18.022  0.358  18.411
summary_POWSC 16.900  0.272  17.182
Power_Disc    15.991  0.618  16.623
Power_Cont    12.354  0.391  12.757
runDE          8.925  0.146   9.082
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/POWSC.Rcheck/00check.log’
for details.



Installation output

POWSC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL POWSC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘POWSC’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (POWSC)

Tests output

POWSC.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(POWSC)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: MAST
> 
> test_check("POWSC")
(4.62,7.57] (7.57,8.53] (8.53,9.59] (9.59,10.8] (10.8,15.2] 
   6.374777    6.374777    6.632438    6.632438   19.096520 
(4.97,7.08] (7.08,7.94] (7.94,8.89] (8.89,9.93] (9.93,11.1] (11.1,15.4] 
   1.510573    5.995587    5.995587    6.058978    6.448522    7.348194 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 32.458   1.048  33.510 

Example timings

POWSC.Rcheck/POWSC-Ex.timings

nameusersystemelapsed
Est2Phase1.8390.0391.880
Power_Cont12.354 0.39112.757
Power_Disc15.991 0.61816.623
Simulate2SCE1.2940.0211.315
SimulateMultiSCEs2.6190.0292.650
plot_POWSC19.186 0.44519.644
runDE8.9250.1469.082
runPOWSC18.022 0.35818.411
summary_POWSC16.900 0.27217.182