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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:POWSC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings POWSC_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/POWSC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘POWSC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘POWSC’ version ‘1.6.0’
* 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 loading without being on the library search path ... 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    13.216  0.251  13.534
summary_POWSC 12.468  0.115  12.725
runPOWSC      11.978  0.156  12.159
Power_Disc     9.012  0.207   9.221
Power_Cont     8.873  0.312   9.185
runDE          5.447  0.032   5.495
* 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 ...
  ‘POWSC.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/POWSC.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL POWSC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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(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, aperm, 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 
 25.298   1.197  26.583