Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 1855/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.29.0  (landing page)
Davide Risso
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/scone
git_branch: devel
git_last_commit: 91519d5
git_last_commit_date: 2024-04-30 10:55:37 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for scone on palomino6

To the developers/maintainers of the scone package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scone.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: scone
Version: 1.29.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scone.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scone_1.29.0.tar.gz
StartedAt: 2024-07-16 03:50:02 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 04:03:07 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 785.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scone.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scone.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scone_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/scone.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scone/DESCRIPTION' ... OK
* this is package 'scone' version '1.29.0'
* 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 whether package 'scone' 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 code 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
sconeReport: no visible global function definition for
  'visNetworkOutput'
sconeReport: no visible global function definition for 'plotlyOutput'
sconeReport : server: no visible global function definition for
  'renderVisNetwork'
sconeReport : server: no visible global function definition for '%>%'
sconeReport : server: no visible global function definition for
  'visNetwork'
sconeReport : server: no visible global function definition for
  'visHierarchicalLayout'
sconeReport : server: no visible global function definition for
  'visGroups'
sconeReport : server: no visible global function definition for
  'visEdges'
sconeReport : server: no visible global function definition for
  'visOptions'
sconeReport : server: no visible global function definition for
  'visLegend'
sconeReport : server: no visible global function definition for
  'visNetworkProxy'
sconeReport : server: no visible global function definition for
  'visSelectNodes'
sconeReport : server: no visible global function definition for
  'plot_ly'
sconeReport : server: no visible global function definition for
  'ggplot'
sconeReport : server: no visible global function definition for 'aes'
sconeReport : server: no visible global function definition for
  'geom_bar'
sconeReport : server: no visible global function definition for 'ylim'
sconeReport : server: no visible global function definition for 'labs'
sconeReport : server: no visible global function definition for 'theme'
sconeReport : server: no visible global function definition for
  'element_blank'
sconeReport : server: no visible global function definition for
  'ggplotly'
sconeReport : server: no visible global function definition for
  'geom_violin'
sconeReport : server: no visible global function definition for
  'coord_cartesian'
sconeReport : server: no visible global function definition for
  'scale_fill_manual'
sconeReport : server: no visible global function definition for
  'geom_point'
sconeReport : server: no visible global function definition for
  'guides'
Undefined global functions or variables:
  %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin
  ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork
  scale_fill_manual theme visEdges visGroups visHierarchicalLayout
  visLegend visNetwork visNetworkOutput visNetworkProxy visOptions
  visSelectNodes ylim
* checking Rd files ... NOTE
checkRd: (-1) estimate_ziber.Rd:57: Lost braces; missing escapes or markup?
    57 | expression rate (Z in {0,1}). Detection conditioned on expression is a 
       |                       ^
checkRd: (-1) estimate_ziber.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_ziber.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:59: Lost braces; missing escapes or markup?
    59 | expression rate (Z in {0,1}). Detection conditioned on expression is a 
       |                       ^
checkRd: (-1) fast_estimate_ziber.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fast_estimate_ziber.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup?
    23 |   y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}).
       |     ^
checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup?
    23 |   y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}).
       |               ^
checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup?
    23 |   y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}).
       |                                      ^
checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup?
    23 |   y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}).
       |                                                 ^
checkRd: (-1) impute_expectation.Rd:23: Lost braces; missing escapes or markup?
    23 |   y_{ij}* = y_{ij} * Pr( No Drop | y_{ij}) + mu_{i} * Pr( Drop | y_{ij}).
       |                                                                    ^
checkRd: (-1) metric_sample_filter.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) metric_sample_filter.Rd:105-106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) metric_sample_filter.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) metric_sample_filter.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) scone.Rd:126-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:145-146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:147-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scone.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) score_matrix.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) score_matrix.Rd:100-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) score_matrix.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:85-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_matrix.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
* 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' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/scone.Rcheck/00check.log'
for details.


Installation output

scone.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scone
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'scone' ...
** 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 (scone)

Tests output

scone.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(scone)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("scone")
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
> > > > > > > > [ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
  74.53    7.98  374.00 

Example timings

scone.Rcheck/scone-Ex.timings

nameusersystemelapsed
CLR_FN000
DESEQ_FN000
FQ_FN000
PSINORM_FN000
PsiNorm0.280.000.29
SCRAN_FN0.750.210.98
SUM_FN000
SconeExperiment-class0.100.000.09
TMM_FN000
UQ_FN000
biplot_color0.010.000.02
biplot_interactive0.20.00.2
control_genes0.020.010.03
estimate_ziber0.020.020.04
factor_sample_filter0.000.050.04
fast_estimate_ziber0.060.000.06
get_bio0.030.000.04
get_design0.370.000.37
get_negconruv0.040.000.03
get_normalized0.070.010.10
get_params0.030.000.03
get_qc0.050.000.04
get_scores0.080.020.10
impute_expectation0.020.000.01
impute_null000
lm_adjust000
make_design000
metric_sample_filter0.010.000.02
scone0.200.010.22
sconeReport0.100.000.09
scone_easybake0.080.000.08
score_matrix000
select_methods0.090.000.09
simple_FNR_params0.020.000.02