Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-18 11:36:25 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1906/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.28.0  (landing page)
Davide Risso
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/scone
git_branch: RELEASE_3_19
git_last_commit: 298a397
git_last_commit_date: 2024-04-30 10:55:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for scone on nebbiolo1


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: 1.28.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scone_1.28.0.tar.gz
StartedAt: 2024-05-18 02:47:04 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 02:55:59 -0400 (Sat, 18 May 2024)
EllapsedTime: 534.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: scone.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scone_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scone.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.28.0’
* 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 ‘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 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
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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    2. └─scone::scone(...)
    3.   └─scone (local) .local(x, ...)
    4.     ├─BiocParallel::bplapply(...)
    5.     └─BiocParallel::bplapply(...)
    6.       └─BiocParallel:::.bpinit(...)
    7.         ├─BiocParallel::bpstart(BPPARAM)
    8.         └─BiocParallel::bpstart(BPPARAM)
    9.           └─BiocParallel (local) .local(x, ...)
   10.             └─BiocParallel:::.bpfork(nnodes, .hostname(x), .port(x))
   11.               └─BiocParallel:::.bpforkConnect(...)
   12.                 └─base::socketConnection(host, port, TRUE, TRUE, "a+b", timeout = connect_timeout)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/scone.Rcheck/00check.log’
for details.


Installation output

scone.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scone
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
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")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 59 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_bpparam.R:31:5'): all back-ends work ───────────────────────────
Error in `socketConnection(host, port, TRUE, TRUE, "a+b", timeout = connect_timeout)`: cannot open the connection
Backtrace:
     ▆
  1. ├─scone::scone(...) at test_bpparam.R:31:5
  2. └─scone::scone(...)
  3.   └─scone (local) .local(x, ...)
  4.     ├─BiocParallel::bplapply(...)
  5.     └─BiocParallel::bplapply(...)
  6.       └─BiocParallel:::.bpinit(...)
  7.         ├─BiocParallel::bpstart(BPPARAM)
  8.         └─BiocParallel::bpstart(BPPARAM)
  9.           └─BiocParallel (local) .local(x, ...)
 10.             └─BiocParallel:::.bpfork(nnodes, .hostname(x), .port(x))
 11.               └─BiocParallel:::.bpforkConnect(...)
 12.                 └─base::socketConnection(host, port, TRUE, TRUE, "a+b", timeout = connect_timeout)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 59 ]
Error: Test failures
Execution halted

Example timings

scone.Rcheck/scone-Ex.timings

nameusersystemelapsed
CLR_FN0.0020.0000.002
DESEQ_FN0.0020.0000.002
FQ_FN0.0030.0000.003
PSINORM_FN0.0020.0000.002
PsiNorm0.3290.0040.333
SCRAN_FN1.0700.1321.202
SUM_FN0.0010.0000.000
SconeExperiment-class0.1280.0030.132
TMM_FN0.0030.0000.004
UQ_FN0.0010.0000.002
biplot_color0.0120.0000.012
biplot_interactive0.2360.0040.240
control_genes0.0170.0000.017
estimate_ziber0.0840.0000.083
factor_sample_filter0.0510.0040.055
fast_estimate_ziber0.0310.0000.031
get_bio0.0380.0000.039
get_design0.4510.0000.450
get_negconruv0.0390.0030.042
get_normalized0.10.00.1
get_params0.0330.0040.036
get_qc0.0510.0000.051
get_scores0.10.00.1
impute_expectation0.0010.0000.000
impute_null000
lm_adjust0.0040.0000.004
make_design0.0010.0000.002
metric_sample_filter0.0030.0040.007
scone0.2490.0160.265
sconeReport0.0930.0030.097
scone_easybake0.0950.0000.094
score_matrix0.0040.0000.003
select_methods0.1020.0000.102
simple_FNR_params0.0200.0000.021