| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:27 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the scone package: - Please 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 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. |
| Package 1794/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scone 1.23.1 (landing page) Davide Risso
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: scone |
| Version: 1.23.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scone_1.23.1.tar.gz |
| StartedAt: 2023-02-07 14:59:02 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 15:10:39 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 697.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scone.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scone_1.23.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scone.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.23.1’
* 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 ‘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 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
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 ... 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 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:
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")
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘PsiNorm.Rmd’ using ‘UTF-8’... OK
‘sconeTutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘PsiNorm.Rmd’ using rmarkdown
Killed
--- re-building ‘sconeTutorial.Rmd’ using rmarkdown
Killed
SUMMARY: processing the following files failed:
‘PsiNorm.Rmd’ ‘sconeTutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/scone.Rcheck/00check.log’
for details.
scone.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scone ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
scone.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> 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, sort, table,
tapply, union, unique, unsplit, which.max, which.min
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: 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")
Killed
scone.Rcheck/scone-Ex.timings
| name | user | system | elapsed | |
| CLR_FN | 0.002 | 0.000 | 0.002 | |
| DESEQ_FN | 0.002 | 0.000 | 0.001 | |
| FQ_FN | 0.002 | 0.000 | 0.003 | |
| PSINORM_FN | 0.002 | 0.000 | 0.002 | |
| PsiNorm | 0.440 | 0.000 | 0.441 | |
| SCRAN_FN | 2.465 | 0.036 | 2.545 | |
| SUM_FN | 0 | 0 | 0 | |
| SconeExperiment-class | 0.148 | 0.008 | 0.156 | |
| TMM_FN | 0.004 | 0.000 | 0.004 | |
| UQ_FN | 0.002 | 0.000 | 0.001 | |
| biplot_color | 0.008 | 0.004 | 0.012 | |
| biplot_interactive | 0.287 | 0.044 | 0.332 | |
| control_genes | 0.017 | 0.000 | 0.019 | |
| estimate_ziber | 0.092 | 0.004 | 0.096 | |
| factor_sample_filter | 0.062 | 0.000 | 0.064 | |
| fast_estimate_ziber | 0.039 | 0.000 | 0.039 | |
| get_bio | 0.05 | 0.00 | 0.05 | |
| get_design | 0.581 | 0.000 | 0.581 | |
| get_negconruv | 0.060 | 0.000 | 0.059 | |
| get_normalized | 0.140 | 0.000 | 0.141 | |
| get_params | 0.044 | 0.016 | 0.059 | |
| get_qc | 0.064 | 0.004 | 0.068 | |
| get_scores | 0.137 | 0.012 | 0.149 | |
| impute_expectation | 0 | 0 | 0 | |
| impute_null | 0 | 0 | 0 | |
| lm_adjust | 0.005 | 0.000 | 0.004 | |
| make_design | 0.002 | 0.000 | 0.002 | |
| metric_sample_filter | 0.008 | 0.000 | 0.010 | |
| scone | 0.314 | 0.044 | 0.358 | |
| sconeReport | 0.146 | 0.000 | 0.146 | |
| scone_easybake | 0.145 | 0.000 | 0.145 | |
| score_matrix | 0.004 | 0.000 | 0.004 | |
| select_methods | 0.140 | 0.004 | 0.144 | |
| simple_FNR_params | 0.030 | 0.000 | 0.031 | |