Davide Risso
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 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) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:20 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1847/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scone 1.29.0 (landing page) Davide Risso
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the scone package: - 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. |
| Package: scone |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scone_1.29.0.tar.gz |
| StartedAt: 2024-05-20 02:00:14 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 02:11:22 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 667.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scone.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scone_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/scone.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* 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 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 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/scone.Rcheck/00check.log’
for details.
scone.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scone ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 0 | WARN 0 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
70.786 8.246 274.590
scone.Rcheck/scone-Ex.timings
| name | user | system | elapsed | |
| CLR_FN | 0.002 | 0.000 | 0.003 | |
| DESEQ_FN | 0.002 | 0.001 | 0.002 | |
| FQ_FN | 0.003 | 0.001 | 0.003 | |
| PSINORM_FN | 0.002 | 0.001 | 0.003 | |
| PsiNorm | 0.376 | 0.005 | 0.383 | |
| SCRAN_FN | 1.176 | 0.107 | 1.289 | |
| SUM_FN | 0.000 | 0.000 | 0.001 | |
| SconeExperiment-class | 0.135 | 0.002 | 0.136 | |
| TMM_FN | 0.004 | 0.001 | 0.004 | |
| UQ_FN | 0.001 | 0.001 | 0.002 | |
| biplot_color | 0.013 | 0.002 | 0.014 | |
| biplot_interactive | 0.293 | 0.005 | 0.299 | |
| control_genes | 0.022 | 0.010 | 0.032 | |
| estimate_ziber | 0.038 | 0.002 | 0.038 | |
| factor_sample_filter | 0.102 | 0.008 | 0.109 | |
| fast_estimate_ziber | 0.026 | 0.001 | 0.026 | |
| get_bio | 0.035 | 0.000 | 0.036 | |
| get_design | 0.503 | 0.003 | 0.508 | |
| get_negconruv | 0.043 | 0.000 | 0.044 | |
| get_normalized | 0.104 | 0.001 | 0.106 | |
| get_params | 0.038 | 0.001 | 0.040 | |
| get_qc | 0.062 | 0.002 | 0.064 | |
| get_scores | 0.109 | 0.009 | 0.118 | |
| impute_expectation | 0.001 | 0.000 | 0.001 | |
| impute_null | 0.000 | 0.001 | 0.001 | |
| lm_adjust | 0.004 | 0.000 | 0.005 | |
| make_design | 0.001 | 0.000 | 0.001 | |
| metric_sample_filter | 0.007 | 0.002 | 0.008 | |
| scone | 0.259 | 0.018 | 0.277 | |
| sconeReport | 0.105 | 0.001 | 0.106 | |
| scone_easybake | 0.102 | 0.001 | 0.103 | |
| score_matrix | 0.004 | 0.001 | 0.003 | |
| select_methods | 0.104 | 0.001 | 0.105 | |
| simple_FNR_params | 0.021 | 0.000 | 0.021 | |