Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 345/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cicero 1.23.0 (landing page) Hannah Pliner
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the cicero package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cicero.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. |
Package: cicero |
Version: 1.23.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cicero.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cicero_1.23.0.tar.gz |
StartedAt: 2024-06-10 00:55:06 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:04:51 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 584.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cicero.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cicero.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cicero_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/cicero.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'cicero/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cicero' version '1.23.0' * 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 'cicero' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 aggregate_nearby_peaks: no visible binding for global variable 'val' annotate_cds_by_site: no visible binding for global variable 'row_name' assemble_connections : <anonymous>: no visible global function definition for 'patterns' assemble_connections: no visible binding for global variable 'value' estimateDispersionsForCellDataSet: no visible global function definition for 'cooks.distance' estimateSizeFactorsSimp: no visible global function definition for 'sizeFactors<-' find_overlapping_ccans: no visible binding for global variable 'CCAN' generate_windows: no visible binding for global variable 'V1' parametricDispersionFit: no visible global function definition for 'glm' parametricDispersionFit: no visible global function definition for 'Gamma' plot_accessibility_in_pseudotime: no visible binding for global variable 'f_id' plot_accessibility_in_pseudotime: no visible binding for global variable 'Var1' Undefined global functions or variables: CCAN Gamma V1 Var1 cooks.distance f_id glm patterns row_name sizeFactors<- val value Consider adding importFrom("stats", "Gamma", "cooks.distance", "glm") to your NAMESPACE file. * 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 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/cicero.Rcheck/00check.log' for details.
cicero.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cicero ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'cicero' ... ** 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 (cicero)
cicero.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > library(testthat) > library(cicero) Loading required package: monocle Loading required package: Matrix 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, 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: ggplot2 Loading required package: VGAM Loading required package: stats4 Loading required package: splines Loading required package: DDRTree Loading required package: irlba Loading required package: Gviz Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid > > test_check("cicero") [1] "Successful cicero models: 283" [1] "Other models: " Zero or one element in range 30 [1] "Models with errors: 0" [1] "Coaccessibility cutoff used: 0.25" [1] "Generating fData ranges" [1] "Generating feature data ranges" [1] "Determining overlaps" [1] "Assigning labels" [1] "Merging to fData table" [1] "Generating fData ranges" [1] "Generating feature data ranges" [1] "Determining overlaps" [1] "Assigning labels" [1] "Merging to fData table" [1] "Generating fData ranges" [1] "Reading data file" [1] "Generating feature data ranges" [1] "Determining overlaps" [1] "Assigning labels" [1] "Merging to fData table" [ FAIL 0 | WARN 1 | SKIP 22 | PASS 211 ] ══ Skipped tests (22) ══════════════════════════════════════════════════════════ • On Bioconductor (22): 'test-plotting.R:37:3', 'test-plotting.R:46:3', 'test-plotting.R:55:3', 'test-plotting.R:77:3', 'test-plotting.R:105:3', 'test-plotting.R:148:3', 'test-plotting.R:167:3', 'test-plotting.R:220:3', 'test-plotting.R:246:3', 'test-plotting.R:279:3', 'test-plotting.R:329:3', 'test-plotting.R:351:3', 'test-plotting.R:362:3', 'test-plotting.R:390:3', 'test-plotting.R:416:3', 'test-plotting.R:429:3', 'test-plotting.R:445:3', 'test-plotting.R:455:3', 'test-plotting.R:472:3', 'test-runCicero.R:141:3', 'test-runCicero.R:259:3', 'test-runCicero.R:302:3' [ FAIL 0 | WARN 1 | SKIP 22 | PASS 211 ] Deleting unused snapshots: • plotting/basic-bar-high-breaks.svg • plotting/basic-bar-one.svg • plotting/basic-bar.svg • plotting/basic-connections-all-bp.svg • plotting/basic-connections-chr-bp1.svg • plotting/basic-connections-chr.svg • plotting/basic-connections-comparison-plot.svg • plotting/basic-connections-high-comparison-cutoff.svg • plotting/basic-connections-high-cutoff.svg • plotting/basic-connections-include-axis-track.svg • plotting/basic-connections-plot-bad-chr.svg • plotting/basic-connections-plot-comparison-cutoff.svg • plotting/basic-connections-plot-cutoff.svg • plotting/basic-connections-plot-dt.svg • plotting/basic-connections-plot-with-viewpoint-change-colors.svg • plotting/basic-connections-plot-with-viewpoint-no-comp.svg • plotting/basic-connections-plot-with-viewpoint.svg • plotting/basic-connections-plot.svg • plotting/comparison-connection-color-color-column.svg • plotting/comparison-connection-color-comparison-connection-width.svg • plotting/comparison-connection-color-type-column-coaccess-no-legend.svg • plotting/comparison-connection-color-type-column-coaccess.svg • plotting/comparison-connection-color-type-column.svg • plotting/comparison-connection-color.svg • plotting/comparison-peak-color-color-column.svg • plotting/comparison-peak-color-logical-column.svg • plotting/comparison-peak-color-type-column.svg • plotting/comparison-peak-color.svg • plotting/comparison-ymax-plus-cutoff.svg • plotting/comparison-ymax.svg • plotting/connection-color-color-column.svg • plotting/connection-color-connection-width.svg • plotting/connection-color-type-column-coaccess-no-legend.svg • plotting/connection-color-type-column-coaccess.svg • plotting/connection-color-type-column.svg • plotting/connection-color.svg • plotting/connection-ymax-plus-cutoff.svg • plotting/connection-ymax.svg • plotting/connections-plot-with-collapsetranscripts-gene.svg • plotting/connections-plot-with-collapsetranscripts-longest.svg • plotting/connections-plot-with-collapsetranscripts-meta.svg • plotting/connections-plot-with-collapsetranscripts-shortest.svg • plotting/connections-plot-with-collapsetranscripts-true.svg • plotting/connections-plot-with-comparison-color.svg • plotting/connections-plot-with-comparison-peak-color-hex.svg • plotting/connections-plot-with-comparison-peak-color.svg • plotting/connections-plot-with-comparison.svg • plotting/connections-plot-with-gene-model-color.svg • plotting/connections-plot-with-gene-model-no-genes.svg • plotting/connections-plot-with-gene-model-with-comparison.svg • plotting/connections-plot-with-gene-model.svg • plotting/peak-color-color-column.svg • plotting/peak-color-logical-column.svg • plotting/peak-color-type-column.svg • plotting/peak-color.svg > > proc.time() user system elapsed 128.25 6.68 135.12
cicero.Rcheck/cicero-Ex.timings
name | user | system | elapsed | |
aggregate_by_cell_bin | 0 | 0 | 0 | |
aggregate_nearby_peaks | 1.11 | 0.08 | 1.20 | |
annotate_cds_by_site | 0.82 | 0.03 | 0.86 | |
assemble_connections | 3.29 | 0.12 | 3.43 | |
build_gene_activity_matrix | 4.01 | 0.14 | 4.18 | |
compare_connections | 0 | 0 | 0 | |
df_for_coords | 0.02 | 0.00 | 0.01 | |
estimate_distance_parameter | 2.70 | 0.16 | 2.86 | |
find_overlapping_ccans | 0.05 | 0.00 | 0.05 | |
find_overlapping_coordinates | 0.06 | 0.00 | 0.07 | |
generate_ccans | 0 | 0 | 0 | |
generate_cicero_models | 2.14 | 0.12 | 2.26 | |
make_atac_cds | 0.34 | 0.02 | 0.36 | |
make_cicero_cds | 0 | 0 | 0 | |
normalize_gene_activities | 3.82 | 0.18 | 4.00 | |
plot_accessibility_in_pseudotime | 0 | 0 | 0 | |
plot_connections | 4.07 | 0.08 | 4.14 | |
ranges_for_coords | 0.08 | 0.00 | 0.08 | |
run_cicero | 2.55 | 0.14 | 2.69 | |