| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:11 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the cicero package: - Please 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 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 318/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cicero 1.12.1 (landing page) Hannah Pliner
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: cicero |
| Version: 1.12.1 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cicero_1.12.1.tar.gz |
| StartedAt: 2022-04-12 06:49:06 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 06:56:20 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 434.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: cicero.Rcheck |
| Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cicero_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/cicero.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cicero/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cicero’ version ‘1.12.1’ * 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 ‘cicero’ 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 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' 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' 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 V1 Var1 f_id patterns row_name sizeFactors<- val value * 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’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: • 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 Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/cicero.Rcheck/00check.log’ for details.
cicero.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL cicero ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-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.fail
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> 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, 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
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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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 1 | WARN 6 | SKIP 21 | PASS 212 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (21)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-runCicero.R:305:3): find_overlapping_ccans works ──────────────
nrow(over) not equal to 4.
1/1 mismatches
[1] 2 - 4 == -2
[ FAIL 1 | WARN 6 | SKIP 21 | PASS 212 ]
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
Error: Test failures
Execution halted
cicero.Rcheck/cicero-Ex.timings
| name | user | system | elapsed | |
| aggregate_by_cell_bin | 0.002 | 0.000 | 0.002 | |
| aggregate_nearby_peaks | 2.282 | 0.084 | 2.318 | |
| annotate_cds_by_site | 0.680 | 0.064 | 0.727 | |
| assemble_connections | 3.000 | 0.060 | 3.054 | |
| build_gene_activity_matrix | 3.425 | 0.160 | 3.546 | |
| compare_connections | 0 | 0 | 0 | |
| df_for_coords | 0.002 | 0.000 | 0.002 | |
| estimate_distance_parameter | 3.323 | 0.104 | 3.426 | |
| find_overlapping_ccans | 0.05 | 0.00 | 0.05 | |
| find_overlapping_coordinates | 0.046 | 0.000 | 0.046 | |
| generate_ccans | 0.000 | 0.000 | 0.001 | |
| generate_cicero_models | 1.578 | 0.064 | 1.642 | |
| make_atac_cds | 0.250 | 0.004 | 0.255 | |
| make_cicero_cds | 1.569 | 0.024 | 1.593 | |
| normalize_gene_activities | 2.291 | 0.016 | 2.268 | |
| plot_accessibility_in_pseudotime | 0 | 0 | 0 | |
| plot_connections | 3.797 | 0.084 | 3.882 | |
| ranges_for_coords | 0.102 | 0.000 | 0.101 | |
| run_cicero | 1.976 | 0.048 | 2.017 | |