Hannah Pliner
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/cicero |
| git_branch: devel |
| git_last_commit: ff77b2c |
| git_last_commit_date: 2024-10-29 10:31:55 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 345/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cicero 1.25.0 (landing page) Hannah Pliner
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: cicero |
| Version: 1.25.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cicero_1.25.0.tar.gz |
| StartedAt: 2024-12-24 05:20:23 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 05:31:10 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 646.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cicero.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cicero_1.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cicero.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cicero/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cicero’ version ‘1.25.0’
* 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 ‘cicero’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/cicero.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
aggregate_nearby_peaks: no visible binding for global variable 'val'
annotate_cds_by_site: no visible binding for global variable 'row_name'
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 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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
build_gene_activity_matrix 5.054 0.1 5.156
* 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: 5 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/cicero.Rcheck/00check.log’
for details.
cicero.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL cicero ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘cicero’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (cicero)
cicero.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(cicero)
Loading required package: monocle
Loading required package: Matrix
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
Warning: program compiled against libxml 212 using older 211
>
> 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
156.790 3.150 160.056
cicero.Rcheck/cicero-Ex.timings
| name | user | system | elapsed | |
| aggregate_by_cell_bin | 0.003 | 0.000 | 0.002 | |
| aggregate_nearby_peaks | 1.188 | 0.012 | 1.192 | |
| annotate_cds_by_site | 0.709 | 0.028 | 0.734 | |
| assemble_connections | 4.101 | 0.080 | 4.191 | |
| build_gene_activity_matrix | 5.054 | 0.100 | 5.156 | |
| compare_connections | 0.001 | 0.000 | 0.000 | |
| df_for_coords | 0.002 | 0.000 | 0.002 | |
| estimate_distance_parameter | 4.291 | 0.004 | 4.304 | |
| find_overlapping_ccans | 0.056 | 0.000 | 0.055 | |
| find_overlapping_coordinates | 0.058 | 0.000 | 0.058 | |
| generate_ccans | 0 | 0 | 0 | |
| generate_cicero_models | 2.687 | 0.008 | 2.700 | |
| make_atac_cds | 0.348 | 0.000 | 0.349 | |
| make_cicero_cds | 0 | 0 | 0 | |
| normalize_gene_activities | 4.838 | 0.024 | 4.864 | |
| plot_accessibility_in_pseudotime | 0.000 | 0.000 | 0.001 | |
| plot_connections | 4.123 | 0.004 | 4.134 | |
| ranges_for_coords | 0.069 | 0.000 | 0.070 | |
| run_cicero | 3.171 | 0.004 | 3.182 | |