Hannah Pliner
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/cicero |
| git_branch: RELEASE_3_16 |
| git_last_commit: 11394fb |
| git_last_commit_date: 2023-02-25 16:10:49 -0400 (Sat, 25 Feb 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 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 329/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cicero 1.16.2 (landing page) Hannah Pliner
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: cicero |
| Version: 1.16.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cicero.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cicero_1.16.2.tar.gz |
| StartedAt: 2023-04-10 19:23:17 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:30:46 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 448.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cicero.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cicero.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cicero_1.16.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/cicero.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.2’
* 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'
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
assemble_connections 4.151 0.170 6.283
estimate_distance_parameter 3.195 0.141 5.822
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/cicero.Rcheck/00check.log’
for details.
cicero.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cicero ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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
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 0 | WARN 0 | SKIP 22 | PASS 211 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (22)
[ FAIL 0 | WARN 0 | 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
105.926 2.450 109.325
cicero.Rcheck/cicero-Ex.timings
| name | user | system | elapsed | |
| aggregate_by_cell_bin | 0.002 | 0.002 | 0.004 | |
| aggregate_nearby_peaks | 2.009 | 0.031 | 2.047 | |
| annotate_cds_by_site | 0.564 | 0.018 | 0.586 | |
| assemble_connections | 4.151 | 0.170 | 6.283 | |
| build_gene_activity_matrix | 2.384 | 0.109 | 4.019 | |
| compare_connections | 0 | 0 | 0 | |
| df_for_coords | 0.002 | 0.000 | 0.002 | |
| estimate_distance_parameter | 3.195 | 0.141 | 5.822 | |
| find_overlapping_ccans | 0.032 | 0.000 | 0.033 | |
| find_overlapping_coordinates | 0.035 | 0.000 | 0.036 | |
| generate_ccans | 0.000 | 0.000 | 0.001 | |
| generate_cicero_models | 1.548 | 0.066 | 1.629 | |
| make_atac_cds | 0.250 | 0.006 | 0.256 | |
| make_cicero_cds | 0 | 0 | 0 | |
| normalize_gene_activities | 3.221 | 0.090 | 3.338 | |
| plot_accessibility_in_pseudotime | 0 | 0 | 0 | |
| plot_connections | 3.019 | 0.032 | 3.077 | |
| ranges_for_coords | 0.060 | 0.001 | 0.064 | |
| run_cicero | 1.924 | 0.071 | 2.010 | |