Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-30 11:37:01 -0400 (Sat, 30 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 344/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cicero 1.18.0  (landing page)
Hannah Pliner
Snapshot Date: 2023-09-29 14:00:14 -0400 (Fri, 29 Sep 2023)
git_url: https://git.bioconductor.org/packages/cicero
git_branch: RELEASE_3_17
git_last_commit: b6a7b66
git_last_commit_date: 2023-04-25 11:04:55 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for cicero on merida1


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.

raw results


Summary

Package: cicero
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2023-09-29 23:49:22 -0400 (Fri, 29 Sep 2023)
EndedAt: 2023-09-30 00:09:12 -0400 (Sat, 30 Sep 2023)
EllapsedTime: 1189.9 seconds
RetCode: 0
Status:   OK  
CheckDir: cicero.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/cicero.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cicero/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cicero’ version ‘1.18.0’
* 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 ... 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        5.762  0.228   8.928
estimate_distance_parameter 4.987  0.129   7.391
build_gene_activity_matrix  4.677  0.210   7.033
plot_connections            4.828  0.041   7.015
normalize_gene_activities   4.554  0.082   6.627
run_cicero                  4.001  0.083   5.935
* 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-3.17-bioc/meat/cicero.Rcheck/00check.log’
for details.



Installation output

cicero.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cicero
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output

cicero.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 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
> 
> 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 (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 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 
223.342   4.476 317.458 

Example timings

cicero.Rcheck/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.0040.0050.014
aggregate_nearby_peaks3.0340.0444.340
annotate_cds_by_site1.1550.0661.763
assemble_connections5.7620.2288.928
build_gene_activity_matrix4.6770.2107.033
compare_connections000
df_for_coords0.0030.0010.004
estimate_distance_parameter4.9870.1297.391
find_overlapping_ccans0.0920.0010.158
find_overlapping_coordinates0.0950.0010.160
generate_ccans0.0010.0000.001
generate_cicero_models3.2850.0754.838
make_atac_cds0.5950.0180.874
make_cicero_cds0.0010.0010.001
normalize_gene_activities4.5540.0826.627
plot_accessibility_in_pseudotime0.0000.0000.001
plot_connections4.8280.0417.015
ranges_for_coords0.1200.0010.174
run_cicero4.0010.0835.935