Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:09:57 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for cicero on merida1


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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 315/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cicero 1.13.0  (landing page)
Hannah Pliner
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/cicero
git_branch: master
git_last_commit: e4e2d36
git_last_commit_date: 2021-10-26 12:47:09 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  NO, package depends on 'monocle' which is not available
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'monocle' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'monocle' which is not available

Summary

Package: cicero
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2022-01-21 23:13:39 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 23:26:31 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 772.1 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cicero.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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'
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 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
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
estimate_distance_parameter 5.768  0.078   5.858
build_gene_activity_matrix  5.290  0.084   5.382
normalize_gene_activities   5.210  0.052   5.270
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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)

Tests output

cicero.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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 9 | SKIP 21 | PASS 206 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (21)

[ FAIL 0 | WARN 9 | SKIP 21 | PASS 206 ]
> 
> proc.time()
   user  system elapsed 
199.573   2.959 205.845 

Example timings

cicero.Rcheck/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.0030.0020.004
aggregate_nearby_peaks2.9160.0282.947
annotate_cds_by_site0.9700.0391.010
assemble_connections4.3090.1464.464
build_gene_activity_matrix5.2900.0845.382
compare_connections0.0010.0010.000
df_for_coords0.0030.0000.003
estimate_distance_parameter5.7680.0785.858
find_overlapping_ccans0.0780.0000.078
find_overlapping_coordinates0.0820.0000.083
generate_ccans0.0010.0010.000
generate_cicero_models4.0540.0614.123
make_atac_cds0.4490.0060.456
make_cicero_cds4.0010.0684.074
normalize_gene_activities5.2100.0525.270
plot_accessibility_in_pseudotime0.0010.0010.000
plot_connections4.4240.0264.461
ranges_for_coords0.1060.0010.106
run_cicero3.6540.0643.723