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CHECK report for cicero on malbec1

This page was generated on 2021-05-05 12:09:35 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the cicero package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 303/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cicero 1.8.1  (landing page)
Hannah Pliner
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/cicero
Branch: RELEASE_3_12
Last Commit: ffa460e
Last Changed Date: 2020-12-08 07:26:19 -0400 (Tue, 08 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: cicero
Version: 1.8.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cicero_1.8.1.tar.gz
StartedAt: 2021-05-05 00:06:51 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 00:17:24 -0400 (Wed, 05 May 2021)
EllapsedTime: 633.0 seconds
RetCode: 0
Status:   OK  
CheckDir: cicero.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cicero_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/cicero.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.1’
* 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'
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 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
normalize_gene_activities 5.328  0.032   5.358
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/cicero.Rcheck/00check.log’
for details.



Installation output

cicero.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL cicero
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output

cicero.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid

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

[ FAIL 0 | WARN 9 | SKIP 21 | PASS 206 ]
> 
> proc.time()
   user  system elapsed 
160.152   0.880 162.546 

Example timings

cicero.Rcheck/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.0000.0000.003
aggregate_nearby_peaks1.3320.0161.319
annotate_cds_by_site1.6240.0001.620
assemble_connections3.5280.0963.690
build_gene_activity_matrix4.2560.0364.280
compare_connections000
df_for_coords0.0040.0000.002
estimate_distance_parameter4.1440.0604.220
find_overlapping_ccans0.0480.0000.048
find_overlapping_coordinates0.0720.0000.074
generate_ccans000
generate_cicero_models2.2560.0442.302
make_atac_cds0.3520.0000.358
make_cicero_cds3.3960.0043.409
normalize_gene_activities5.3280.0325.358
plot_accessibility_in_pseudotime000
plot_connections3.6120.0363.651
ranges_for_coords0.0520.0000.054
run_cicero3.240.043.28