Package: cicero

Version: 1.0.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cicero.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cicero_1.0.15.tar.gz

StartedAt: 2019-04-15 23:00:49 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:09:49 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 540.1 seconds

RetCode: 0

Status:  OK

CheckDir: cicero.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cicero.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cicero_1.0.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cicero.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.15’
* 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'
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'
Undefined global functions or variables:
  CCAN V1 f_id 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 or elapsed time > 5s
                             user system elapsed
build_gene_activity_matrix  7.204  1.377   6.184
normalize_gene_activities   5.132  1.382   4.545
estimate_distance_parameter 6.046  0.166   6.270
assemble_connections        5.307  0.205   5.562
* 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-3.8-bioc/meat/cicero.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cicero
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cicero’ ...
** R
** data
** 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
* DONE (cicero)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
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:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 199 SKIPPED: 19 FAILED: 0
> 
> proc.time()
   user  system elapsed 
159.719  21.402 149.947 

name	user	system	elapsed
aggregate_by_cell_bin	0.367	0.006	0.375
aggregate_nearby_peaks	2.973	0.066	3.295
annotate_cds_by_site	1.296	0.050	1.356
assemble_connections	5.307	0.205	5.562
build_gene_activity_matrix	7.204	1.377	6.184
compare_connections	0	0	0
df_for_coords	0.003	0.000	0.003
estimate_distance_parameter	6.046	0.166	6.270
find_overlapping_ccans	0.055	0.001	0.056
find_overlapping_coordinates	0.057	0.000	0.058
generate_ccans	0	0	0
generate_cicero_models	4.042	0.132	4.204
make_atac_cds	0.770	0.018	0.792
make_cicero_cds	3.842	0.145	4.027
normalize_gene_activities	5.132	1.382	4.545
plot_accessibility_in_pseudotime	0.000	0.001	0.000
plot_connections	3.512	0.197	3.357
ranges_for_coords	0.054	0.000	0.055
run_cicero	4.060	0.151	4.237