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CHECK report for cicero on celaya2

This page was generated on 2019-10-16 13:03:24 -0400 (Wed, 16 Oct 2019).

Package 277/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cicero 1.2.0
Hannah Pliner
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/cicero
Branch: RELEASE_3_9
Last Commit: 1690071
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cicero
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2019-10-16 01:28:51 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:40:35 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 704.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cicero.Rcheck
Warnings: 0

Command output

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### Running 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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'
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  7.471  0.882   7.931
normalize_gene_activities   6.963  0.561   5.381
assemble_connections        6.932  0.398   7.767
estimate_distance_parameter 6.641  0.421   7.089
make_cicero_cds             5.380  0.390   5.851
aggregate_nearby_peaks      4.318  0.920   4.261
* 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-3.9-bioc/meat/cicero.Rcheck/00check.log’
for details.



Installation output

cicero.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cicero’ ...
** using staged installation
** 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 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 object is masked from 'package:Matrix':

    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, 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, 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 | WARNINGS: 851 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
181.188   8.505 182.495 

Example timings

cicero.Rcheck/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.4470.0150.462
aggregate_nearby_peaks4.3180.9204.261
annotate_cds_by_site1.5360.1051.632
assemble_connections6.9320.3987.767
build_gene_activity_matrix7.4710.8827.931
compare_connections0.0010.0010.000
df_for_coords0.0050.0010.005
estimate_distance_parameter6.6410.4217.089
find_overlapping_ccans0.0730.0010.074
find_overlapping_coordinates0.0740.0010.075
generate_ccans0.0010.0010.001
generate_cicero_models4.1160.2584.405
make_atac_cds1.0220.0291.053
make_cicero_cds5.3800.3905.851
normalize_gene_activities6.9630.5615.381
plot_accessibility_in_pseudotime000
plot_connections4.7480.1974.632
ranges_for_coords0.0340.0010.035
run_cicero4.1880.2464.421