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CHECK report for cicero on tokay2

This page was generated on 2019-04-09 12:42:16 -0400 (Tue, 09 Apr 2019).

Package 272/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cicero 1.1.4
Hannah Pliner
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cicero
Branch: master
Last Commit: de54582
Last Changed Date: 2019-02-19 20:02:12 -0400 (Tue, 19 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: cicero
Version: 1.1.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cicero.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cicero_1.1.4.tar.gz
StartedAt: 2019-04-09 01:47:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:59:42 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 720.9 seconds
RetCode: 1
Status:  ERROR  
CheckDir: cicero.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cicero.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cicero_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cicero/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cicero' version '1.1.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
estimate_distance_parameter 6.84   0.34    7.18
build_gene_activity_matrix  5.41   0.55    5.93
assemble_connections        5.53   0.28    5.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
build_gene_activity_matrix 5.73    0.3    5.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 180 SKIPPED: 19 FAILED: 19
  1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30) 
  2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50) 
  3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#65) 
  4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#74) 
  5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#91) 
  6. Failure: assemble_connections gives output (@test-runCicero.R#152) 
  7. Failure: assemble_connections gives output (@test-runCicero.R#160) 
  8. Failure: run_cicero gives output (@test-runCicero.R#172) 
  9. Failure: run_cicero gives output (@test-runCicero.R#177) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 180 SKIPPED: 19 FAILED: 19
  1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30) 
  2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50) 
  3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#65) 
  4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#74) 
  5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#91) 
  6. Failure: assemble_connections gives output (@test-runCicero.R#152) 
  7. Failure: assemble_connections gives output (@test-runCicero.R#160) 
  8. Failure: run_cicero gives output (@test-runCicero.R#172) 
  9. Failure: run_cicero gives output (@test-runCicero.R#177) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck/00check.log'
for details.

Installation output

cicero.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cicero_1.1.4.tar.gz && rm -rf cicero.buildbin-libdir && mkdir cicero.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cicero.buildbin-libdir cicero_1.1.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cicero_1.1.4.zip && rm cicero_1.1.4.tar.gz cicero_1.1.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  714k  100  714k    0     0  9891k      0 --:--:-- --:--:-- --:--:-- 10.7M

install for i386

* installing *source* package 'cicero' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cicero'
    finding HTML links ... done
    aggregate_by_cell_bin                   html  
    aggregate_nearby_peaks                  html  
    annotate_cds_by_site                    html  
    assemble_connections                    html  
    build_gene_activity_matrix              html  
    cell_data                               html  
    cicero-package                          html  
    cicero_data                             html  
    compare_connections                     html  
    df_for_coords                           html  
    estimate_distance_parameter             html  
    find_overlapping_ccans                  html  
    find_overlapping_coordinates            html  
    gene_annotation_sample                  html  
    generate_ccans                          html  
    generate_cicero_models                  html  
    human.hg19.genome                       html  
    make_atac_cds                           html  
    make_cicero_cds                         html  
    make_sparse_matrix                      html  
    normalize_gene_activities               html  
    plot_accessibility_in_pseudotime        html  
    plot_connections                        html  
    ranges_for_coords                       html  
    run_cicero                              html  
** 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

install for x64

* installing *source* package 'cicero' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cicero' as cicero_1.1.4.zip
* DONE (cicero)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cicero' successfully unpacked and MD5 sums checked

Tests output

cicero.Rcheck/tests_i386/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("cicero")
-- 1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30)  ----
ncol(exprs(cicero_cds)) not equal to 36.
1/1 mismatches
[1] 34 - 36 == -2

-- 2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50)  ----
ncol(exprs(cicero_cds)) not equal to 36.
1/1 mismatches
[1] 34 - 36 == -2

-- 3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R
`mean_alpha` not equal to 2.030655.
1/1 mismatches
[1] 2.25 - 2.03 == 0.219

-- 4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R
`mean_alpha` not equal to 2.030655.
1/1 mismatches
[1] 2.25 - 2.03 == 0.219

-- 5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#9
No distance_parameters calculated
1: testthat::expect_warning(alphas <- estimate_distance_parameter(cicero_cds, window = 10000, 
       maxit = 100, sample_num = 2, distance_constraint = 5000, distance_parameter_convergence = 1e-22, 
       genomic_coords = sample_genome)) at testthat/test-runCicero.R:91
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
       out$push(condition)
       invokeRestart("muffleWarning")
   })
5: eval_bare(get_expr(quo), get_env(quo))
6: estimate_distance_parameter(cicero_cds, window = 10000, maxit = 100, sample_num = 2, 
       distance_constraint = 5000, distance_parameter_convergence = 1e-22, genomic_coords = sample_genome)
7: stop("No distance_parameters calculated")

-- 6. Failure: assemble_connections gives output (@test-runCicero.R#152)  ------
con_list[[1]]$w[1, 2] not equal to 1.028059.
1/1 mismatches
[1] 0.866 - 1.03 == -0.162

[1] "Successful cicero models:  283"
[1] "Other models: "

Zero or one element in range 
                          30 
[1] "Models with errors:  0"
-- 7. Failure: assemble_connections gives output (@test-runCicero.R#160)  ------
cons$coaccess[1] not equal to 0.908402.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

-- 8. Failure: run_cicero gives output (@test-runCicero.R#172)  ----------------
cons$coaccess[1] not equal to 0.9083997.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

-- 9. Failure: run_cicero gives output (@test-runCicero.R#177)  ----------------
cons$coaccess[1] not equal to 0.9083997.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

[1] "Coaccessibility cutoff used: 0.25"
-- 10. Failure: find_overlapping_ccans works (@test-runCicero.R#228)  ----------
nrow(over) not equal to 40.
1/1 mismatches
[1] 100 - 40 == 60

-- 11. Failure: find_overlapping_ccans works (@test-runCicero.R#230)  ----------
nrow(over) not equal to 2.
1/1 mismatches
[1] 4 - 2 == 2

-- 12. Failure: (unknown) (@test-runCicero.R#246)  -----------------------------
unnorm_ga[1, 1] not equal to 1.183498.
1/1 mismatches
[1] 1.19 - 1.18 == 0.0113

-- 13. Failure: build_gene_activity_matrix works (@test-runCicero.R#255)  ------
unnorm_ga[1, 1] not equal to 1.183498.
1/1 mismatches
[1] 1.19 - 1.18 == 0.0113

-- 14. Failure: normalize_gene_activities works (@test-runCicero.R#267)  -------
cicero_gene_activities[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 15. Failure: normalize_gene_activities works (@test-runCicero.R#278)  -------
cicero_gene_activities1[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 16. Failure: normalize_gene_activities works (@test-runCicero.R#282)  -------
cicero_gene_activities2[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 17. Failure: normalize_gene_activities works (@test-runCicero.R#289)  -------
cicero_gene_activities[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 18. Failure: normalize_gene_activities works (@test-runCicero.R#300)  -------
cicero_gene_activities1[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 19. Failure: normalize_gene_activities works (@test-runCicero.R#304)  -------
cicero_gene_activities2[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

[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: 180 SKIPPED: 19 FAILED: 19
1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30) 
2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50) 
3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#65) 
4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#74) 
5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#91) 
6. Failure: assemble_connections gives output (@test-runCicero.R#152) 
7. Failure: assemble_connections gives output (@test-runCicero.R#160) 
8. Failure: run_cicero gives output (@test-runCicero.R#172) 
9. Failure: run_cicero gives output (@test-runCicero.R#177) 
1. ...

Error: testthat unit tests failed
Execution halted

cicero.Rcheck/tests_x64/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("cicero")
-- 1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30)  ----
ncol(exprs(cicero_cds)) not equal to 36.
1/1 mismatches
[1] 34 - 36 == -2

-- 2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50)  ----
ncol(exprs(cicero_cds)) not equal to 36.
1/1 mismatches
[1] 34 - 36 == -2

-- 3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R
`mean_alpha` not equal to 2.030655.
1/1 mismatches
[1] 2.25 - 2.03 == 0.219

-- 4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R
`mean_alpha` not equal to 2.030655.
1/1 mismatches
[1] 2.25 - 2.03 == 0.219

-- 5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#9
No distance_parameters calculated
1: testthat::expect_warning(alphas <- estimate_distance_parameter(cicero_cds, window = 10000, 
       maxit = 100, sample_num = 2, distance_constraint = 5000, distance_parameter_convergence = 1e-22, 
       genomic_coords = sample_genome)) at testthat/test-runCicero.R:91
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
       out$push(condition)
       invokeRestart("muffleWarning")
   })
5: eval_bare(get_expr(quo), get_env(quo))
6: estimate_distance_parameter(cicero_cds, window = 10000, maxit = 100, sample_num = 2, 
       distance_constraint = 5000, distance_parameter_convergence = 1e-22, genomic_coords = sample_genome)
7: stop("No distance_parameters calculated")

-- 6. Failure: assemble_connections gives output (@test-runCicero.R#152)  ------
con_list[[1]]$w[1, 2] not equal to 1.028059.
1/1 mismatches
[1] 0.866 - 1.03 == -0.162

[1] "Successful cicero models:  283"
[1] "Other models: "

Zero or one element in range 
                          30 
[1] "Models with errors:  0"
-- 7. Failure: assemble_connections gives output (@test-runCicero.R#160)  ------
cons$coaccess[1] not equal to 0.908402.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

-- 8. Failure: run_cicero gives output (@test-runCicero.R#172)  ----------------
cons$coaccess[1] not equal to 0.9083997.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

-- 9. Failure: run_cicero gives output (@test-runCicero.R#177)  ----------------
cons$coaccess[1] not equal to 0.9083997.
1/1 mismatches
[1] 0.877 - 0.908 == -0.0309

[1] "Coaccessibility cutoff used: 0.25"
-- 10. Failure: find_overlapping_ccans works (@test-runCicero.R#228)  ----------
nrow(over) not equal to 40.
1/1 mismatches
[1] 100 - 40 == 60

-- 11. Failure: find_overlapping_ccans works (@test-runCicero.R#230)  ----------
nrow(over) not equal to 2.
1/1 mismatches
[1] 4 - 2 == 2

-- 12. Failure: (unknown) (@test-runCicero.R#246)  -----------------------------
unnorm_ga[1, 1] not equal to 1.183498.
1/1 mismatches
[1] 1.19 - 1.18 == 0.0113

-- 13. Failure: build_gene_activity_matrix works (@test-runCicero.R#255)  ------
unnorm_ga[1, 1] not equal to 1.183498.
1/1 mismatches
[1] 1.19 - 1.18 == 0.0113

-- 14. Failure: normalize_gene_activities works (@test-runCicero.R#267)  -------
cicero_gene_activities[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 15. Failure: normalize_gene_activities works (@test-runCicero.R#278)  -------
cicero_gene_activities1[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 16. Failure: normalize_gene_activities works (@test-runCicero.R#282)  -------
cicero_gene_activities2[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 17. Failure: normalize_gene_activities works (@test-runCicero.R#289)  -------
cicero_gene_activities[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 18. Failure: normalize_gene_activities works (@test-runCicero.R#300)  -------
cicero_gene_activities1[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

-- 19. Failure: normalize_gene_activities works (@test-runCicero.R#304)  -------
cicero_gene_activities2[1, 1] not equal to 0.008026735.
1/1 mismatches
[1] 0.00857 - 0.00803 == 0.000546

[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: 180 SKIPPED: 19 FAILED: 19
1. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#30) 
2. Failure: make_cicero_cds aggregates correctly (@test-runCicero.R#50) 
3. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#65) 
4. Failure: estimate_distance_parameter gives correct mean (@test-runCicero.R#74) 
5. Error: estimate_distance_parameter gives correct mean (@test-runCicero.R#91) 
6. Failure: assemble_connections gives output (@test-runCicero.R#152) 
7. Failure: assemble_connections gives output (@test-runCicero.R#160) 
8. Failure: run_cicero gives output (@test-runCicero.R#172) 
9. Failure: run_cicero gives output (@test-runCicero.R#177) 
1. ...

Error: testthat unit tests failed
Execution halted

Example timings

cicero.Rcheck/examples_i386/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.680.020.68
aggregate_nearby_peaks2.720.092.81
annotate_cds_by_site1.070.081.17
assemble_connections5.530.285.93
build_gene_activity_matrix5.410.555.93
compare_connections000
df_for_coords000
estimate_distance_parameter6.840.347.18
find_overlapping_ccans0.050.000.05
find_overlapping_coordinates0.030.000.03
generate_ccans000
generate_cicero_models2.450.062.52
make_atac_cds0.780.020.79
make_cicero_cds4.280.144.43
normalize_gene_activities3.990.254.25
plot_accessibility_in_pseudotime000
plot_connections2.970.002.96
ranges_for_coords0.030.000.04
run_cicero3.480.143.62

cicero.Rcheck/examples_x64/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.280.020.29
aggregate_nearby_peaks2.600.052.64
annotate_cds_by_site0.910.060.98
assemble_connections4.420.144.57
build_gene_activity_matrix5.730.305.98
compare_connections000
df_for_coords0.020.000.02
estimate_distance_parameter3.410.173.57
find_overlapping_ccans0.010.000.02
find_overlapping_coordinates0.030.000.03
generate_ccans000
generate_cicero_models2.020.132.14
make_atac_cds0.480.030.51
make_cicero_cds3.420.143.56
normalize_gene_activities4.020.204.20
plot_accessibility_in_pseudotime000
plot_connections3.530.053.58
ranges_for_coords0.030.000.03
run_cicero2.640.062.70