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CHECK report for cicero on malbec2

This page was generated on 2019-04-09 11:51:57 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cicero_1.1.4.tar.gz
StartedAt: 2019-04-08 23:27:54 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:36:08 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 493.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: cicero.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cicero_1.1.4.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.4’
* 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 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
normalize_gene_activities   8.381  0.116   6.713
build_gene_activity_matrix  7.837  0.145   6.247
assemble_connections        5.512  0.055   5.714
estimate_distance_parameter 5.310  0.028   5.641
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck/00check.log’
for details.

Installation output

cicero.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cicero
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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.fail


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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: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
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/cicero-Ex.timings

nameusersystemelapsed
aggregate_by_cell_bin0.2940.0000.294
aggregate_nearby_peaks4.3300.0463.197
annotate_cds_by_site2.0320.0201.505
assemble_connections5.5120.0555.714
build_gene_activity_matrix7.8370.1456.247
compare_connections0.0010.0000.000
df_for_coords0.0030.0000.003
estimate_distance_parameter5.3100.0285.641
find_overlapping_ccans0.0440.0000.043
find_overlapping_coordinates0.0480.0000.049
generate_ccans000
generate_cicero_models3.1230.0323.185
make_atac_cds0.7200.0040.724
make_cicero_cds2.5920.0362.639
normalize_gene_activities8.3810.1166.713
plot_accessibility_in_pseudotime000
plot_connections3.0220.0133.037
ranges_for_coords0.0420.0000.042
run_cicero4.3760.0694.257