Multiple platform build/check report for BioC 3.14 - CHECK results for cicero on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: cicero

Version: 1.12.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cicero.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cicero_1.12.1.tar.gz

StartedAt: 2022-04-12 17:18:36 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:30:39 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 722.3 seconds

RetCode: 1

Status: ERROR

CheckDir: cicero.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cicero.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cicero_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cicero.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.12.1'
* 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 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'
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'
estimateSizeFactorsSimp: no visible global function definition for
  'sizeFactors<-'
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 sizeFactors<- 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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:
  * plotting/connections-plot-with-collapsetranscripts-true.svg
  * plotting/connections-plot-with-comparison-color.svg
  * plotting/connections-plot-with-comparison-peak-color-hex.svg
  * plotting/connections-plot-with-comparison-peak-color.svg
  * plotting/connections-plot-with-comparison.svg
  * plotting/connections-plot-with-gene-model-color.svg
  * plotting/connections-plot-with-gene-model-no-genes.svg
  * plotting/connections-plot-with-gene-model-with-comparison.svg
  * plotting/connections-plot-with-gene-model.svg
  * plotting/peak-color-color-column.svg
  * plotting/peak-color-logical-column.svg
  * plotting/peak-color-type-column.svg
  * plotting/peak-color.svg
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  * plotting/connections-plot-with-collapsetranscripts-true.svg
  * plotting/connections-plot-with-comparison-color.svg
  * plotting/connections-plot-with-comparison-peak-color-hex.svg
  * plotting/connections-plot-with-comparison-peak-color.svg
  * plotting/connections-plot-with-comparison.svg
  * plotting/connections-plot-with-gene-model-color.svg
  * plotting/connections-plot-with-gene-model-no-genes.svg
  * plotting/connections-plot-with-gene-model-with-comparison.svg
  * plotting/connections-plot-with-gene-model.svg
  * plotting/peak-color-color-column.svg
  * plotting/peak-color-logical-column.svg
  * plotting/peak-color-type-column.svg
  * plotting/peak-color.svg
  Error: Test failures
  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-3.14-bioc/meat/cicero.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cicero_1.12.1.tar.gz && rm -rf cicero.buildbin-libdir && mkdir cicero.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cicero.buildbin-libdir cicero_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cicero_1.12.1.zip && rm cicero_1.12.1.tar.gz cicero_1.12.1.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  923k  100  923k    0     0   932k      0 --:--:-- --:--:-- --:--:--  932k
100  923k  100  923k    0     0   932k      0 --:--:-- --:--:-- --:--:--  932k

install for i386

* 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
  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_1.12.1.zip
* DONE (cicero)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cicero' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:Matrix':

    expand, unname

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

    I, expand.grid, unname

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] "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"
[ FAIL 1 | WARN 6 | SKIP 21 | PASS 212 ]

== Skipped tests ===============================================================
* On Bioconductor (21)

== Failed tests ================================================================
-- Failure (test-runCicero.R:305:3): find_overlapping_ccans works --------------
nrow(over) not equal to 4.
1/1 mismatches
[1] 2 - 4 == -2

[ FAIL 1 | WARN 6 | SKIP 21 | PASS 212 ]
Deleting unused snapshots:
* plotting/basic-bar-high-breaks.svg
* plotting/basic-bar-one.svg
* plotting/basic-bar.svg
* plotting/basic-connections-all-bp.svg
* plotting/basic-connections-chr-bp1.svg
* plotting/basic-connections-chr.svg
* plotting/basic-connections-comparison-plot.svg
* plotting/basic-connections-high-comparison-cutoff.svg
* plotting/basic-connections-high-cutoff.svg
* plotting/basic-connections-include-axis-track.svg
* plotting/basic-connections-plot-bad-chr.svg
* plotting/basic-connections-plot-comparison-cutoff.svg
* plotting/basic-connections-plot-cutoff.svg
* plotting/basic-connections-plot-dt.svg
* plotting/basic-connections-plot-with-viewpoint-change-colors.svg
* plotting/basic-connections-plot-with-viewpoint-no-comp.svg
* plotting/basic-connections-plot-with-viewpoint.svg
* plotting/basic-connections-plot.svg
* plotting/comparison-connection-color-color-column.svg
* plotting/comparison-connection-color-comparison-connection-width.svg
* plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
* plotting/comparison-connection-color-type-column-coaccess.svg
* plotting/comparison-connection-color-type-column.svg
* plotting/comparison-connection-color.svg
* plotting/comparison-peak-color-color-column.svg
* plotting/comparison-peak-color-logical-column.svg
* plotting/comparison-peak-color-type-column.svg
* plotting/comparison-peak-color.svg
* plotting/comparison-ymax-plus-cutoff.svg
* plotting/comparison-ymax.svg
* plotting/connection-color-color-column.svg
* plotting/connection-color-connection-width.svg
* plotting/connection-color-type-column-coaccess-no-legend.svg
* plotting/connection-color-type-column-coaccess.svg
* plotting/connection-color-type-column.svg
* plotting/connection-color.svg
* plotting/connection-ymax-plus-cutoff.svg
* plotting/connection-ymax.svg
* plotting/connections-plot-with-collapsetranscripts-gene.svg
* plotting/connections-plot-with-collapsetranscripts-longest.svg
* plotting/connections-plot-with-collapsetranscripts-meta.svg
* plotting/connections-plot-with-collapsetranscripts-shortest.svg
* plotting/connections-plot-with-collapsetranscripts-true.svg
* plotting/connections-plot-with-comparison-color.svg
* plotting/connections-plot-with-comparison-peak-color-hex.svg
* plotting/connections-plot-with-comparison-peak-color.svg
* plotting/connections-plot-with-comparison.svg
* plotting/connections-plot-with-gene-model-color.svg
* plotting/connections-plot-with-gene-model-no-genes.svg
* plotting/connections-plot-with-gene-model-with-comparison.svg
* plotting/connections-plot-with-gene-model.svg
* plotting/peak-color-color-column.svg
* plotting/peak-color-logical-column.svg
* plotting/peak-color-type-column.svg
* plotting/peak-color.svg
Error: Test failures
Execution halted


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:Matrix':

    expand, unname

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

    I, expand.grid, unname

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] "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"
[ FAIL 1 | WARN 6 | SKIP 21 | PASS 212 ]

== Skipped tests ===============================================================
* On Bioconductor (21)

== Failed tests ================================================================
-- Failure (test-runCicero.R:305:3): find_overlapping_ccans works --------------
nrow(over) not equal to 4.
1/1 mismatches
[1] 2 - 4 == -2

[ FAIL 1 | WARN 6 | SKIP 21 | PASS 212 ]
Deleting unused snapshots:
* plotting/basic-bar-high-breaks.svg
* plotting/basic-bar-one.svg
* plotting/basic-bar.svg
* plotting/basic-connections-all-bp.svg
* plotting/basic-connections-chr-bp1.svg
* plotting/basic-connections-chr.svg
* plotting/basic-connections-comparison-plot.svg
* plotting/basic-connections-high-comparison-cutoff.svg
* plotting/basic-connections-high-cutoff.svg
* plotting/basic-connections-include-axis-track.svg
* plotting/basic-connections-plot-bad-chr.svg
* plotting/basic-connections-plot-comparison-cutoff.svg
* plotting/basic-connections-plot-cutoff.svg
* plotting/basic-connections-plot-dt.svg
* plotting/basic-connections-plot-with-viewpoint-change-colors.svg
* plotting/basic-connections-plot-with-viewpoint-no-comp.svg
* plotting/basic-connections-plot-with-viewpoint.svg
* plotting/basic-connections-plot.svg
* plotting/comparison-connection-color-color-column.svg
* plotting/comparison-connection-color-comparison-connection-width.svg
* plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
* plotting/comparison-connection-color-type-column-coaccess.svg
* plotting/comparison-connection-color-type-column.svg
* plotting/comparison-connection-color.svg
* plotting/comparison-peak-color-color-column.svg
* plotting/comparison-peak-color-logical-column.svg
* plotting/comparison-peak-color-type-column.svg
* plotting/comparison-peak-color.svg
* plotting/comparison-ymax-plus-cutoff.svg
* plotting/comparison-ymax.svg
* plotting/connection-color-color-column.svg
* plotting/connection-color-connection-width.svg
* plotting/connection-color-type-column-coaccess-no-legend.svg
* plotting/connection-color-type-column-coaccess.svg
* plotting/connection-color-type-column.svg
* plotting/connection-color.svg
* plotting/connection-ymax-plus-cutoff.svg
* plotting/connection-ymax.svg
* plotting/connections-plot-with-collapsetranscripts-gene.svg
* plotting/connections-plot-with-collapsetranscripts-longest.svg
* plotting/connections-plot-with-collapsetranscripts-meta.svg
* plotting/connections-plot-with-collapsetranscripts-shortest.svg
* plotting/connections-plot-with-collapsetranscripts-true.svg
* plotting/connections-plot-with-comparison-color.svg
* plotting/connections-plot-with-comparison-peak-color-hex.svg
* plotting/connections-plot-with-comparison-peak-color.svg
* plotting/connections-plot-with-comparison.svg
* plotting/connections-plot-with-gene-model-color.svg
* plotting/connections-plot-with-gene-model-no-genes.svg
* plotting/connections-plot-with-gene-model-with-comparison.svg
* plotting/connections-plot-with-gene-model.svg
* plotting/peak-color-color-column.svg
* plotting/peak-color-logical-column.svg
* plotting/peak-color-type-column.svg
* plotting/peak-color.svg
Error: Test failures
Execution halted

name	user	system	elapsed
aggregate_by_cell_bin	0.00	0.02	0.01
aggregate_nearby_peaks	1.80	0.35	2.16
annotate_cds_by_site	0.69	0.04	0.71
assemble_connections	3.58	0.07	3.75
build_gene_activity_matrix	3.64	0.36	4.00
compare_connections	0	0	0
df_for_coords	0.01	0.00	0.02
estimate_distance_parameter	3.64	0.21	3.84
find_overlapping_ccans	0.07	0.00	0.07
find_overlapping_coordinates	0.04	0.00	0.04
generate_ccans	0	0	0
generate_cicero_models	1.88	0.06	1.94
make_atac_cds	0.26	0.01	0.28
make_cicero_cds	2.69	0.10	2.78
normalize_gene_activities	2.52	0.05	2.57
plot_accessibility_in_pseudotime	0	0	0
plot_connections	2.97	0.00	2.96
ranges_for_coords	0.09	0.00	0.10
run_cicero	2.16	0.09	2.25

name	user	system	elapsed
aggregate_by_cell_bin	0.00	0.02	0.01
aggregate_nearby_peaks	2.20	0.04	2.25
annotate_cds_by_site	0.64	0.02	0.66
assemble_connections	2.93	0.14	3.06
build_gene_activity_matrix	3.76	0.12	3.89
compare_connections	0	0	0
df_for_coords	0	0	0
estimate_distance_parameter	4.24	0.11	4.35
find_overlapping_ccans	0.06	0.00	0.06
find_overlapping_coordinates	0.04	0.00	0.05
generate_ccans	0	0	0
generate_cicero_models	1.96	0.02	1.97
make_atac_cds	0.28	0.00	0.28
make_cicero_cds	1.77	0.06	1.83
normalize_gene_activities	3.47	0.09	3.56
plot_accessibility_in_pseudotime	0	0	0
plot_connections	3.30	0.08	3.37
ranges_for_coords	0.07	0.00	0.08
run_cicero	2.99	0.07	3.04

CHECK results for cicero on tokay2

Summary

Command output

Installation output

Tests output

Example timings