| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:37:39 -0400 (Tue, 09 Apr 2019).
| Package 272/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cicero 1.1.4 Hannah Pliner
| 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 |
| Package: cicero |
| Version: 1.1.4 |
| 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_1.1.4.tar.gz |
| StartedAt: 2019-04-08 23:54:49 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-09 00:03:47 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 538.1 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_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cicero.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.4’
* 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
build_gene_activity_matrix 8.033 2.248 6.160
normalize_gene_activities 7.023 1.442 6.190
estimate_distance_parameter 5.917 0.171 6.142
* 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.
cicero.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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’ ... ** 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)
cicero.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, 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
157.302 24.163 145.458
cicero.Rcheck/cicero-Ex.timings
| name | user | system | elapsed | |
| aggregate_by_cell_bin | 0.344 | 0.007 | 0.351 | |
| aggregate_nearby_peaks | 3.592 | 0.766 | 2.820 | |
| annotate_cds_by_site | 1.562 | 0.420 | 1.381 | |
| assemble_connections | 4.270 | 0.367 | 4.232 | |
| build_gene_activity_matrix | 8.033 | 2.248 | 6.160 | |
| compare_connections | 0.000 | 0.000 | 0.001 | |
| df_for_coords | 0.003 | 0.000 | 0.004 | |
| estimate_distance_parameter | 5.917 | 0.171 | 6.142 | |
| find_overlapping_ccans | 0.049 | 0.000 | 0.050 | |
| find_overlapping_coordinates | 0.057 | 0.000 | 0.057 | |
| generate_ccans | 0.000 | 0.001 | 0.001 | |
| generate_cicero_models | 3.071 | 0.113 | 3.212 | |
| make_atac_cds | 0.660 | 0.012 | 0.684 | |
| make_cicero_cds | 2.953 | 0.106 | 3.083 | |
| normalize_gene_activities | 7.023 | 1.442 | 6.190 | |
| plot_accessibility_in_pseudotime | 0.002 | 0.002 | 0.000 | |
| plot_connections | 3.632 | 0.234 | 3.483 | |
| ranges_for_coords | 0.039 | 0.000 | 0.040 | |
| run_cicero | 4.076 | 0.166 | 4.251 | |