Christophe Georgescu
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/infercnv |
| Branch: RELEASE_3_10 |
| Last Commit: a67b785 |
| Last Changed Date: 2019-12-06 16:26:18 -0400 (Fri, 06 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:22 -0400 (Wed, 15 Apr 2020).
| Package 845/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| infercnv 1.2.1 Christophe Georgescu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: infercnv |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings infercnv_1.2.1.tar.gz |
| StartedAt: 2020-04-15 03:11:12 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:19:23 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 490.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: infercnv.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings infercnv_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/infercnv.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.2.1’
* 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 ‘infercnv’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
inferCNVBayesNet 251.315 4.883 222.644
run 15.249 0.274 15.656
apply_median_filtering 8.940 0.172 9.203
* 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-3.10-bioc/meat/infercnv.Rcheck/00check.log’
for details.
infercnv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL infercnv ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘infercnv’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (infercnv)
infercnv.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> #!/usr/bin/env Rscript
>
> library(testthat)
> library(infercnv)
>
> test_check("infercnv")
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 03:19:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 03:19:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 03:19:15] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-04-15 03:19:15] window length < 2, returning original unmodified data
WARN [2020-04-15 03:19:15] window length < 2, returning original unmodified data
INFO [2020-04-15 03:19:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-04-15 03:19:15] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2020-04-15 03:19:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-04-15 03:19:15] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2020-04-15 03:19:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-04-15 03:19:15] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-04-15 03:19:15] outlier bounds defined between: -0.5 - 17.75
INFO [2020-04-15 03:19:15] ::order_reduce:Start.
INFO [2020-04-15 03:19:15] ::order_reduce:Start.
INFO [2020-04-15 03:19:15] .order_reduce(): expr and order match.
INFO [2020-04-15 03:19:15] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 03:19:15] ::order_reduce:Start.
INFO [2020-04-15 03:19:15] .order_reduce(): expr and order match.
INFO [2020-04-15 03:19:15] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 03:19:15] ::order_reduce:Start.
INFO [2020-04-15 03:19:15] ::process_data:order_reduce:The position file and the expression file row (gene) names do not match.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.835 0.677 11.528
infercnv.Rcheck/infercnv-Ex.timings
| name | user | system | elapsed | |
| CreateInfercnvObject | 0.113 | 0.009 | 0.121 | |
| apply_median_filtering | 8.940 | 0.172 | 9.203 | |
| filterHighPNormals | 0.016 | 0.002 | 0.017 | |
| inferCNVBayesNet | 251.315 | 4.883 | 222.644 | |
| plot_cnv | 1.318 | 0.179 | 1.411 | |
| plot_per_group | 2.858 | 0.388 | 3.094 | |
| run | 15.249 | 0.274 | 15.656 | |
| sample_object | 0.038 | 0.004 | 0.044 | |