| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:07 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the infercnv package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/infercnv.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 971/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| infercnv 1.14.2 (landing page) Christophe Georgescu
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: infercnv |
| Version: 1.14.2 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings infercnv_1.14.2.tar.gz |
| StartedAt: 2023-04-10 21:24:16 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:32:10 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 473.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: infercnv.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings infercnv_1.14.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/infercnv.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.14.2’
* 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 loading without being on the library search path ... 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 ... NOTE
.whole_dataset_leiden_subclustering_per_chr: no visible binding for
global variable ‘tumor_group’
Undefined global functions or variables:
tumor_group
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
inferCNVBayesNet 183.385 3.607 157.935
run 12.122 0.712 12.833
* 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 ...
‘inferCNV.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/infercnv.Rcheck/00check.log’
for details.
infercnv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL infercnv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.
> #!/usr/bin/env Rscript
>
> library(testthat)
> library(infercnv)
>
> test_check("infercnv")
INFO [2023-04-10 21:31:05] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:05] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-10 21:31:06] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:06] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-10 21:31:06] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:06] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-10 21:31:06] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:06] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-10 21:31:06] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:06] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-10 21:31:06] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-10 21:31:06] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-10 21:31:06] -subtracting expr per gene, use_bounds=TRUE
WARN [2023-04-10 21:31:06] window length < 2, returning original unmodified data
WARN [2023-04-10 21:31:06] window length < 2, returning original unmodified data
INFO [2023-04-10 21:31:06] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2023-04-10 21:31:06] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2023-04-10 21:31:06] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2023-04-10 21:31:06] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2023-04-10 21:31:06] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2023-04-10 21:31:06] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2023-04-10 21:31:06] outlier bounds defined between: -0.5 - 17.75
INFO [2023-04-10 21:31:06] ::order_reduce:Start.
INFO [2023-04-10 21:31:06] ::order_reduce:Start.
INFO [2023-04-10 21:31:06] .order_reduce(): expr and order match.
INFO [2023-04-10 21:31:06] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-04-10 21:31:06] ::order_reduce:Start.
INFO [2023-04-10 21:31:06] .order_reduce(): expr and order match.
INFO [2023-04-10 21:31:06] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-04-10 21:31:06] ::order_reduce:Start.
INFO [2023-04-10 21:31:06] ::process_data:order_reduce:The position file and the expression file row (gene) names do not match.
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
>
> proc.time()
user system elapsed
10.219 0.640 10.843
infercnv.Rcheck/infercnv-Ex.timings
| name | user | system | elapsed | |
| CreateInfercnvObject | 0.169 | 0.004 | 0.173 | |
| apply_median_filtering | 4.350 | 0.123 | 4.474 | |
| color.palette | 0.003 | 0.000 | 0.003 | |
| filterHighPNormals | 0.014 | 0.000 | 0.014 | |
| inferCNVBayesNet | 183.385 | 3.607 | 157.935 | |
| plot_cnv | 0.623 | 0.055 | 0.679 | |
| plot_per_group | 1.181 | 0.068 | 1.248 | |
| run | 12.122 | 0.712 | 12.833 | |
| sample_object | 0.028 | 0.000 | 0.027 | |