| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:09 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 960/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| infercnv 1.15.0 (landing page) Christophe Georgescu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: infercnv |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings infercnv_1.15.0.tar.gz |
| StartedAt: 2023-02-07 05:08:07 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 05:17:56 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 588.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: infercnv.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings infercnv_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/infercnv.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.15.0’
* 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 ... WARNING
Undocumented arguments in documentation object 'run'
‘per_chr_hmm_subclusters_references’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 220.779 1.795 195.684
run 14.847 0.236 15.089
apply_median_filtering 6.409 0.072 6.482
* 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: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/infercnv.Rcheck/00check.log’
for details.
infercnv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL infercnv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-02-07 05:16:31] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-02-07 05:16:31] subtracting mean(normal) per gene per cell across all data
INFO [2023-02-07 05:16:31] -subtracting expr per gene, use_bounds=TRUE
WARN [2023-02-07 05:16:31] window length < 2, returning original unmodified data
WARN [2023-02-07 05:16:31] window length < 2, returning original unmodified data
INFO [2023-02-07 05:16:31] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2023-02-07 05:16:31] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2023-02-07 05:16:31] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2023-02-07 05:16:32] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2023-02-07 05:16:32] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2023-02-07 05:16:32] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2023-02-07 05:16:32] outlier bounds defined between: -0.5 - 17.75
INFO [2023-02-07 05:16:32] ::order_reduce:Start.
INFO [2023-02-07 05:16:32] ::order_reduce:Start.
INFO [2023-02-07 05:16:32] .order_reduce(): expr and order match.
INFO [2023-02-07 05:16:32] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-02-07 05:16:32] ::order_reduce:Start.
INFO [2023-02-07 05:16:32] .order_reduce(): expr and order match.
INFO [2023-02-07 05:16:32] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-02-07 05:16:32] ::order_reduce:Start.
INFO [2023-02-07 05:16:32] ::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
14.421 0.403 14.838
infercnv.Rcheck/infercnv-Ex.timings
| name | user | system | elapsed | |
| CreateInfercnvObject | 0.857 | 0.008 | 0.866 | |
| apply_median_filtering | 6.409 | 0.072 | 6.482 | |
| color.palette | 0.003 | 0.000 | 0.003 | |
| filterHighPNormals | 0.016 | 0.000 | 0.016 | |
| inferCNVBayesNet | 220.779 | 1.795 | 195.684 | |
| plot_cnv | 0.857 | 0.045 | 0.883 | |
| plot_per_group | 1.415 | 0.068 | 1.485 | |
| plot_subclusters | 0.650 | 0.012 | 0.662 | |
| run | 14.847 | 0.236 | 15.089 | |
| sample_object | 0.031 | 0.000 | 0.031 | |