Christophe Georgescu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/infercnv |
| git_branch: master |
| git_last_commit: 8cf9302 |
| git_last_commit_date: 2022-02-03 16:07:46 -0400 (Thu, 03 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:48 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 934/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| infercnv 1.11.2 (landing page) Christophe Georgescu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: infercnv |
| Version: 1.11.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:infercnv.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings infercnv_1.11.2.tar.gz |
| StartedAt: 2022-03-17 19:22:26 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:28:25 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 359.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: infercnv.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:infercnv.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings infercnv_1.11.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/infercnv.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'infercnv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'infercnv' version '1.11.2'
* 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 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 ... NOTE
.parameterize_random_cluster_heights: no visible global function
definition for 'parllelDist'
Undefined global functions or variables:
parllelDist
* 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 166.36 1.19 168.83
run 10.60 0.08 10.67
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/infercnv.Rcheck/00check.log'
for details.
infercnv.Rcheck/00install.out
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###
### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL infercnv
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'infercnv'
finding HTML links ... done
CreateInfercnvObject html
HMM_states html
MCMC_inferCNV-class html
add_to_seurat html
apply_median_filtering html
color.palette html
filterHighPNormals html
inferCNVBayesNet html
infercnv-class html
infercnv-package html
infercnv_annots_example html
infercnv_data_example html
infercnv_genes_example html
infercnv_object_example html
mcmc_obj html
plot_cnv html
plot_per_group html
run html
sample_object html
validate_infercnv_obj 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
* DONE (infercnv)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'zFPKM' is missing or broken
done
infercnv.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> #!/usr/bin/env Rscript
>
> library(testthat)
> library(infercnv)
>
> test_check("infercnv")
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2022-03-17 19:28:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2022-03-17 19:28:15] subtracting mean(normal) per gene per cell across all data
INFO [2022-03-17 19:28:15] -subtracting expr per gene, use_bounds=TRUE
WARN [2022-03-17 19:28:15] window length < 2, returning original unmodified data
WARN [2022-03-17 19:28:15] window length < 2, returning original unmodified data
INFO [2022-03-17 19:28:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2022-03-17 19:28:15] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2022-03-17 19:28:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2022-03-17 19:28:15] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2022-03-17 19:28:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2022-03-17 19:28:15] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2022-03-17 19:28:15] outlier bounds defined between: -0.5 - 17.75
INFO [2022-03-17 19:28:15] ::order_reduce:Start.
INFO [2022-03-17 19:28:15] ::order_reduce:Start.
INFO [2022-03-17 19:28:15] .order_reduce(): expr and order match.
INFO [2022-03-17 19:28:15] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2022-03-17 19:28:15] ::order_reduce:Start.
INFO [2022-03-17 19:28:15] .order_reduce(): expr and order match.
INFO [2022-03-17 19:28:15] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2022-03-17 19:28:15] ::order_reduce:Start.
INFO [2022-03-17 19:28:15] ::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
5.82 0.71 6.54
infercnv.Rcheck/infercnv-Ex.timings
| name | user | system | elapsed | |
| CreateInfercnvObject | 0.06 | 0.01 | 0.07 | |
| apply_median_filtering | 4.16 | 0.03 | 4.19 | |
| color.palette | 0 | 0 | 0 | |
| filterHighPNormals | 0.02 | 0.00 | 0.01 | |
| inferCNVBayesNet | 166.36 | 1.19 | 168.83 | |
| plot_cnv | 1.17 | 0.21 | 1.38 | |
| plot_per_group | 1.51 | 0.34 | 1.87 | |
| run | 10.60 | 0.08 | 10.67 | |
| sample_object | 0.03 | 0.01 | 0.05 | |