Christophe Georgescu
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/infercnv |
| Branch: RELEASE_3_11 |
| Last Commit: c422114 |
| Last Changed Date: 2020-04-27 15:26:59 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE infercnv PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 876/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| infercnv 1.4.0 Christophe Georgescu
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: infercnv |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:infercnv.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings infercnv_1.4.0.tar.gz |
| StartedAt: 2020-10-17 05:12:42 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:29:55 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1032.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: infercnv.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:infercnv.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings infercnv_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.plot_cnv_references: no visible binding for global variable
'infercnv_obj'
Undefined global functions or variables:
infercnv_obj
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
inferCNVBayesNet 206.64 0.84 307.97
run 11.84 0.05 11.89
apply_median_filtering 5.00 0.35 5.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
inferCNVBayesNet 267.53 0.86 269.61
run 14.47 0.03 14.50
apply_median_filtering 7.29 0.05 7.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck/00check.log'
for details.
infercnv.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/infercnv_1.4.0.tar.gz && rm -rf infercnv.buildbin-libdir && mkdir infercnv.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=infercnv.buildbin-libdir infercnv_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL infercnv_1.4.0.zip && rm infercnv_1.4.0.tar.gz infercnv_1.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
56 3762k 56 2112k 0 0 11.8M 0 --:--:-- --:--:-- --:--:-- 12.2M
100 3762k 100 3762k 0 0 19.4M 0 --:--:-- --:--:-- --:--:-- 20.0M
install for i386
* 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
annots html
apply_median_filtering html
color.palette html
data html
filterHighPNormals html
genes html
inferCNVBayesNet html
infercnv-class html
infercnv-package html
infercnv_obj 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
install for x64
* installing *source* package 'infercnv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'infercnv' as infercnv_1.4.0.zip
* DONE (infercnv)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'infercnv' successfully unpacked and MD5 sums checked
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infercnv.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:34] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:34] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-10-17 05:29:34] window length < 2, returning original unmodified data
WARN [2020-10-17 05:29:34] window length < 2, returning original unmodified data
INFO [2020-10-17 05:29:34] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-10-17 05:29:34] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2020-10-17 05:29:34] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-10-17 05:29:34] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2020-10-17 05:29:34] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-10-17 05:29:34] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-10-17 05:29:34] outlier bounds defined between: -0.5 - 17.75
INFO [2020-10-17 05:29:34] ::order_reduce:Start.
INFO [2020-10-17 05:29:34] ::order_reduce:Start.
INFO [2020-10-17 05:29:34] .order_reduce(): expr and order match.
INFO [2020-10-17 05:29:34] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 05:29:34] ::order_reduce:Start.
INFO [2020-10-17 05:29:34] .order_reduce(): expr and order match.
INFO [2020-10-17 05:29:34] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 05:29:34] ::order_reduce:Start.
INFO [2020-10-17 05:29:35] ::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
9.78 0.90 10.68
|
infercnv.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 05:29:45] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 05:29:45] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 05:29:45] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-10-17 05:29:45] window length < 2, returning original unmodified data
WARN [2020-10-17 05:29:45] window length < 2, returning original unmodified data
INFO [2020-10-17 05:29:45] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-10-17 05:29:45] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30
INFO [2020-10-17 05:29:45] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-10-17 05:29:45] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15
INFO [2020-10-17 05:29:45] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-10-17 05:29:45] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-10-17 05:29:45] outlier bounds defined between: -0.5 - 17.75
INFO [2020-10-17 05:29:46] ::order_reduce:Start.
INFO [2020-10-17 05:29:46] ::order_reduce:Start.
INFO [2020-10-17 05:29:46] .order_reduce(): expr and order match.
INFO [2020-10-17 05:29:46] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 05:29:46] ::order_reduce:Start.
INFO [2020-10-17 05:29:46] .order_reduce(): expr and order match.
INFO [2020-10-17 05:29:46] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 05:29:46] ::order_reduce:Start.
INFO [2020-10-17 05:29:46] ::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
10.12 0.45 10.57
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infercnv.Rcheck/examples_i386/infercnv-Ex.timings
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infercnv.Rcheck/examples_x64/infercnv-Ex.timings
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