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CHECK report for infercnv on tokay1

This page was generated on 2020-04-15 12:32:28 -0400 (Wed, 15 Apr 2020).

Package 845/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.2.1
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)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: infercnv
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:infercnv.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings infercnv_1.2.1.tar.gz
StartedAt: 2020-04-15 04:02:50 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:17:17 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 867.1 seconds
RetCode: 0
Status:  OK  
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:infercnv.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings infercnv_1.2.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/infercnv.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.2.1'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
inferCNVBayesNet       295.79   1.44  298.25
run                     12.02   0.06   12.08
apply_median_filtering   5.56   0.20    5.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
inferCNVBayesNet       261.82   0.72  262.64
run                     11.23   0.06   11.30
apply_median_filtering   7.33   0.08    7.41
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/infercnv.Rcheck/00check.log'
for details.

Installation output

infercnv.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/infercnv_1.2.1.tar.gz && rm -rf infercnv.buildbin-libdir && mkdir infercnv.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=infercnv.buildbin-libdir infercnv_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL infercnv_1.2.1.zip && rm infercnv_1.2.1.tar.gz infercnv_1.2.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3758k  100 3758k    0     0  65.0M      0 --:--:-- --:--:-- --:--:-- 69.2M

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  
    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_1.2.1.zip
* DONE (infercnv)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'infercnv' successfully unpacked and MD5 sums checked

Tests output

infercnv.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:01] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-04-15 04:17:01] window length < 2, returning original unmodified data
WARN [2020-04-15 04:17:01] window length < 2, returning original unmodified data
INFO [2020-04-15 04:17:01] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-04-15 04:17:01] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2020-04-15 04:17:01] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-04-15 04:17:01] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2020-04-15 04:17:01] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-04-15 04:17:01] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-04-15 04:17:01] outlier bounds defined between: -0.5 - 17.75
INFO [2020-04-15 04:17:02] ::order_reduce:Start.
INFO [2020-04-15 04:17:02] ::order_reduce:Start.
INFO [2020-04-15 04:17:02] .order_reduce(): expr and order match.
INFO [2020-04-15 04:17:02] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 04:17:02] ::order_reduce:Start.
INFO [2020-04-15 04:17:02] .order_reduce(): expr and order match.
INFO [2020-04-15 04:17:02] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 04:17:02] ::order_reduce:Start.
INFO [2020-04-15 04:17:02] ::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 
   7.39    0.78    8.15

infercnv.Rcheck/tests_x64/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-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 [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-04-15 04:17:10] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-04-15 04:17:10] subtracting mean(normal) per gene per cell across all data
INFO [2020-04-15 04:17:10] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-04-15 04:17:10] window length < 2, returning original unmodified data
WARN [2020-04-15 04:17:10] window length < 2, returning original unmodified data
INFO [2020-04-15 04:17:10] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-04-15 04:17:10] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2020-04-15 04:17:10] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-04-15 04:17:10] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2020-04-15 04:17:10] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-04-15 04:17:10] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-04-15 04:17:10] outlier bounds defined between: -0.5 - 17.75
INFO [2020-04-15 04:17:10] ::order_reduce:Start.
INFO [2020-04-15 04:17:10] ::order_reduce:Start.
INFO [2020-04-15 04:17:10] .order_reduce(): expr and order match.
INFO [2020-04-15 04:17:10] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 04:17:10] ::order_reduce:Start.
INFO [2020-04-15 04:17:10] .order_reduce(): expr and order match.
INFO [2020-04-15 04:17:10] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-04-15 04:17:10] ::order_reduce:Start.
INFO [2020-04-15 04:17:10] ::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 
   8.06    0.40    8.45

Example timings

infercnv.Rcheck/examples_i386/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.050.070.11
apply_median_filtering5.560.205.76
filterHighPNormals0.020.000.02
inferCNVBayesNet295.79 1.44298.25
plot_cnv1.140.221.39
plot_per_group2.020.472.53
run12.02 0.0612.08
sample_object0.030.010.04

infercnv.Rcheck/examples_x64/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.070.000.08
apply_median_filtering7.330.087.41
filterHighPNormals0.010.000.02
inferCNVBayesNet261.82 0.72262.64
plot_cnv0.790.120.92
plot_per_group2.100.242.33
run11.23 0.0611.30
sample_object0.020.000.01