Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-26 14:06:50 -0400 (Tue, 26 Oct 2021).

CHECK results for ADImpute on riesling1

To the developers/maintainers of the ADImpute package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADImpute.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 19/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADImpute 1.3.0  (landing page)
Ana Carolina Leote
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/ADImpute
git_branch: master
git_last_commit: 47331f1
git_last_commit_date: 2021-05-19 12:57:20 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  

Summary

Package: ADImpute
Version: 1.3.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADImpute.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ADImpute_1.3.0.tar.gz
StartedAt: 2021-10-26 00:16:42 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 00:22:22 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 340.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ADImpute.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADImpute.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ADImpute_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/ADImpute.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ADImpute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ADImpute' version '1.3.0'
* package encoding: UTF-8
* 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 'ADImpute' 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 ... WARNING
'::' or ':::' imports not declared from:
  'SCRABBLE' 'scImpute'
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 WARNING
See
  'D:/biocbuild/bbs-3.14-bioc/meat/ADImpute.Rcheck/00check.log'
for details.



Installation output

ADImpute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ADImpute_1.3.0.tar.gz && rm -rf ADImpute.buildbin-libdir && mkdir ADImpute.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ADImpute.buildbin-libdir ADImpute_1.3.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ADImpute_1.3.0.zip && rm ADImpute_1.3.0.tar.gz ADImpute_1.3.0.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 1951k  100 1951k    0     0  4327k      0 --:--:-- --:--:-- --:--:-- 4337k

install for i386

* installing *source* package 'ADImpute' ...
** 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 'ADImpute'
    finding HTML links ... done
    ArrangeData                             html  
    CenterData                              html  
    CheckArguments_Impute                   html  
    ChooseMethod                            html  
    Combine                                 html  
    ComputeMSEGenewise                      html  
    CreateArgCheck                          html  
    CreateTrainData                         html  
    DataCheck_Matrix                        html  
    DataCheck_Network                       html  
    DataCheck_SingleCellExperiment          html  
    DataCheck_TrLength                      html  
    EvaluateMethods                         html  
    GetDropoutProbabilities                 html  
    HandleBiologicalZeros                   html  
    Impute                                  html  
    ImputeBaseline                          html  
    ImputeDrImpute                          html  
    ImputeNPDropouts                        html  
    ImputeNetParallel                       html  
    ImputeNetwork                           html  
    ImputePredictiveDropouts                html  
    ImputeSAVER                             html  
    MaskData                                html  
    MaskerPerGene                           html  
    NormalizeRPM                            html  
    NormalizeTPM                            html  
    PseudoInverseSolution_percell           html  
    ReadData                                html  
    ReturnChoice                            html  
    ReturnOut                               html  
    SetBiologicalZeros                      html  
    SplitData                               html  
    WriteCSV                                html  
    WriteTXT                                html  
    demo_data                               html  
    demo_net                                html  
    demo_sce                                html  
    network.coefficients                    html  
    transcript_length                       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 'ADImpute' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADImpute' as ADImpute_1.3.0.zip
* DONE (ADImpute)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'ADImpute' successfully unpacked and MD5 sums checked

Tests output

ADImpute.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(ADImpute)
> 
> test_check("ADImpute")
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 31 percent. 
46 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 84 percent. 
After impute : 59 percent. 
25 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 84 percent. 
After impute : 63 percent. 
22 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 42 percent. 
34 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 47 percent. 
30 percent of zeros are imputed. 
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
  33.65    0.70   62.81 

ADImpute.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> library(testthat)
> library(ADImpute)
> 
> test_check("ADImpute")
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 31 percent. 
46 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 84 percent. 
After impute : 59 percent. 
25 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 84 percent. 
After impute : 63 percent. 
22 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 42 percent. 
34 percent of zeros are imputed. 
Calculating Spearman distance. 
Calculating Pearson distance. 
 Clustering for k : 10
 Clustering for k : 11
 Clustering for k : 12
 Clustering for k : 13
 Clustering for k : 14
 Clustering for k : 15
cls object have 12 number of clustering sets.


 Zero percentage : 
Before impute : 76 percent. 
After impute : 47 percent. 
30 percent of zeros are imputed. 
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
  37.62    0.98   63.78 

Example timings

ADImpute.Rcheck/examples_i386/ADImpute-Ex.timings

nameusersystemelapsed
EvaluateMethods1.580.081.65
Impute0.480.023.25
NormalizeRPM0.020.000.01
NormalizeTPM0.830.000.83
WriteCSV000
WriteTXT000

ADImpute.Rcheck/examples_x64/ADImpute-Ex.timings

nameusersystemelapsed
EvaluateMethods1.360.161.52
Impute0.400.073.69
NormalizeRPM000
NormalizeTPM0.720.000.72
WriteCSV0.010.000.02
WriteTXT000