Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-04-13 12:07:23 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for sparseDOSSA on tokay2


To the developers/maintainers of the sparseDOSSA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sparseDOSSA.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.

raw results

Package 1840/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparseDOSSA 1.18.0  (landing page)
Boyu Ren, Emma Schwager
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/sparseDOSSA
git_branch: RELEASE_3_14
git_last_commit: 19015de
git_last_commit_date: 2021-10-26 12:32:01 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sparseDOSSA
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparseDOSSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sparseDOSSA_1.18.0.tar.gz
StartedAt: 2022-04-13 03:17:01 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 03:18:43 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 102.1 seconds
RetCode: 0
Status:   OK  
CheckDir: sparseDOSSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparseDOSSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sparseDOSSA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sparseDOSSA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sparseDOSSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sparseDOSSA' version '1.18.0'
* 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 'sparseDOSSA' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
sparseDOSSA 5.19   0.03    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
sparseDOSSA 5.86   0.02    5.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'RunTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'RunTests.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: OK


Installation output

sparseDOSSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/sparseDOSSA_1.18.0.tar.gz && rm -rf sparseDOSSA.buildbin-libdir && mkdir sparseDOSSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sparseDOSSA.buildbin-libdir sparseDOSSA_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sparseDOSSA_1.18.0.zip && rm sparseDOSSA_1.18.0.tar.gz sparseDOSSA_1.18.0.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
 35  568k   35  204k    0     0   605k      0 --:--:-- --:--:-- --:--:--  606k
100  568k  100  568k    0     0   896k      0 --:--:-- --:--:-- --:--:--  896k

install for i386

* installing *source* package 'sparseDOSSA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sparseDOSSA'
    finding HTML links ... done
    sparseDOSSA                             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 'sparseDOSSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sparseDOSSA' as sparseDOSSA_1.18.0.zip
* DONE (sparseDOSSA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sparseDOSSA' successfully unpacked and MD5 sums checked

Tests output

sparseDOSSA.Rcheck/tests_i386/RunTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> BiocGenerics:::testPackage("sparseDOSSA")
Parameters BEFORE Calibration File
Length exp NA Length vdMu NA length vdSD NA length vdPercentZero NA Read depth 8030
Parameters AFTER Calibration File (if no calibration file is used, defaults are shown)
Length exp 1 Length vdMu 1 length vdSD 1 length vdPercentZero 1 Read depth 8030 Feature Count 300
func_generate_random_lognormal_matrix START
start funcGenerateFeatureParameters
funcGenerateFeatureParameters: Generating vdExp Vector.
LogMu 2.39794758911363 LogSD 1.33357395233333 Threshold 26.178898826878
funcGenerateFeatureParameters: Generating vdSD Vector.
funcGenerateFeatureParameters: Generating vdMu Vector.
funcGenerateFeatureParameters: Generating vdPercentZero Vector.
***Scale***
1
***vdPercentZero***
0.3876521595863820.5012820479589080.6426777338705610.6437241888648060.7660754409368890.97850870467247
stop funcGenerateFeatureParameters
func_generate_random_lognormal_matrix: START Making features
Start funcShuffleMatrix
stop func_generate_random_lognormal_matrix
start func_generate_random_lognormal_with_outliers
Stop func_generate_random_lognormal_with_outliers
start func_generate_random_lognormal_with_multivariate_spikes
stop func_generate_random_lognormal_with_multivariate_spikes


RUNIT TEST PROTOCOL -- Wed Apr 13 03:18:27 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sparseDOSSA RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In sparseDOSSA(bugs_to_spike = 0, calibrate = NA, datasetCount = 1,  :
  number of associations = 0, and no spike file specified; no bug-bug spike-ins will be done.
> 
> proc.time()
   user  system elapsed 
   7.34    0.25    7.62 

sparseDOSSA.Rcheck/tests_x64/RunTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> BiocGenerics:::testPackage("sparseDOSSA")
Parameters BEFORE Calibration File
Length exp NA Length vdMu NA length vdSD NA length vdPercentZero NA Read depth 8030
Parameters AFTER Calibration File (if no calibration file is used, defaults are shown)
Length exp 1 Length vdMu 1 length vdSD 1 length vdPercentZero 1 Read depth 8030 Feature Count 300
func_generate_random_lognormal_matrix START
start funcGenerateFeatureParameters
funcGenerateFeatureParameters: Generating vdExp Vector.
LogMu 2.39794758911363 LogSD 1.33357395233333 Threshold 26.178898826878
funcGenerateFeatureParameters: Generating vdSD Vector.
funcGenerateFeatureParameters: Generating vdMu Vector.
funcGenerateFeatureParameters: Generating vdPercentZero Vector.
***Scale***
1
***vdPercentZero***
0.3876521595863820.5012820479589080.6426777338705610.6437241888648060.7660754409368890.97850870467247
stop funcGenerateFeatureParameters
func_generate_random_lognormal_matrix: START Making features
Start funcShuffleMatrix
stop func_generate_random_lognormal_matrix
start func_generate_random_lognormal_with_outliers
Stop func_generate_random_lognormal_with_outliers
start func_generate_random_lognormal_with_multivariate_spikes
stop func_generate_random_lognormal_with_multivariate_spikes


RUNIT TEST PROTOCOL -- Wed Apr 13 03:18:36 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sparseDOSSA RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In sparseDOSSA(bugs_to_spike = 0, calibrate = NA, datasetCount = 1,  :
  number of associations = 0, and no spike file specified; no bug-bug spike-ins will be done.
> 
> proc.time()
   user  system elapsed 
   8.68    0.21    8.89 

Example timings

sparseDOSSA.Rcheck/examples_i386/sparseDOSSA-Ex.timings

nameusersystemelapsed
sparseDOSSA5.190.035.22

sparseDOSSA.Rcheck/examples_x64/sparseDOSSA-Ex.timings

nameusersystemelapsed
sparseDOSSA5.860.025.99