Package: sparseDOSSA

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparseDOSSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sparseDOSSA_1.6.1.tar.gz

StartedAt: 2019-04-13 05:39:44 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:42:20 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 156.7 seconds

RetCode: 0

Status:  OK

CheckDir: sparseDOSSA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparseDOSSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sparseDOSSA_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sparseDOSSA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 or elapsed time > 5s
            user system elapsed
sparseDOSSA 7.09   0.03    7.12
** running examples for arch 'x64' ... OK
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sparseDOSSA_1.6.1.tar.gz && rm -rf sparseDOSSA.buildbin-libdir && mkdir sparseDOSSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sparseDOSSA.buildbin-libdir sparseDOSSA_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sparseDOSSA_1.6.1.zip && rm sparseDOSSA_1.6.1.tar.gz sparseDOSSA_1.6.1.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  570k  100  570k    0     0  13.4M      0 --:--:-- --:--:-- --:--:-- 15.0M

install for i386

* installing *source* package 'sparseDOSSA' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'sparseDOSSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sparseDOSSA' as sparseDOSSA_1.6.1.zip
* DONE (sparseDOSSA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sparseDOSSA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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***
0.3881161055321170.5018004809438940.639949873162620.6427238281898810.7660289948565550.97850870467247
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 -- Sat Apr 13 05:42:09 2019 
*********************************************** 
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 
   8.06    0.29    8.64 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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***
0.3881161055321170.5018004809438940.639949873162620.6427238281898810.7660289948565550.97850870467247
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 -- Sat Apr 13 05:42:16 2019 
*********************************************** 
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 
   7.32    0.23    7.54