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CHECK report for SeqSQC on tokay1

This page was generated on 2019-04-13 11:28:31 -0400 (Sat, 13 Apr 2019).

Package 1426/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqSQC 1.4.0
Qian Liu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SeqSQC
Branch: RELEASE_3_8
Last Commit: 6a30e5e
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: SeqSQC
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqSQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SeqSQC_1.4.0.tar.gz
StartedAt: 2019-04-13 05:26:46 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:35:53 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 547.4 seconds
RetCode: 0
Status:  OK  
CheckDir: SeqSQC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqSQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SeqSQC_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqSQC.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 'SeqSQC/DESCRIPTION' ... OK
* this is package 'SeqSQC' version '1.4.0'
* package encoding: UTF-8
* 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 'SeqSQC' 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
LoadVfile  174.05   8.53  183.20
Inbreeding   4.84   0.17    5.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
LoadVfile 115.82   7.98  124.97
* 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: OK


Installation output

SeqSQC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SeqSQC_1.4.0.tar.gz && rm -rf SeqSQC.buildbin-libdir && mkdir SeqSQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqSQC.buildbin-libdir SeqSQC_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SeqSQC_1.4.0.zip && rm SeqSQC_1.4.0.tar.gz SeqSQC_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
100 3068k  100 3068k    0     0  44.9M      0 --:--:-- --:--:-- --:--:-- 48.3M

install for i386

* installing *source* package 'SeqSQC' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SeqSQC'
    finding HTML links ... done
    CCDS.Hs37.3.reduced_chr1.bed            html  
    IBDCheck                                html  
    IBDRemove                               html  
    Inbreeding                              html  
    LoadVfile                               html  
    MissingRate                             html  
    PCACheck                                html  
    RenderReport                            html  
    SeqOpen                                 html  
    SeqSQC-class                            html  
    SeqSQC-package                          html  
    SexCheck                                html  
    example.gds                             html  
    example.seqfile.Rdata                   html  
    example_sub.vcf                         html  
    plotQC                                  html  
    problemList                             html  
    sampleAnnotation.txt                    html  
    sampleQC                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SeqSQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqSQC' as SeqSQC_1.4.0.zip
* DONE (SeqSQC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SeqSQC' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

SeqSQC.Rcheck/tests_i386/testthat.Rout


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.

> library(testthat)
> library(SeqSQC)
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: AnnotationHub
Loading required package: SNPRelate
Loading required package: gdsfmt
SNPRelate
> 
> test_check("SeqSQC")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.96    0.37    4.32 

SeqSQC.Rcheck/tests_x64/testthat.Rout


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.

> library(testthat)
> library(SeqSQC)
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: AnnotationHub
Loading required package: SNPRelate
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
> 
> test_check("SeqSQC")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.20    0.21    4.40 

Example timings

SeqSQC.Rcheck/examples_i386/SeqSQC-Ex.timings

nameusersystemelapsed
IBDCheck0.850.031.44
IBDRemove0.700.020.72
Inbreeding4.840.175.01
LoadVfile174.05 8.53183.20
MissingRate0.230.030.27
PCACheck0.830.020.84
RenderReport2.870.453.86
SeqOpen0.040.000.03
SeqSQC-class000
SexCheck0.420.000.48
plotQC0.280.000.29
problemList0.020.000.01
sampleQC000

SeqSQC.Rcheck/examples_x64/SeqSQC-Ex.timings

nameusersystemelapsed
IBDCheck0.610.030.64
IBDRemove0.760.020.79
Inbreeding4.060.254.31
LoadVfile115.82 7.98124.97
MissingRate0.180.000.18
PCACheck0.710.020.72
RenderReport3.470.264.14
SeqOpen0.040.000.05
SeqSQC-class0.020.000.02
SexCheck0.400.040.42
plotQC0.340.000.35
problemList0.010.000.01
sampleQC000