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CHECK report for nondetects on tokay1

This page was generated on 2018-04-12 13:24:02 -0400 (Thu, 12 Apr 2018).

Package 946/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nondetects 2.8.0
Valeriia Sherina
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/nondetects
Branch: RELEASE_3_6
Last Commit: 9d87241
Last Changed Date: 2017-10-30 12:40:13 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: nondetects
Version: 2.8.0
Command: rm -rf nondetects.buildbin-libdir nondetects.Rcheck && mkdir nondetects.buildbin-libdir nondetects.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nondetects.buildbin-libdir nondetects_2.8.0.tar.gz >nondetects.Rcheck\00install.out 2>&1 && cp nondetects.Rcheck\00install.out nondetects-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=nondetects.buildbin-libdir --install="check:nondetects-install.out" --force-multiarch --no-vignettes --timings nondetects_2.8.0.tar.gz
StartedAt: 2018-04-12 01:50:08 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:59:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 550.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: nondetects.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf nondetects.buildbin-libdir nondetects.Rcheck && mkdir nondetects.buildbin-libdir nondetects.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nondetects.buildbin-libdir nondetects_2.8.0.tar.gz >nondetects.Rcheck\00install.out 2>&1 && cp nondetects.Rcheck\00install.out nondetects-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=nondetects.buildbin-libdir --install="check:nondetects-install.out" --force-multiarch --no-vignettes --timings nondetects_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/nondetects.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nondetects/DESCRIPTION' ... OK
* this is package 'nondetects' version '2.8.0'
* 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 'nondetects' can be installed ... OK
* checking installed package size ... OK
* checking package 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'nondetects.Rmd', 'nondetects.bib'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
qpcrImpute 101.28      0  101.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
qpcrImpute 133.36   0.04  133.44
* 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 PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/nondetects.Rcheck/00check.log'
for details.

Installation output

nondetects.Rcheck/00install.out


install for i386

* installing *source* package 'nondetects' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'nondetects'
    finding HTML links ... done
    nature2008                              html  
    oncogene2013                            html  
    qpcrImpute                              html  
    sagmb2011                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nondetects' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nondetects' as nondetects_2.8.0.zip
* DONE (nondetects)
In R CMD INSTALL
In R CMD INSTALL

Tests output

nondetects.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("nondetects")

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, cbind, colMeans, colSums, colnames, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

˜0 + nrep
<environment: 0x0d0dcb7c>
[1] "1 / 100"
-1586.32350454531
[1] "2 / 100"
-1532.33373645459
[1] "3 / 100"
-1506.64379697505
[1] "4 / 100"
-1494.38792762004
[1] "5 / 100"
-1487.58174346804
[1] "6 / 100"
-1483.22776877085
[1] "7 / 100"
-1480.31128960294
[1] "8 / 100"
-1478.31967542131
[1] "9 / 100"
-1476.94980050437
[1] "10 / 100"
-1475.99499358357
[1] "Single"


RUNIT TEST PROTOCOL -- Thu Apr 12 01:56:54 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
nondetects RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 115.03    0.10  115.25

nondetects.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("nondetects")

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, cbind, colMeans, colSums, colnames, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

˜0 + nrep
<environment: 0x0000000020e69650>
[1] "1 / 100"
-1586.32350454531
[1] "2 / 100"
-1532.33373645459
[1] "3 / 100"
-1506.64379697505
[1] "4 / 100"
-1494.38792762004
[1] "5 / 100"
-1487.58174346804
[1] "6 / 100"
-1483.22776877085
[1] "7 / 100"
-1480.31128960294
[1] "8 / 100"
-1478.31967542131
[1] "9 / 100"
-1476.94980050437
[1] "10 / 100"
-1475.99499358357
[1] "Single"


RUNIT TEST PROTOCOL -- Thu Apr 12 01:59:15 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
nondetects RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 139.71    0.20  140.00

Example timings

nondetects.Rcheck/examples_i386/nondetects-Ex.timings

nameusersystemelapsed
nature20080.020.010.03
oncogene20130.010.000.02
qpcrImpute101.28 0.00101.28
sagmb20110.010.000.02

nondetects.Rcheck/examples_x64/nondetects-Ex.timings

nameusersystemelapsed
nature20080.000.030.04
oncogene20130.030.000.03
qpcrImpute133.36 0.04133.44
sagmb20110.020.000.02