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CHECK report for plethy on tokay2

This page was generated on 2019-10-16 12:27:58 -0400 (Wed, 16 Oct 2019).

Package 1220/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plethy 1.22.0
Daniel Bottomly
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/plethy
Branch: RELEASE_3_9
Last Commit: 14c7a57
Last Changed Date: 2019-05-02 11:53:42 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plethy
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plethy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plethy_1.22.0.tar.gz
StartedAt: 2019-10-16 06:01:56 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:07:19 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 322.8 seconds
RetCode: 0
Status:  OK  
CheckDir: plethy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plethy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plethy_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/plethy.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plethy/DESCRIPTION' ... OK
* this is package 'plethy' version '1.22.0'
* 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 'plethy' 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'csv.to.table' 'find.break.ranges.integer' 'fix.time' 'multi.grep'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate.sample.buxco :  :  :  :
  : no visible global function definition for 'rnorm'
make.db.package: no visible global function definition for
  'packageDescription'
mvtsplot.data.frame: no visible global function definition for 'colors'
mvtsplot.data.frame: no visible global function definition for 'par'
mvtsplot.data.frame: no visible global function definition for 'layout'
mvtsplot.data.frame: no visible global function definition for
  'strwidth'
mvtsplot.data.frame: no visible global function definition for 'abline'
mvtsplot.data.frame: no visible global function definition for 'mtext'
mvtsplot.data.frame: no visible global function definition for 'plot'
mvtsplot.data.frame: no visible global function definition for 'bxp'
mvtsplot.data.frame : : no visible binding for global
  variable 'median'
mvtsplot.data.frame: no visible global function definition for 'lines'
mvtsplot.data.frame: no visible global function definition for 'Axis'
mvtsplot.data.frame: no visible global function definition for 'legend'
retrieveMatrix,BuxcoDB: no visible global function definition for
  'terms'
tsplot,BuxcoDB: no visible binding for global variable 'Days'
tsplot,BuxcoDB: no visible binding for global variable 'Value'
tsplot,BuxcoDB: no visible binding for global variable 'Sample_Name'
Undefined global functions or variables:
  Axis Days Sample_Name Value abline bxp colors layout legend lines
  median mtext packageDescription par plot rnorm strwidth terms
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
             "lines", "mtext", "par", "plot", "strwidth")
  importFrom("stats", "median", "rnorm", "terms")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
* 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
utilities 8.05   0.15   10.36
parsing   5.82   0.12    7.41
plethy    5.15   0.10    5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
utilities 5.31   0.22    5.54
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/plethy.Rcheck/00check.log'
for details.

Installation output

plethy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/plethy_1.22.0.tar.gz && rm -rf plethy.buildbin-libdir && mkdir plethy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plethy.buildbin-libdir plethy_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL plethy_1.22.0.zip && rm plethy_1.22.0.tar.gz plethy_1.22.0.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  861k  100  861k    0     0  6487k      0 --:--:-- --:--:-- --:--:-- 6733k

install for i386

* installing *source* package 'plethy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'plethy'
    finding HTML links ... done
    BuxcoDB                                 html  
    add_query_funcs                         html  
    dbImport                                html  
    parsing                                 html  
    plethy                                  html  
    utilities                               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 'plethy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plethy' as plethy_1.22.0.zip
* DONE (plethy)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'plethy' successfully unpacked and MD5 sums checked

Tests output

plethy.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("plethy")

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: reshape2
Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp2JkMOF\file1f087cec204c in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
Starting sample sample_1
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Processing breakpoint 3
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Processing breakpoint 4
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Processing breakpoint 6
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Reached the end of the file, writing remaining data
Starting sample sample_3
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Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp2JkMOF\file1f086372c38 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_1
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Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp2JkMOF\file1f0859ce66d7 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_4
Sample written
Processing breakpoint 2
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Reached the end of the file, writing remaining data
Starting sample sample_5
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Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp2JkMOF\file1f08319d715f in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
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Reached the end of the file, writing remaining data
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Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp2JkMOF\file1f08445a4eb3 in chunks of 10000
Starting chunk 1
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Processing breakpoint 7
Starting sample sample_1
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Reached the end of the file, writing remaining data
Starting sample sample_2
Sample written


RUNIT TEST PROTOCOL -- Wed Oct 16 06:06:00 2019 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
plethy RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  85.12    1.42   86.95

plethy.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("plethy")

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: reshape2
Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpQL713q\file11142817c81 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
Starting sample sample_1
Sample written
Starting sample sample_2
Sample written
Processing breakpoint 3
Starting sample sample_2
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Starting sample sample_3
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Processing breakpoint 4
Starting sample sample_1
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Processing breakpoint 5
Starting sample sample_1
Sample written
Starting sample sample_2
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Processing breakpoint 6
Starting sample sample_2
Sample written
Starting sample sample_3
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_3
Sample written
Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpQL713q\file111470382622 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_1
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Sample written
Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpQL713q\file11144a433f44 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_4
Sample written
Processing breakpoint 2
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Sample written
Reached the end of the file, writing remaining data
Starting sample sample_5
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Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpQL713q\file11143c7be01 in chunks of 10000
Starting chunk 1
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Processing breakpoint 1
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Reached the end of the file, writing remaining data
Starting sample sample_2
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Sample written
Processing C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpQL713q\file11144154437b in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
Starting sample sample_2
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Processing breakpoint 3
Starting sample sample_1
Sample written
Processing breakpoint 4
Starting sample sample_2
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Processing breakpoint 5
Starting sample sample_1
Sample written
Processing breakpoint 6
Starting sample sample_2
Sample written
Processing breakpoint 7
Starting sample sample_1
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_2
Sample written


RUNIT TEST PROTOCOL -- Wed Oct 16 06:07:10 2019 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
plethy RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  68.29    1.35   69.78

Example timings

plethy.Rcheck/examples_i386/plethy-Ex.timings

nameusersystemelapsed
BuxcoDB0.880.091.46
add_query_funcs0.290.040.32
dbImport0.470.060.61
parsing5.820.127.41
plethy5.150.105.25
utilities 8.05 0.1510.36

plethy.Rcheck/examples_x64/plethy-Ex.timings

nameusersystemelapsed
BuxcoDB1.260.131.39
add_query_funcs0.330.000.33
dbImport0.610.050.89
parsing3.700.094.46
plethy3.500.113.61
utilities5.310.225.54