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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plethy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plethy_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/plethy.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.39.0’
* 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 for sufficient/correct file permissions ... 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
* 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 : <anonymous> : <anonymous> : <anonymous> :
  <anonymous>: 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 ‘bxp’
mvtsplot.data.frame : <anonymous>: 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 rnorm strwidth terms
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
             "lines", "mtext", "par", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ERROR in test.csv.to.table: Error in is.data.frame(dta) && nrow(dta) == 1 && colnames(dta) == c("rat",  : 
    'length = 3' in coercion to 'logical(1)'
  ERROR in test.make.break.dta: Error in is.list(basic.result) && names(basic.result) == c("break.dta",  : 
    'length = 2' in coercion to 'logical(1)'
  
  Test files with failing tests
  
     test_check_helpers.R 
       test.csv.to.table 
       test.make.break.dta 
  
  
  Error in BiocGenerics:::testPackage("plethy") : 
    unit tests failed for package plethy
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/plethy.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plethy
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘plethy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (plethy)

R version 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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:stats':

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: reshape2
Processing /tmp/Rtmp3h1JAv/file15c6edcfb4ca 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
Sample written
Processing breakpoint 4
Starting sample sample_1
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Starting sample sample_3
Sample written
Processing breakpoint 5
Starting sample sample_1
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Starting sample sample_2
Sample written
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
Timing stopped at: 0.002 0 0.002
Error in is.data.frame(dta) && nrow(dta) == 1 && colnames(dta) == c("rat",  : 
  'length = 3' in coercion to 'logical(1)'
Processing /tmp/Rtmp3h1JAv/file15c6e47bbe9ef 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
Sample written
Starting sample sample_2
Sample written
Starting sample sample_3
Sample written
Processing /tmp/Rtmp3h1JAv/file15c6e2220ec70 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_4
Sample written
Processing breakpoint 2
Starting sample sample_4
Sample written
Starting sample sample_5
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_5
Sample written
Processing /tmp/Rtmp3h1JAv/file15c6e3f533b4f 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
Sample written
Processing breakpoint 4
Starting sample sample_3
Sample written
Starting sample sample_4
Sample written
Processing breakpoint 5
Starting sample sample_2
Sample written
Starting sample sample_4
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_2
Sample written
Starting sample sample_5
Sample written
Timing stopped at: 0.014 0.001 0.015
Error in is.list(basic.result) && names(basic.result) == c("break.dta",  : 
  'length = 2' in coercion to 'logical(1)'
In addition: Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In sanity.check.time(cur.samp.break$sec.from.start, maxTime(ret.list) *  :
  Found ( 14620 / 15300 ) timepoints greater than maximum expected time length for sample sample_5 , break.num: 6 , computing relative to new minimum
Processing /tmp/Rtmp3h1JAv/file15c6e3c55b78c 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
Sample written
Processing breakpoint 3
Starting sample sample_1
Sample written
Processing breakpoint 4
Starting sample sample_2
Sample written
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 -- Mon Jun 26 21:38:05 2023 
*********************************************** 
Number of test functions: 23 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
plethy RUnit Tests - 23 test functions, 2 errors, 0 failures
ERROR in test.csv.to.table: Error in is.data.frame(dta) && nrow(dta) == 1 && colnames(dta) == c("rat",  : 
  'length = 3' in coercion to 'logical(1)'
ERROR in test.make.break.dta: Error in is.list(basic.result) && names(basic.result) == c("break.dta",  : 
  'length = 2' in coercion to 'logical(1)'

Test files with failing tests

   test_check_helpers.R 
     test.csv.to.table 
     test.make.break.dta 


Error in BiocGenerics:::testPackage("plethy") : 
  unit tests failed for package plethy
Execution halted