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CHECK report for DelayedDataFrame on tokay2

This page was generated on 2019-04-09 12:43:18 -0400 (Tue, 09 Apr 2019).

Package 404/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DelayedDataFrame 0.99.9
Qian Liu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DelayedDataFrame
Branch: master
Last Commit: 705c967
Last Changed Date: 2018-11-08 15:12:05 -0400 (Thu, 08 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: DelayedDataFrame
Version: 0.99.9
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedDataFrame.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DelayedDataFrame_0.99.9.tar.gz
StartedAt: 2019-04-09 02:11:48 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:14:13 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 145.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: DelayedDataFrame.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedDataFrame.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DelayedDataFrame_0.99.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DelayedDataFrame.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DelayedDataFrame/DESCRIPTION' ... OK
* this is package 'DelayedDataFrame' version '0.99.9'
* package encoding: UTF-8
* 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 'DelayedDataFrame' 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
Unexported object imported by a ':::' call: 'BiocGenerics:::replaceSlots'
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'DelayedDataFrame,ANY,ANY,ANY'
  generic '[' and siglist 'LazyIndex,ANY,ANY,ANY'
  generic '[<-' and siglist 'DelayedDataFrame,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  17: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
  18: `as<-`(`*tmp*`, Classi, value = obj)
  19: asMethod(object, Class, value)
  20: as(from, "DataFrame", TRUE)
  21: asMethod(object)
  22: DataFrame(listData, row.names = rownames(from))
  23: stop("cannot coerce class \"", class(listData[[i]])[1L], "\" to a DataFrame")
  
  == testthat results  ===========================================================
  OK: 109 SKIPPED: 0 FAILED: 2
  1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-method.R#145) 
  2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#220) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  17: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
  18: `as<-`(`*tmp*`, Classi, value = obj)
  19: asMethod(object, Class, value)
  20: as(from, "DataFrame", TRUE)
  21: asMethod(object)
  22: DataFrame(listData, row.names = rownames(from))
  23: stop("cannot coerce class \"", class(listData[[i]])[1L], "\" to a DataFrame")
  
  == testthat results  ===========================================================
  OK: 109 SKIPPED: 0 FAILED: 2
  1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-method.R#145) 
  2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#220) 
  
  Error: testthat unit tests failed
  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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DelayedDataFrame.Rcheck/00check.log'
for details.

Installation output

DelayedDataFrame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DelayedDataFrame_0.99.9.tar.gz && rm -rf DelayedDataFrame.buildbin-libdir && mkdir DelayedDataFrame.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedDataFrame.buildbin-libdir DelayedDataFrame_0.99.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DelayedDataFrame_0.99.9.zip && rm DelayedDataFrame_0.99.9.tar.gz DelayedDataFrame_0.99.9.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  191k  100  191k    0     0  2912k      0 --:--:-- --:--:-- --:--:-- 3245k

install for i386

* installing *source* package 'DelayedDataFrame' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DelayedDataFrame'
    finding HTML links ... done
    DelayedDataFrame-class                  html  
    DelayedDataFrame-method                 html  
    LazyIndex-class                         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 'DelayedDataFrame' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DelayedDataFrame' as DelayedDataFrame_0.99.9.zip
* DONE (DelayedDataFrame)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DelayedDataFrame' successfully unpacked and MD5 sums checked

Tests output

DelayedDataFrame.Rcheck/tests_i386/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(DelayedDataFrame)
Loading required package: S4Vectors
Loading required package: stats4
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, 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


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: DelayedArray
Loading required package: matrixStats
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("DelayedDataFrame")
-- 1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-me
invalid class "DelayedDataFrame" object: 
    '.index(x)' must be of same length of 'ncols(x)'
1: `[<-`(`*tmp*`, 1:5, 1, value = c("e", "d", "c", "b", "a")) at testthat/test_DelayedDataFrame-method.R:145
2: `[<-`(`*tmp*`, 1:5, 1, value = c("e", "d", "c", "b", "a"))
3: callNextMethod()
4: .nextMethod(x = x, i = i, j = j, value = value)
5: mergeROWS(extractCOLS(x, j), i, value)
6: extractCOLS(x, j)
7: extractCOLS(x, j)
8: initialize(x, listData = new_listData, elementMetadata = new_mcols)
9: initialize(x, listData = new_listData, elementMetadata = new_mcols)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)

-- 2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#2
cannot coerce class "list" to a DataFrame
1: `[[<-`(`*tmp*`, "da0", value = structure(c(6L, 8L, 10L, 3L, 2L, 9L, 1L, 5L, 4L, 7L
   ), .Dim = 10L)) at testthat/test_DelayedDataFrame-method.R:220
2: `[[<-`(`*tmp*`, "da0", value = structure(c(6L, 8L, 10L, 3L, 2L, 9L, 1L, 5L, 4L, 7L
   ), .Dim = 10L))
3: callNextMethod(x, i, value = value)
4: eval(call, callEnv)
5: eval(call, callEnv)
6: .nextMethod(x, i, value = value)
7: setListElement(x, i, value)
8: setListElement(x, i, value)
9: .replace_list_element(x, i2, value)
10: `[<-`(`*tmp*`, i, value = new("DelayedDataFrame", lazyIndex = new("LazyIndex", index = 1L, 
       listData = list(NULL), elementType = "ANY", elementMetadata = NULL, metadata = list()), 
       rownames = NULL, nrows = 10L, listData = list(da0 = structure(c(6L, 8L, 10L, 
       3L, 2L, 9L, 1L, 5L, 4L, 7L), .Dim = 10L)), elementType = "ANY", elementMetadata = NULL, 
       metadata = list()))
...
14: replaceCOLS(x, i, value)
15: replaceCOLS(x, i, value)
16: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
17: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
18: `as<-`(`*tmp*`, Classi, value = obj)
19: asMethod(object, Class, value)
20: as(from, "DataFrame", TRUE)
21: asMethod(object)
22: DataFrame(listData, row.names = rownames(from))
23: stop("cannot coerce class \"", class(listData[[i]])[1L], "\" to a DataFrame")

== testthat results  ===========================================================
OK: 109 SKIPPED: 0 FAILED: 2
1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-method.R#145) 
2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#220) 

Error: testthat unit tests failed
Execution halted

DelayedDataFrame.Rcheck/tests_x64/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(DelayedDataFrame)
Loading required package: S4Vectors
Loading required package: stats4
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, 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


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: DelayedArray
Loading required package: matrixStats
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("DelayedDataFrame")
-- 1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-me
invalid class "DelayedDataFrame" object: 
    '.index(x)' must be of same length of 'ncols(x)'
1: `[<-`(`*tmp*`, 1:5, 1, value = c("e", "d", "c", "b", "a")) at testthat/test_DelayedDataFrame-method.R:145
2: `[<-`(`*tmp*`, 1:5, 1, value = c("e", "d", "c", "b", "a"))
3: callNextMethod()
4: .nextMethod(x = x, i = i, j = j, value = value)
5: mergeROWS(extractCOLS(x, j), i, value)
6: extractCOLS(x, j)
7: extractCOLS(x, j)
8: initialize(x, listData = new_listData, elementMetadata = new_mcols)
9: initialize(x, listData = new_listData, elementMetadata = new_mcols)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)

-- 2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#2
cannot coerce class "list" to a DataFrame
1: `[[<-`(`*tmp*`, "da0", value = structure(c(6L, 8L, 7L, 4L, 9L, 1L, 3L, 2L, 5L, 10L
   ), .Dim = 10L)) at testthat/test_DelayedDataFrame-method.R:220
2: `[[<-`(`*tmp*`, "da0", value = structure(c(6L, 8L, 7L, 4L, 9L, 1L, 3L, 2L, 5L, 10L
   ), .Dim = 10L))
3: callNextMethod(x, i, value = value)
4: eval(call, callEnv)
5: eval(call, callEnv)
6: .nextMethod(x, i, value = value)
7: setListElement(x, i, value)
8: setListElement(x, i, value)
9: .replace_list_element(x, i2, value)
10: `[<-`(`*tmp*`, i, value = new("DelayedDataFrame", lazyIndex = new("LazyIndex", index = 1L, 
       listData = list(NULL), elementType = "ANY", elementMetadata = NULL, metadata = list()), 
       rownames = NULL, nrows = 10L, listData = list(da0 = structure(c(6L, 8L, 7L, 4L, 
       9L, 1L, 3L, 2L, 5L, 10L), .Dim = 10L)), elementType = "ANY", elementMetadata = NULL, 
       metadata = list()))
...
14: replaceCOLS(x, i, value)
15: replaceCOLS(x, i, value)
16: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
17: initialize(x, sl, rownames = .make_rownames(x, ri, ri, value), nrows = max_len)
18: `as<-`(`*tmp*`, Classi, value = obj)
19: asMethod(object, Class, value)
20: as(from, "DataFrame", TRUE)
21: asMethod(object)
22: DataFrame(listData, row.names = rownames(from))
23: stop("cannot coerce class \"", class(listData[[i]])[1L], "\" to a DataFrame")

== testthat results  ===========================================================
OK: 109 SKIPPED: 0 FAILED: 2
1. Error: [<-,DelayedDataFrame 2-D subseting works (@test_DelayedDataFrame-method.R#145) 
2. Error: [[<-,DelayedDataFrame is correct (@test_DelayedDataFrame-method.R#220) 

Error: testthat unit tests failed
Execution halted

Example timings

DelayedDataFrame.Rcheck/examples_i386/DelayedDataFrame-Ex.timings

nameusersystemelapsed
DelayedDataFrame-class0.110.000.11

DelayedDataFrame.Rcheck/examples_x64/DelayedDataFrame-Ex.timings

nameusersystemelapsed
DelayedDataFrame-class0.20.00.2