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fix revdep check failure issue. Now all works
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2 changes: 1 addition & 1 deletion NEWS.md
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# fastDummies 1.6.3

* Fix bug where inputting a vector or a one column data.frame returned an issue. Now
will convert the vector to a data.frame and return that. Closes #23 by @Garyf20.
will convert the vector to a data.frame and return that. Will name each column ".data_". Closes #23 by @Garyf20.
* Fix bug where `remove_most_frequent_dummy` wasn't working right when there was a
tie for which value was the most frequent. Closes #22 by eden70.

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2 changes: 1 addition & 1 deletion R/dummy_cols.R
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Expand Up @@ -67,7 +67,7 @@ dummy_cols <- function(.data,
}

if (is.vector(.data)) {
.data <- data.frame(x = .data, stringsAsFactors = FALSE)
.data <- data.frame(.data = .data, stringsAsFactors = FALSE)
}

data_type <- check_type(.data)
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1 change: 1 addition & 0 deletions cran-comments.md
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Expand Up @@ -16,3 +16,4 @@ There were no ERRORs or WARNINGs or NOTES.
## Reverse dependencies

There are five reverse dependencies. revdepcheck::revdep_check() returns OK for all five.

2 changes: 1 addition & 1 deletion docs/articles/making-dummy-rows.html
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2 changes: 1 addition & 1 deletion docs/pkgdown.yml
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Expand Up @@ -4,5 +4,5 @@ pkgdown_sha: ~
articles:
making-dummy-rows: making-dummy-rows.html
making-dummy-variables: making-dummy-variables.html
last_built: 2020-11-08T13:43Z
last_built: 2020-11-28T16:25Z

47 changes: 47 additions & 0 deletions revdep/README.md
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# Platform

|field |value |
|:--------|:----------------------------|
|version |R version 4.0.2 (2020-06-22) |
|os |Windows 10 x64 |
|system |x86_64, mingw32 |
|ui |RStudio |
|language |(EN) |
|collate |English_United States.1252 |
|ctype |English_United States.1252 |
|tz |America/Chicago |
|date |2020-11-28 |

# Dependencies

|package |old |new |<U+0394> |
|:-----------|:------|:------|:--|
|fastDummies |1.6.2 |1.6.3 |* |
|assertthat |0.2.1 |0.2.1 | |
|cli |2.2.0 |2.2.0 | |
|crayon |1.3.4 |1.3.4 | |
|data.table |1.13.2 |1.13.2 | |
|digest |0.6.27 |0.6.27 | |
|ellipsis |0.3.1 |0.3.1 | |
|fansi |0.4.1 |0.4.1 | |
|glue |1.4.2 |1.4.2 | |
|lifecycle |0.2.0 |0.2.0 | |
|magrittr |2.0.1 |2.0.1 | |
|pillar |1.4.7 |1.4.7 | |
|pkgconfig |2.0.3 |2.0.3 | |
|rlang |0.4.9 |0.4.9 | |
|stringi |1.5.3 |1.5.3 | |
|stringr |1.4.0 |1.4.0 | |
|tibble |3.0.4 |3.0.4 | |
|utf8 |1.1.4 |1.1.4 | |
|vctrs |0.3.5 |0.3.5 | |

# Revdeps

## Failed to check (2)

|package |version |error |warning |note |
|:-------|:-------|:-----|:-------|:----|
|bnpa |? | | | |
|drf |? | | | |

Binary file added revdep/checks/DMCFB/DMCFB_1.4.0.tar.gz
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138 changes: 138 additions & 0 deletions revdep/checks/DMCFB/new/DMCFB.Rcheck/00check.log
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* using log directory 'C:/Users/user/Dropbox/R_project/fastDummies/revdep/checks/DMCFB/new/DMCFB.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --no-build-vignettes'
* checking for file 'DMCFB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DMCFB' version '1.4.0'
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DMCFB' can be installed ... WARNING
Found the following significant warnings:
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'matrixStats' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'BiocParallel' was built under R version 4.0.3
See 'C:/Users/user/Dropbox/R_project/fastDummies/revdep/checks/DMCFB/new/DMCFB.Rcheck/00install.out' for details.
* 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 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'DMCFB-Ex.R' failed
The error most likely occurred in:

> ### Name: findDMCFB-method
> ### Title: findDMCFB method
> ### Aliases: findDMCFB-method findDMCFB,BSDMC-method findDMCFB
>
> ### ** Examples
>
> set.seed(1980)
> nr <- 1000
> nc <- 4
> metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
> methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
> methl <- methc / metht
> r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
> names(r1) <- 1:nr
> cd1 <- DataFrame(
+ Group = rep(c("G1", "G2"), each = nc / 2),
+ row.names = LETTERS[1:nc]
+ )
> OBJ1 <- cBSDMC(
+ rowRanges = r1, methReads = methc, totalReads = metht,
+ methLevels = methl, colData = cd1
+ )
> OBJ2 <- findDMCFB(OBJ1,
+ bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
+ alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
+ )
------------------------------------------------------------
Running Bayesian functional regression model ...
The priors's SD = 0.3033, estimated from data ...
Number of assigned cores: 2 ...
------------------------------------------------------------
Fitted model:
logit(MethRead/ReadDepth) ~ F(Group)
------------------------------------------------------------
Creating 1 batches of genomic positions ...
Running batch 1/1; chr1; 1000 positions; Region [ 1, 1000]; Date 2020-11-28 11:33:41
Warning: namespace 'DMCFB' is not available and has been replaced
by .GlobalEnv when processing object '<unknown>'
Loading required package: DMCFB
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'DMCFB'
Warning: namespace 'DMCFB' is not available and has been replaced
by .GlobalEnv when processing object '<unknown>'
Error: BiocParallel errors
element index: 1, 2
first error: unable to find required package 'DMCFB'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
 5.  +-BiocParallel::bplapply(mylist, .fitpar, BPPARAM = optbp)
 6.  \-BiocParallel::bplapply(mylist, .fitpar, BPPARAM = optbp)

Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'DMCFB'
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'DMCFB'
== testthat results ===========================================================
Error (test-findDMCFB.R:12:5): test findDMCFB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... NONE
'DMCFB.Rmd' using 'UTF-8'... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 2 ERRORs, 1 WARNING
68 changes: 68 additions & 0 deletions revdep/checks/DMCFB/new/DMCFB.Rcheck/00install.out
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* installing *source* package 'DMCFB' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package 'SummarizedExperiment' was built under R version 4.0.3
2: package 'MatrixGenerics' was built under R version 4.0.3
3: package 'matrixStats' was built under R version 4.0.3
4: package 'GenomicRanges' was built under R version 4.0.3
5: package 'BiocGenerics' was built under R version 4.0.3
6: package 'S4Vectors' was built under R version 4.0.3
7: package 'IRanges' was built under R version 4.0.3
8: package 'GenomeInfoDb' was built under R version 4.0.3
9: package 'Biobase' was built under R version 4.0.3
10: package 'BiocParallel' was built under R version 4.0.3
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'matrixStats' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'BiocParallel' was built under R version 4.0.3
*** arch - x64
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'matrixStats' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'BiocParallel' was built under R version 4.0.3
** testing if installed package can be loaded from final location
*** arch - i386
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'matrixStats' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'BiocParallel' was built under R version 4.0.3
*** arch - x64
Warning: package 'SummarizedExperiment' was built under R version 4.0.3
Warning: package 'MatrixGenerics' was built under R version 4.0.3
Warning: package 'matrixStats' was built under R version 4.0.3
Warning: package 'GenomicRanges' was built under R version 4.0.3
Warning: package 'BiocGenerics' was built under R version 4.0.3
Warning: package 'S4Vectors' was built under R version 4.0.3
Warning: package 'IRanges' was built under R version 4.0.3
Warning: package 'GenomeInfoDb' was built under R version 4.0.3
Warning: package 'Biobase' was built under R version 4.0.3
Warning: package 'BiocParallel' was built under R version 4.0.3
** testing if installed package keeps a record of temporary installation path
* DONE (DMCFB)
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