Last updated on 2024-06-14 01:52:35 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| animint2 | 1 | 7 | 5 | |
| atime | 1 | 12 | ||
| aum | 1 | 12 | ||
| binsegRcpp | 1 | 12 | ||
| directlabels | 1 | 12 | ||
| FLOPART | 1 | 12 | ||
| inlinedocs | 13 | |||
| LOPART | 1 | 12 | ||
| mlr3resampling | 1 | 12 | ||
| nc | 2 | 1 | 10 | |
| neuroblastoma | 8 | 5 | ||
| PeakError | 1 | 12 | ||
| PeakSegDisk | 1 | 1 | 11 | |
| PeakSegDP | 1 | 12 | ||
| PeakSegJoint | 1 | 12 | ||
| PeakSegOptimal | 1 | 12 | ||
| penaltyLearning | 1 | 12 | ||
| plotHMM | 1 | 12 | ||
| WeightedROC | 1 | 9 | 3 |
Current CRAN status: ERROR: 1, NOTE: 7, OK: 5
Version: 2024.1.24
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
stat_unique.html:110:1 (stat_unique.Rd:65): Warning: trimming empty <li>
stat_unique.html:109:1 (stat_unique.Rd:65): Warning: trimming empty <ul>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 2024.1.24
Check: package dependencies
Result: ERROR
Package required but not available: ‘reshape2’
Packages suggested but not available for checking:
'gh', 'gistr', 'testthat', 'devtools', 'Hmisc', 'ggplot2'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.4.23
Check: package dependencies
Result: ERROR
Package required but not available: ‘bench’
Packages suggested but not available for checking:
'ggplot2', 'testthat', 'readr', 'dplyr', 'tidyr'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2023.6.14
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'testthat', 'ggplot2', 'penaltyLearning', 'atime', 'ggrepel'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.6.14
Check: examples
Result: ERROR
Running examples in ‘aum-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aum_line_search
> ### Title: aum line search
> ### Aliases: aum_line_search
>
> ### ** Examples
>
>
> if(require("data.table"))setDTthreads(1L)#for CRAN check.
Loading required package: data.table
>
> ## Example 1: two binary data.
> (bin.diffs <- aum::aum_diffs_binary(c(0,1)))
Key: <example, pred>
example pred fp_diff fn_diff
<int> <num> <num> <num>
1: 0 0 1 0
2: 1 0 0 -1
> if(requireNamespace("ggplot2"))plot(bin.diffs)
Loading required namespace: ggplot2
Failed with error: ‘there is no package called ‘ggplot2’’
> bin.line.search <- aum::aum_line_search(bin.diffs, pred.vec=c(10,-10))
> if(requireNamespace("ggplot2"))plot(bin.line.search)
Loading required namespace: ggplot2
Failed with error: ‘there is no package called ‘ggplot2’’
>
> ## Example 2: two changepoint examples, one with three breakpoints.
> data(neuroblastomaProcessed, package="penaltyLearning", envir=environment())
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘penaltyLearning’
Calls: data -> find.package
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.6.14
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘speed-comparison.Rmd’ using knitr
Quitting from lines 22-44 [unnamed-chunk-1] (speed-comparison.Rmd)
Error: processing vignette 'speed-comparison.Rmd' failed with diagnostics:
there is no package called 'penaltyLearning'
--- failed re-building ‘speed-comparison.Rmd’
SUMMARY: processing the following file failed:
‘speed-comparison.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2023.8.31
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'penaltyLearning', 'ggplot2', 'testthat'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.8.31
Check: examples
Result: ERROR
Running examples in ‘binsegRcpp-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: random_set_vec
> ### Title: random set vec
> ### Aliases: random_set_vec
>
> ### ** Examples
>
>
> library(data.table)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.8.31
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘comparisons.Rmd’ using knitr
Quitting from lines 94-95 [unnamed-chunk-8] (comparisons.Rmd)
Error: processing vignette 'comparisons.Rmd' failed with diagnostics:
there is no package called 'penaltyLearning'
--- failed re-building ‘comparisons.Rmd’
--- re-building ‘cross-validation.Rmd’ using knitr
--- finished re-building ‘cross-validation.Rmd’
SUMMARY: processing the following file failed:
‘comparisons.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 1, OK: 12
Version: 2024.1.21
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ggplot2', 'alphahull', 'dplyr', 'ggthemes', 'testthat'
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2023.8.31
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.8.31
Check: tests
Result: ERROR
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 1, OK: 12
Version: 2020.6.29
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.4.14
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'animint2', 'testthat'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.4.14
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ResamplingSameOtherCV.Rmd’ using rmarkdown
--- finished re-building ‘ResamplingSameOtherCV.Rmd’
--- re-building ‘ResamplingSameOtherSizesCV.Rmd’ using rmarkdown
Quitting from lines 36-52 [simulationScatter] (ResamplingSameOtherSizesCV.Rmd)
Error: processing vignette 'ResamplingSameOtherSizesCV.Rmd' failed with diagnostics:
there is no package called 'animint2'
--- failed re-building ‘ResamplingSameOtherSizesCV.Rmd’
--- re-building ‘ResamplingVariableSizeTrainCV.Rmd’ using rmarkdown
--- finished re-building ‘ResamplingVariableSizeTrainCV.Rmd’
SUMMARY: processing the following file failed:
‘ResamplingSameOtherSizesCV.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 2, NOTE: 1, OK: 10
Version: 2024.2.21
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'testthat', 'ggplot2', 'tidyr', 'reshape2', 'arrow'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.2.21
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘v0-overview.Rmd’ using rmarkdown
--- finished re-building ‘v0-overview.Rmd’
--- re-building ‘v1-capture-first.Rmd’ using rmarkdown
--- finished re-building ‘v1-capture-first.Rmd’
--- re-building ‘v2-capture-all.Rmd’ using rmarkdown
--- finished re-building ‘v2-capture-all.Rmd’
--- re-building ‘v3-capture-melt.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'tidyr''
--- finished re-building ‘v3-capture-melt.Rmd’
--- re-building ‘v4-comparisons.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'reshape2''
Failed with error: 'there is no package called 'tidyr''
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nc.Rcheck/vign_test/nc/vignettes/v4-comparisons_files/figure-html/unnamed-chunk-19-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7166 bytes
Input file size = 8021 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6754
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6754
Output IDAT size = 6754 bytes (412 bytes decrease)
Output file size = 6832 bytes (1189 bytes = 14.82% decrease)
Failed with error: 'there is no package called 'tidyr''
Failed with error: 'there is no package called 'tidyr''
Quitting from lines 671-687 [unnamed-chunk-21] (v4-comparisons.Rmd)
Error: processing vignette 'v4-comparisons.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘v4-comparisons.Rmd’
--- re-building ‘v5-helpers.Rmd’ using rmarkdown
--- finished re-building 'v5-helpers.Rmd'
--- re-building ‘v6-engines.Rmd’ using rmarkdown
--- finished re-building ‘v6-engines.Rmd’
--- re-building ‘v7-capture-glob.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'arrow''
Failed with error: 'there is no package called 'arrow''
Failed with error: 'there is no package called 'arrow''
--- finished re-building ‘v7-capture-glob.Rmd’
SUMMARY: processing the following file failed:
‘v4-comparisons.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.2.21
Check: examples
Result: ERROR
Running examples in ‘nc-Ex.R’ failed
The error most likely occurred in:
> ### Name: capture_first_glob
> ### Title: capture first glob
> ### Aliases: capture_first_glob
>
> ### ** Examples
>
>
> data.table::setDTthreads(1)
>
> ## Example 0: iris data, one file per species.
> library(data.table)
> dir.create(iris.dir <- tempfile())
> icsv <- function(sp)file.path(iris.dir, paste0(sp, ".csv"))
> data.table(iris)[, fwrite(.SD, icsv(Species)), by=Species]
Empty data.table (0 rows and 1 cols): Species
> dir(iris.dir)
[1] "setosa.csv" "versicolor.csv" "virginica.csv"
> data.table::fread(file.path(iris.dir,"setosa.csv"), nrows=2)
Sepal.Length Sepal.Width Petal.Length Petal.Width
<num> <num> <num> <num>
1: 5.1 3.5 1.4 0.2
2: 4.9 3.0 1.4 0.2
> (iglob <- file.path(iris.dir,"*.csv"))
[1] "/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpxNPzlE/file463c41145017/*.csv"
> nc::capture_first_glob(iglob, Species="[^/]+", "[.]csv")
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
<char> <num> <num> <num> <num>
1: setosa 5.1 3.5 1.4 0.2
2: setosa 4.9 3.0 1.4 0.2
3: setosa 4.7 3.2 1.3 0.2
4: setosa 4.6 3.1 1.5 0.2
5: setosa 5.0 3.6 1.4 0.2
---
146: virginica 6.7 3.0 5.2 2.3
147: virginica 6.3 2.5 5.0 1.9
148: virginica 6.5 3.0 5.2 2.0
149: virginica 6.2 3.4 5.4 2.3
150: virginica 5.9 3.0 5.1 1.8
>
> ## Example 1: four files, two capture groups, custom read function.
> db <- system.file("extdata/chip-seq-chunk-db", package="nc", mustWork=TRUE)
> suffix <- if(interactive())"gz" else "head"
> (glob <- paste0(db, "/*/*/counts/*", suffix))
[1] "/Volumes/Builds/packages/big-sur-arm64/results/4.4/nc.Rcheck/nc/extdata/chip-seq-chunk-db/*/*/counts/*head"
> Sys.glob(glob)
[1] "/Volumes/Builds/packages/big-sur-arm64/results/4.4/nc.Rcheck/nc/extdata/chip-seq-chunk-db/H3K36me3_AM_immune/9/counts/McGill0101.bedGraph.head"
[2] "/Volumes/Builds/packages/big-sur-arm64/results/4.4/nc.Rcheck/nc/extdata/chip-seq-chunk-db/H3K36me3_TDH_other/1/counts/McGill0019.bedGraph.head"
[3] "/Volumes/Builds/packages/big-sur-arm64/results/4.4/nc.Rcheck/nc/extdata/chip-seq-chunk-db/H3K4me3_TDH_immune/9/counts/McGill0024.bedGraph.head"
[4] "/Volumes/Builds/packages/big-sur-arm64/results/4.4/nc.Rcheck/nc/extdata/chip-seq-chunk-db/H3K4me3_XJ_immune/2/counts/McGill0024.bedGraph.head"
> read.bedGraph <- function(f)data.table::fread(
+ f, skip=1, col.names = c("chrom","start", "end", "count"))
> data.chunk.pattern <- list(
+ data="H.*?",
+ "/",
+ chunk="[0-9]+", as.integer)
> (data.chunk.dt <- nc::capture_first_glob(glob, data.chunk.pattern, READ=read.bedGraph))
data chunk chrom start end count
<char> <int> <char> <int> <int> <int>
1: H3K36me3_AM_immune 9 chr10 111456281 111456338 2
2: H3K36me3_AM_immune 9 chr10 111456338 111456381 1
3: H3K36me3_AM_immune 9 chr10 111456381 111459312 0
4: H3K36me3_AM_immune 9 chr10 111459312 111459316 5
5: H3K36me3_AM_immune 9 chr10 111459316 111459409 10
6: H3K36me3_AM_immune 9 chr10 111459409 111459411 8
7: H3K36me3_AM_immune 9 chr10 111459411 111459415 5
8: H3K36me3_AM_immune 9 chr10 111459415 111463412 0
9: H3K36me3_AM_immune 9 chr10 111463412 111463512 2
10: H3K36me3_AM_immune 9 chr10 111463512 111466726 0
11: H3K36me3_TDH_other 1 chr21 43119165 43119386 0
12: H3K36me3_TDH_other 1 chr21 43119386 43119407 1
13: H3K36me3_TDH_other 1 chr21 43119407 43119475 2
14: H3K36me3_TDH_other 1 chr21 43119475 43119502 1
15: H3K36me3_TDH_other 1 chr21 43119502 43119987 0
16: H3K36me3_TDH_other 1 chr21 43119987 43120007 1
17: H3K36me3_TDH_other 1 chr21 43120007 43120086 2
18: H3K36me3_TDH_other 1 chr21 43120086 43120107 1
19: H3K36me3_TDH_other 1 chr21 43120107 43120743 0
20: H3K36me3_TDH_other 1 chr21 43120743 43120789 1
21: H3K4me3_TDH_immune 9 chr1 36926536 36926549 10
22: H3K4me3_TDH_immune 9 chr1 36926549 36926554 9
23: H3K4me3_TDH_immune 9 chr1 36926554 36926565 11
24: H3K4me3_TDH_immune 9 chr1 36926565 36926569 9
25: H3K4me3_TDH_immune 9 chr1 36926569 36926571 8
26: H3K4me3_TDH_immune 9 chr1 36926571 36926580 7
27: H3K4me3_TDH_immune 9 chr1 36926580 36926593 8
28: H3K4me3_TDH_immune 9 chr1 36926593 36926606 7
29: H3K4me3_TDH_immune 9 chr1 36926606 36926622 8
30: H3K4me3_TDH_immune 9 chr1 36926622 36926634 9
31: H3K4me3_XJ_immune 2 chr22 20688396 20688502 0
32: H3K4me3_XJ_immune 2 chr22 20688502 20688602 1
33: H3K4me3_XJ_immune 2 chr22 20688602 20688869 0
34: H3K4me3_XJ_immune 2 chr22 20688869 20688932 2
35: H3K4me3_XJ_immune 2 chr22 20688932 20688934 3
36: H3K4me3_XJ_immune 2 chr22 20688934 20688936 4
37: H3K4me3_XJ_immune 2 chr22 20688936 20688963 5
38: H3K4me3_XJ_immune 2 chr22 20688963 20688968 7
39: H3K4me3_XJ_immune 2 chr22 20688968 20688969 6
40: H3K4me3_XJ_immune 2 chr22 20688969 20688979 5
data chunk chrom start end count
>
> ## Write same data set in Hive partition, then re-read.
> if(requireNamespace("arrow")){
+ path <- tempfile()
+ max_rows_per_file <- if(interactive())3 else 1000
+ arrow::write_dataset(
+ dataset=data.chunk.dt,
+ path=path,
+ format="csv",
+ partitioning=c("data","chunk"),
+ max_rows_per_file=max_rows_per_file)
+ hive.glob <- file.path(path, "*", "*", "*.csv")
+ hive.pattern <- list(
+ nc::field("data","=",".*?"),
+ "/",
+ nc::field("chunk","=",".*?", as.integer),
+ "/",
+ nc::field("part","-","[0-9]+", as.integer))
+ hive.dt <- nc::capture_first_glob(hive.glob, hive.pattern)
+ hive.dt[, .(rows=.N), by=.(data,chunk,part)]
+ }
Loading required namespace: arrow
Error in dataset___HivePartitioning(schm, null_fallback = null_fallback_or_default(null_fallback), :
Cannot call dataset___HivePartitioning(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Calls: <Anonymous> -> <Anonymous> -> dataset___HivePartitioning
Execution halted
Flavor: r-release-macos-arm64
Version: 2024.2.21
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘v0-overview.Rmd’ using rmarkdown
--- finished re-building ‘v0-overview.Rmd’
--- re-building ‘v1-capture-first.Rmd’ using rmarkdown
--- finished re-building ‘v1-capture-first.Rmd’
--- re-building ‘v2-capture-all.Rmd’ using rmarkdown
--- finished re-building ‘v2-capture-all.Rmd’
--- re-building ‘v3-capture-melt.Rmd’ using rmarkdown
--- finished re-building ‘v3-capture-melt.Rmd’
--- re-building ‘v4-comparisons.Rmd’ using rmarkdown
--- finished re-building ‘v4-comparisons.Rmd’
--- re-building ‘v5-helpers.Rmd’ using rmarkdown
--- finished re-building 'v5-helpers.Rmd'
--- re-building ‘v6-engines.Rmd’ using rmarkdown
--- finished re-building ‘v6-engines.Rmd’
--- re-building ‘v7-capture-glob.Rmd’ using rmarkdown
Quitting from lines 152-163 [unnamed-chunk-11] (v7-capture-glob.Rmd)
Error: processing vignette 'v7-capture-glob.Rmd' failed with diagnostics:
Cannot call dataset___HivePartitioning(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
--- failed re-building ‘v7-capture-glob.Rmd’
SUMMARY: processing the following file failed:
‘v7-capture-glob.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-arm64
Version: 2024.2.21
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘arrow’
Flavor: r-release-macos-x86_64
Current CRAN status: NOTE: 8, OK: 5
Version: 2023.9.3
Check: installed package size
Result: NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 7.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 1, OK: 12
Version: 2023.9.4
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, WARN: 1, OK: 11
Version: 2023.11.27
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.11.27
Check: examples
Result: ERROR
Running examples in ‘PeakSegDisk-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakSegFPOP_df
> ### Title: PeakSeg penalized solver for data.frame
> ### Aliases: PeakSegFPOP_df
>
> ### ** Examples
>
>
> ## Simulate a sequence of Poisson count data.
> sim.seg <- function(seg.mean, size.mean=15){
+ seg.size <- rpois(1, size.mean)
+ rpois(seg.size, seg.mean)
+ }
> set.seed(1)
> seg.mean.vec <- c(1.5, 3.5, 0.5, 4.5, 2.5)
> z.list <- lapply(seg.mean.vec, sim.seg)
> z.rep.vec <- unlist(z.list)
>
> ## Plot the simulated data sequence.
> if(require(ggplot2)){
+ count.df <- data.frame(
+ position=seq_along(z.rep.vec),
+ count=z.rep.vec)
+ gg.count <- ggplot()+
+ geom_point(aes(
+ position, count),
+ shape=1,
+ data=count.df)
+ gg.count
+ }
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘ggplot2’
>
> ## Plot the true changes.
> n.segs <- length(seg.mean.vec)
> seg.size.vec <- sapply(z.list, length)
> seg.end.vec <- cumsum(seg.size.vec)
> change.vec <- seg.end.vec[-n.segs]+0.5
> change.df <- data.frame(
+ changepoint=change.vec)
> gg.change <- gg.count+
+ geom_vline(aes(
+ xintercept=changepoint),
+ data=change.df)
Error: object 'gg.count' not found
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.11.27
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Examples.Rnw’ using knitr
Quitting from lines 209-213 [unnamed-chunk-4] (Examples.Rnw)
Error: processing vignette 'Examples.Rnw' failed with diagnostics:
object 'gg.change' not found
--- failed re-building ‘Examples.Rnw’
--- re-building ‘Spatial_correlation.Rmd’ using knitr
--- finished re-building ‘Spatial_correlation.Rmd’
--- re-building ‘Worst_case.Rmd’ using knitr
--- finished re-building ‘Worst_case.Rmd’
SUMMARY: processing the following file failed:
‘Examples.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.11.27
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘Examples.Rnw’ using knitr
Error: processing vignette 'Examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Examples.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.121 \hldef
{sim.seg} \hlkwb{<-} \hlkwa{function}\hldef{(}\hlkwc{seg.mean}\h...
?
! Emergency stop.
l.121
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Examples.Rnw’
--- re-building ‘Spatial_correlation.Rmd’ using knitr
--- finished re-building ‘Spatial_correlation.Rmd’
--- re-building ‘Worst_case.Rmd’ using knitr
--- finished re-building ‘Worst_case.Rmd’
SUMMARY: processing the following file failed:
‘Examples.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.1.24
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ggplot2', 'testthat', 'penaltyLearning'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.1.24
Check: examples
Result: ERROR
Running examples in ‘PeakSegDP-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ### chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
>
> ### ** Examples
>
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.1.24
Check: tests
Result: ERROR
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.1.24
Check: package dependencies
Result: ERROR
Package required but not available: ‘penaltyLearning’
Packages suggested but not available for checking: 'testthat', 'ggplot2'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.1.24
Check: package dependencies
Result: ERROR
Package required but not available: ‘penaltyLearning’
Packages suggested but not available for checking: 'ggplot2', 'testthat'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2024.1.25
Check: package dependencies
Result: ERROR
Package required but not available: ‘ggplot2’
Package suggested but not available for checking: ‘testthat’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 2023.8.28
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.8.28
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘compare_depmixS4.Rmd’ using knitr
** Processing: figure/unnamed-chunk-2-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 29807 bytes
Input file size = 30701 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28437
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 28000
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 28000
Output IDAT size = 28000 bytes (1807 bytes decrease)
Output file size = 28078 bytes (2623 bytes = 8.54% decrease)
Quitting from lines 89-113 [unnamed-chunk-5] (compare_depmixS4.Rmd)
Error: processing vignette 'compare_depmixS4.Rmd' failed with diagnostics:
object 'nb.dt' not found
--- failed re-building ‘compare_depmixS4.Rmd’
--- re-building ‘multiple_sequences.Rmd’ using knitr
Quitting from lines 18-34 [unnamed-chunk-1] (multiple_sequences.Rmd)
Error: processing vignette 'multiple_sequences.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘multiple_sequences.Rmd’
SUMMARY: processing the following files failed:
‘compare_depmixS4.Rmd’ ‘multiple_sequences.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, NOTE: 9, OK: 3
Version: 2020.1.31
Check: Rd files
Result: NOTE
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
10 | integer/numeric with values all in {0=negative,1=positive} or
| ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
| ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 2020.1.31
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2020.1.31
Check: examples
Result: ERROR
Running examples in ‘WeightedROC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WeightedROC
> ### Title: WeightedROC
> ### Aliases: WeightedROC
>
> ### ** Examples
>
>
> ## WeightedROC can compute ROC curves for data sets with variable
> ## weights.
> library(WeightedROC)
> y <- c(-1, -1, 1, 1, 1)
> w <- c(1, 1, 1, 4, 5)
> y.hat <- c(1, 2, 3, 1, 1)
> tp.fp <- WeightedROC(y.hat, y, w)
> if(require(ggplot2)){
+ gg <- ggplot()+
+ geom_path(aes(FPR, TPR), data=tp.fp)+
+ coord_equal()
+ print(gg)
+ }else{
+ plot(TPR~FPR, tp.fp, type="l")
+ }
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘ggplot2’
>
> ## The FN/FP columns can be used to plot weighted error as a
> ## function of threshold.
> error.fun.list <- list(
+ FN=function(df)df$FN,
+ FP=function(df)df$FP,
+ errors=function(df)with(df, FP+FN)
+ )
> all.error.list <- list()
> for(error.type in names(error.fun.list)){
+ error.fun <- error.fun.list[[error.type]]
+ all.error.list[[error.type]] <-
+ data.frame(tp.fp, error.type, weighted.error=error.fun(tp.fp))
+ }
> all.error <- do.call(rbind, all.error.list)
> fp.fn.colors <- c(FP="skyblue",
+ FN="#E41A1C",
+ errors="black")
> ggplot()+
+ scale_color_manual(values=fp.fn.colors)+
+ geom_line(aes(threshold, weighted.error, color=error.type),
+ data=all.error)
Error in ggplot() : could not find function "ggplot"
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2020.1.31
Check: tests
Result: ERROR
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2020.1.31
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Definition.Rnw’ using Sweave
Error: processing vignette 'Definition.Rnw' failed with diagnostics:
chunk 1 (label = curve)
Error in library(ggplot2) : there is no package called ‘ggplot2’
--- failed re-building ‘Definition.Rnw’
SUMMARY: processing the following file failed:
‘Definition.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc