Just for the record, on R-3.3.2 Herve's code fails with the following error:
Error in x[TRUE] <- new("A") :
incompatible types (from S4 to logical) in subassignment type fix
Cheers,
Andrzej
On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>
>> Hi Leonardo,
>>
>> Thanks for hunting down and isolating that bug! I tried to simplify
>> your code even more and was able to get a segfault with just:
>>
>> setClass("A", representation(stuff="numeric"))
>> x <- logical(10)
>> x[TRUE] <- new("A")
>>
>> I get the segfault about 50% of the time on a fresh R session on Mac.
>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>> on El Capitan. I get the segfault on both.
>>
>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>
>
> Any insight from
>
> R -d valgrind -f herve.R
>
> where herve.R contains the code above?
>
> Martin
>
>
>
>> Cheers,
>> H.
>>
>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
>>
>>> Hi bioc-devel,
>>>
>>> This is a story about a bug that took me a long time to trace. The
>>> behaviour was really weird, so I'm sharing the story in case this
>>> helps others in the future. I was originally writing it to request
>>> help, but then I was able to find the issue ^^. The story ends right
>>> now with code that will reproduce the problem with '$<-' from
>>> IRanges/S4Vectors.
>>>
>>>
>>>
>>>
>>> During this Bioc cycle, frequently my package derfinder has failed to
>>> pass R CMD check in OSX. The error is always the same when it appears
>>> and sometimes it shows up in release, but not devel and viceversa.
>>> Right now (3/21/2017) it's visible in both
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>>> ctor.org_checkResults_release_bioc-2DLATEST_derfinder_
>>> morelia-2Dchecksrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
>>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Bw-1Kqy-M_
>>> t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ&s=RS-lsygPtDdgWKAhjA2BcSLk
>>> Vy9RxxshXWAJaBZa_Yc&e=
>>>
>>> and
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>>> ctor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca
>>> 2-2Dchecksrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3X
>>> eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Bw-1Kqy-M_
>>> t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ&s=a_K-yK7w2LEV72lpHrpp0UoK
>>> Rru_7Aad74T5Uk0R-Fo&e=
>>> .
>>> The end of "test-all.Rout.fail" looks like this:
>>>
>>> Loading required package: foreach
>>> Loading required package: iterators
>>> Loading required package: locfit
>>> locfit 1.5-9.1 2013-03-22
>>> getSegments: segmenting
>>> getSegments: splitting
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>> 2017-03-20 02:36:52 findRegions: identifying potential segments
>>> 2017-03-20 02:36:52 findRegions: segmenting information
>>> 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
>>> 16.3681899295041
>>> 2017-03-20 02:36:52 findRegions: identifying candidate regions
>>> 2017-03-20 02:36:52 findRegions: identifying region clusters
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>> 2017-03-20 02:36:52 findRegions: identifying potential segments
>>> 2017-03-20 02:36:52 findRegions: segmenting information
>>> 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
>>> 19.7936614060235
>>> 2017-03-20 02:36:52 findRegions: identifying candidate regions
>>> 2017-03-20 02:36:52 findRegions: identifying region clusters
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>>
>>> *** caught segfault ***
>>> address 0x7f87d2f917e0, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: (function (y, x, cluster, weights, smoothFun, ...) {
>>> hostPackage <- environmentName(environment(smoothFun))
>>> requireNamespace(hostPackage) smoothed <- .runFunFormal(smoothFun,
>>> y = y, x = x, cluster = cluster, weights = weights, ...) if
>>> (any(!smoothed$smoothed)) { smoothed$fitted[!smoothed$smoothed]
>>> <- y[!smoothed$smoothed] } res <- Rle(smoothed$fitted)
>>> return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
>>> dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
>>> weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
>>> verbose = TRUE) { if (is.null(dim(y))) y <-
>>> matrix(y, ncol = 1) if (!is.null(weights) &&
>>> is.null(dim(weights))) weights <- matrix(weights, ncol =
>>> 1) if (is.null(x)) x <- seq(along = y) if
>>> (is.null(weights)) weights <- matrix(1, nrow = nrow(y),
>>> ncol = ncol(y)) Indexes <- split(seq(along = cluster), cluster)
>>> clusterL <- sapply(Indexes, length) smoothed <-
>>> rep(TRUE, nrow(y)) for (i in seq(along = Indexes)) {
>>> if (verbose) if (i%%10000 == 0)
>>> cat(".") Index <- Indexes[[i]] if (clusterL[i]
>>>
>>>> = minNum & sum(rowSums(is.na(y[Index, , drop =
>>>>
>>> FALSE])) == 0) >= minNum) { nn <-
>>> minInSpan/length(Index) for (j in 1:ncol(y)) {
>>> sdata <- data.frame(pos = x[Index], y = y[Index,
>>> j], weights = weights[Index, j]) fit <-
>>> locfit(y ˜ lp(pos, nn = nn, h = bpSpan), data =
>>> sdata, weights = weights, family = "gaussian",
>>> maxk = 10000) pp <- preplot(fit, where = "data", band
>>> = "local", newdata = data.frame(pos = x[Index]))
>>> y[Index, j] <- pp$trans(pp$fit) }
>>> } else { y[Index, ] <- NA
>>> smoothed[Index] <- FALSE } }
>>> return(list(fitted = y, smoothed = smoothed, smoother = "locfit"))
>>> }, verbose = TRUE, minNum = 1435)
>>> 2: .mapply(.FUN, dots, .MoreArgs)
>>> 3: FUN(...)
>>> 4: doTryCatch(return(expr), name, parentenv, handler)
>>> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 6: tryCatchList(expr, classes, parentenv, handlers)
>>> 7: tryCatch({ FUN(...)}, error = handle_error)
>>> 8: withCallingHandlers({ tryCatch({ FUN(...) }, error =
>>> handle_error)}, warning = handle_warning)
>>> 9: FUN(X[[i]], ...)
>>> 10: lapply(X, FUN, ...)
>>> 11: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
>>> .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
>>> 12: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
>>> .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
>>> 13: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
>>> weightChunks, MoreArgs = list(smoothFun = smoothFunction,
>>> ...), BPPARAM = BPPARAM)
>>> 14: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
>>> weightChunks, MoreArgs = list(smoothFun = smoothFunction,
>>> ...), BPPARAM = BPPARAM)
>>> 15: .smootherFstats(fstats = fstats, position = position, weights =
>>> weights, smoothFunction = smoothFunction, ...)
>>> 16: findRegions(prep$position, genomeFstats, "chr21", verbose = TRUE,
>>> smooth = TRUE, minNum = 1435)
>>> 17: eval(exprs, env)
>>> 18: eval(exprs, env)
>>> 19: source_file(path, new.env(parent = env), chdir = TRUE)
>>> 20: force(code)
>>> 21: with_reporter(reporter = reporter, start_end_reporter =
>>> start_end_reporter, { lister$start_file(basename(path))
>>> source_file(path, new.env(parent = env), chdir = TRUE)
>>> end_context() })
>>> 22: FUN(X[[i]], ...)
>>> 23: lapply(paths, test_file, env = env, reporter = current_reporter,
>>> start_end_reporter = FALSE, load_helpers = FALSE)
>>> 24: force(code)
>>> 25: with_reporter(reporter = current_reporter, results <-
>>> lapply(paths, test_file, env = env, reporter = current_reporter,
>>> start_end_reporter = FALSE, load_helpers = FALSE))
>>> 26: test_files(paths, reporter = reporter, env = env, ...)
>>> 27: test_dir(test_path, reporter = reporter, env = env, filter =
>>> filter, ...)
>>> 28: with_top_env(env, { test_dir(test_path, reporter = reporter,
>>> env = env, filter = filter, ...)})
>>> 29: run_tests(package, test_path, filter, reporter, ...)
>>> 30: test_check("derfinder")
>>> An irrecoverable exception occurred. R is aborting now ...
>>>
>>> I was finally able to reproduce this error on my Mac OSX laptop after
>>> running R CMD build and R CMD check (same options as in Bioc) several
>>> times. It took me a while, but I figured out what's the exact code
>>> that's failing. It can be reproduced (noting that it won't always
>>> fail...) in OSX by running:
>>>
>>> library('derfinder')
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>> regs_s3 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, minNum = 1435)
>>>
>>>
>>> Here is the output from my laptop one time it actually failed:
>>>
>>> library('derfinder')
>>>>
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>>
>>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>>> chunksize=1e3,
>>>>
>>> + colsubset=NULL)
>>>
>>>> regs_s3 <- findRegions(prep$position, genomeFstats, 'chr21',
>>>> verbose=TRUE, smooth = TRUE, minNum = 1435)
>>>>
>>> 2017-03-21 16:37:39 findRegions: smoothing
>>>
>>> *** caught segfault ***
>>> address 0x7f958dbf2be0, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: (function (y, x, cluster, weights, smoothFun, ...) {
>>> hostPackage <- environmentName(environment(smoothFun))
>>> requireNamespace(hostPackage) smoothed <- .runFunFormal(smoothFun,
>>> y = y, x = x, cluster = cluster, weights = weights, ...) if
>>> (any(!smoothed$smoothed)) { smoothed$fitted[!smoothed$smoothed]
>>> <- y[!smoothed$smoothed] } res <- Rle(smoothed$fitted)
>>> return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
>>> dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
>>> weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
>>> verbose = TRUE) { if (is.null(dim(y))) y <-
>>> matrix(y, ncol = 1) if (!is.null(weights) &&
>>> is.null(dim(weights))) weights <- matrix(weights, ncol =
>>> 1) if (is.null(x)) x <- seq(along = y) if
>>> (is.null(weights)) weights <- matrix(1, nrow = nrow(y),
>>> ncol = ncol(y)) Indexes <- split(seq(along = cluster), cluster)
>>> clusterL <- sapply(Indexes, length) smoothed <-
>>> rep(TRUE, nrow(y)) for (i in seq(along = Indexes)) {
>>> if (verbose) if (i%%10000 == 0)
>>> cat(".") Index <- Indexes[[i]] if (clusterL[i]
>>>
>>>> = minNum & sum(rowSums(is.na(y[Index, , drop =
>>>>
>>> FALSE])) == 0) >= minNum) { nn <-
>>> minInSpan/length(Index) for (j in 1:ncol(y)) {
>>> sdata <- data.frame(pos = x[Index], y = y[Index,
>>> j], weights = weights[Index, j]) fit <-
>>> locfit(y ~ lp(pos, nn = nn, h = bpSpan), data =
>>> sdata, weights = weights, family = "gaussian",
>>> maxk = 10000) pp <- preplot(fit, where = "data", band
>>> = "local", newdata = data.frame(pos = x[Index]))
>>> y[Index, j] <- pp$trans(pp$fit) }
>>> } else { y[Index, ] <- NA
>>> smoothed[Index] <- FALSE } }
>>> return(list(fitted = y, smoothed = smoothed, smoother = "locfit"))
>>> }, verbose = TRUE, minNum = 1435)
>>> 2: .mapply(.FUN, dots, .MoreArgs)
>>> 3: FUN(...)
>>> 4: doTryCatch(return(expr), name, parentenv, handler)
>>> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 6: tryCatchList(expr, classes, parentenv, handlers)
>>> 7: tryCatch({ FUN(...)}, error = handle_error)
>>> 8: withCallingHandlers({ tryCatch({ FUN(...) }, error =
>>> handle_error)}, warning = handle_warning)
>>> 9: FUN(X[[i]], ...)
>>> 10: lapply(X, FUN, ...)
>>> 11: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
>>> .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
>>> 12: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
>>> .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
>>> 13: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
>>> weightChunks, MoreArgs = list(smoothFun = smoothFunction,
>>> ...), BPPARAM = BPPARAM)
>>> 14: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks,
>>> weightChunks, MoreArgs = list(smoothFun = smoothFunction,
>>> ...), BPPARAM = BPPARAM)
>>> 15: .smootherFstats(fstats = fstats, position = position, weights =
>>> weights, smoothFunction = smoothFunction, ...)
>>> 16: findRegions(prep$position, genomeFstats, "chr21", verbose = TRUE,
>>> smooth = TRUE, minNum = 1435)
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>>
>>> The traceback information ends at's bumphunter::loessByCluster().
>>>
>>>
>>> I have successfully used the following code other times (see below)
>>> where I test the culprit line 100 times. By successfully, I mean that
>>> the code ran without problems... so it was unsuccessful at reproducing
>>> the problem.
>>>
>>> library('derfinder')
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>>
>>> for(i in 1:100) {
>>> print(i)
>>> regs_s3 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, minNum = 1435)
>>> }
>>> options(width = 120)
>>> devtools::session_info()
>>>
>>>
>>> I had several R processes open the one time it did fail, but well,
>>> I've had multiple of them open the times that the code didn't fail. So
>>> having multiple R processes doesn't seem to be an issue.
>>>
>>> The line that triggers the segfault is used simply to test that
>>> passing the argument 'minNum' to bumphunter::loessByCluster() via
>>> '...' works. It's not a relevant test for derfinder and I was tempted
>>> to remove it, although before tracing the bug I talked with Valerie
>>> about not removing it. With the upcoming Bioconductor release I
>>> decided to finally trace the line that triggers the segfault. At this
>>> point I was feeling lost...
>>>
>>>
>>> Running the following code seems to trigger the segfault more often (I
>>> got it like 4 times in a row):
>>>
>>> library('derfinder')
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>> regs_s1 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE)
>>> regs_s2 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, smoothFunction =
>>> bumphunter::runmedByCluster)
>>> regs_s3 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, minNum = 1435)
>>>
>>> But then I can still run the same code without problems on a for loop
>>> for 100 times:
>>>
>>> library('derfinder')
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>>
>>> for(i in 1:100) {
>>> print(i)
>>> regs_s1 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE)
>>> regs_s2 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, smoothFunction =
>>> bumphunter::runmedByCluster)
>>> regs_s3 <- findRegions(prep$position, genomeFstats, 'chr21',
>>> verbose=TRUE, smooth = TRUE, minNum = 1435)
>>> }
>>> options(width = 120)
>>> devtools::session_info()
>>>
>>>
>>>
>>>
>>> I next thought of going through findRegions() to produce simple
>>> objects that could reproduce the error. I had in mine sharing these
>>> objects so it would be easier for others to help me figure out what
>>> was failing. It turns out that this code segfaulted reliably (all the
>>> times I tested it at least):
>>>
>>>
>>> library('derfinder')
>>> library('BiocParallel')
>>> library('IRanges')
>>> prep <- preprocessCoverage(genomeData, cutoff=0, scalefac=32,
>>> chunksize=1e3,
>>> colsubset=NULL)
>>> fstats <- genomeFstats
>>> position <- prep$position
>>> weights <- NULL
>>> cluster <- derfinder:::.clusterMakerRle(position, 300L)
>>> cluster
>>> BPPARAM <- SerialParam()
>>> iChunks <- rep(1, length(cluster))
>>>
>>> fstatsChunks <- split(fstats, iChunks)
>>> posChunks <- split(which(position), iChunks)
>>> clusterChunks <- split(cluster, iChunks)
>>> weightChunks <- vector('list', length = length(unique(iChunks)))
>>>
>>> res <- bpmapply(bumphunter::loessByCluster, fstatsChunks, posChunks,
>>> clusterChunks, weightChunks, MoreArgs = list(minNum = 1435),
>>> BPPARAM = BPPARAM, SIMPLIFY = FALSE)
>>>
>>> y <- fstatsChunks[[1]]
>>> smoothed <- res[[1]]
>>>
>>> ## This segfaults:
>>> if(any(!smoothed$smoothed)) {
>>> smoothed$fitted[!smoothed$smoothed] <- y[!smoothed$smoothed]
>>> }
>>>
>>>
>>> The objects on the line that fail are a list and an Rle:
>>>
>>> y
>>>>
>>> numeric-Rle of length 1434 with 358 runs
>>> Lengths: 1 5
>>> ... 1
>>> Values : 5.109484425367 3.85228949953674 ...
>>> 3.99765511645983
>>>
>>>> lapply(smoothed, head)
>>>>
>>> $fitted
>>> [,1]
>>> [1,] NA
>>> [2,] NA
>>> [3,] NA
>>> [4,] NA
>>> [5,] NA
>>> [6,] NA
>>>
>>> $smoothed
>>> [1] FALSE FALSE FALSE FALSE FALSE FALSE
>>>
>>> $smoother
>>> [1] "loess"
>>>
>>>> table(!smoothed$smoothed)
>>>>
>>>
>>> TRUE
>>> 1434
>>>
>>>> y[!smoothed$smoothed]
>>>>
>>> numeric-Rle of length 1434 with 358 runs
>>> Lengths: 1 5
>>> ... 1
>>> Values : 5.109484425367 3.85228949953674 ...
>>> 3.99765511645983
>>>
>>> So in my derfinder code I was assigning an Rle to a matrix, and that
>>> was the segfault. I have no idea why this doesn't always fail on OSX
>>> and why it never failed on Linux or Windows.
>>>
>>>
>>> This is the super simplified IRanges code that fails:
>>>
>>> library('IRanges')
>>> y <- Rle(runif(10, 1, 1))
>>> smoothed <- list('fitted' = matrix(NA, ncol = 1, nrow = 10),
>>> 'smoothed' = rep(FALSE, 10), smoother = 'loess')
>>> sessionInfo()
>>> smoothed$fitted[!smoothed$smoothed] <- y[!smoothed$smoothed]
>>>
>>> ## Segfault on OSX
>>>
>>> library('IRanges')
>>>> y <- Rle(runif(10, 1, 1))
>>>> smoothed <- list('fitted' = matrix(NA, ncol = 1, nrow = 10),
>>>>
>>> + 'smoothed' = rep(FALSE, 10), smoother = 'loess')
>>>
>>>>
>>>> sessionInfo()
>>>>
>>> R Under development (unstable) (2016-10-26 r71594)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: macOS Sierra 10.12.3
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats4 parallel stats graphics grDevices utils
>>> datasets methods base
>>>
>>> other attached packages:
>>> [1] IRanges_2.9.19 S4Vectors_0.13.15 BiocGenerics_0.21.3
>>>
>>>> smoothed$fitted[!smoothed$smoothed] <- y[!smoothed$smoothed]
>>>>
>>>
>>> *** caught segfault ***
>>> address 0x7fcdc31dffe0, cause 'memory not mapped'
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>>
>>>
>>> ## No problems on Linux
>>>
>>> library('IRanges')
>>>> y <- Rle(runif(10, 1, 1))
>>>> smoothed <- list('fitted' = matrix(NA, ncol = 1, nrow = 10),
>>>>
>>> + 'smoothed' = rep(FALSE, 10), smoother = 'loess')
>>>
>>>>
>>>> sessionInfo()
>>>>
>>> R version 3.3.1 Patched (2016-09-30 r71426)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4 parallel stats graphics grDevices datasets utils
>>> [8] methods base
>>>
>>> other attached packages:
>>> [1] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0
>>> [4] colorout_1.1-2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.3.1
>>>
>>>> smoothed$fitted[!smoothed$smoothed] <- y[!smoothed$smoothed]
>>>>
>>>
>>>
>>> Best,
>>> Leo
>>>
>>>
>>>
>>> The session information for my first tests is below:
>>>
>>> devtools::session_info()
>>>>
>>> Session info
>>> ------------------------------------------------------------
>>> -----------------------------------------------
>>>
>>> setting value
>>> version R Under development (unstable) (2016-10-26 r71594)
>>> system x86_64, darwin13.4.0
>>> ui X11
>>> language (EN)
>>> collate en_US.UTF-8
>>> tz America/New_York
>>> date 2017-03-21
>>>
>>> Packages
>>> ------------------------------------------------------------
>>> ---------------------------------------------------
>>>
>>> package * version date source
>>> acepack 1.4.1 2016-10-29 CRAN (R 3.4.0)
>>> AnnotationDbi 1.37.4 2017-03-10 Bioconductor
>>> assertthat 0.1 2013-12-06 CRAN (R 3.4.0)
>>> backports 1.0.5 2017-01-18 CRAN (R 3.4.0)
>>> base64enc 0.1-3 2015-07-28 CRAN (R 3.4.0)
>>> Biobase 2.35.1 2017-02-23 Bioconductor
>>> BiocGenerics * 0.21.3 2017-01-12 Bioconductor
>>> BiocParallel 1.9.5 2017-01-24 Bioconductor
>>> biomaRt 2.31.4 2017-01-13 Bioconductor
>>> Biostrings 2.43.5 2017-03-19 cran (@2.43.5)
>>> bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
>>> BSgenome 1.43.7 2017-02-24 Bioconductor
>>> bumphunter * 1.15.0 2016-10-23 Bioconductor
>>> checkmate 1.8.2 2016-11-02 CRAN (R 3.4.0)
>>> cluster 2.0.6 2017-03-16 CRAN (R 3.4.0)
>>> codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
>>> colorout * 1.1-2 2016-11-15 Github
>>> (jalvesaq/colorout@6d84420)
>>> colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
>>> crayon 1.3.2 2016-06-28 CRAN (R 3.4.0)
>>> data.table 1.10.4 2017-02-01 CRAN (R 3.4.0)
>>> DBI 0.6 2017-03-09 CRAN (R 3.4.0)
>>> DelayedArray 0.1.7 2017-02-17 Bioconductor
>>> derfinder * 1.9.10 2017-03-17 cran (@1.9.10)
>>> derfinderHelper 1.9.4 2017-03-07 Bioconductor
>>> devtools 1.12.0 2016-12-05 CRAN (R 3.4.0)
>>> digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
>>> doRNG 1.6 2014-03-07 CRAN (R 3.4.0)
>>> foreach * 1.4.3 2015-10-13 CRAN (R 3.4.0)
>>> foreign 0.8-67 2016-09-13 CRAN (R 3.4.0)
>>> Formula 1.2-1 2015-04-07 CRAN (R 3.4.0)
>>> GenomeInfoDb * 1.11.9 2017-02-08 Bioconductor
>>> GenomeInfoDbData 0.99.0 2017-02-14 Bioconductor
>>> GenomicAlignments 1.11.12 2017-03-16 cran (@1.11.12)
>>> GenomicFeatures 1.27.10 2017-03-16 cran (@1.27.10)
>>> GenomicFiles 1.11.4 2017-03-10 Bioconductor
>>> GenomicRanges * 1.27.23 2017-02-25 Bioconductor
>>> ggplot2 2.2.1 2016-12-30 CRAN (R 3.4.0)
>>> gridExtra 2.2.1 2016-02-29 CRAN (R 3.4.0)
>>> gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
>>> Hmisc 4.0-2 2016-12-31 CRAN (R 3.4.0)
>>> htmlTable 1.9 2017-01-26 CRAN (R 3.4.0)
>>> htmltools 0.3.5 2016-03-21 CRAN (R 3.4.0)
>>> htmlwidgets 0.8 2016-11-09 CRAN (R 3.4.0)
>>> IRanges * 2.9.19 2017-03-15 cran (@2.9.19)
>>> iterators * 1.0.8 2015-10-13 CRAN (R 3.4.0)
>>> knitr 1.15.1 2016-11-22 CRAN (R 3.4.0)
>>> lattice 0.20-34 2016-09-06 CRAN (R 3.4.0)
>>> latticeExtra 0.6-28 2016-02-09 CRAN (R 3.4.0)
>>> lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.0)
>>> locfit * 1.5-9.1 2013-04-20 CRAN (R 3.4.0)
>>> magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
>>> Matrix 1.2-8 2017-01-20 CRAN (R 3.4.0)
>>> matrixStats 0.51.0 2016-10-09 CRAN (R 3.4.0)
>>> memoise 1.0.0 2016-01-29 CRAN (R 3.4.0)
>>> munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
>>> nnet 7.3-12 2016-02-02 CRAN (R 3.4.0)
>>> pkgmaker 0.22 2014-05-14 CRAN (R 3.4.0)
>>> plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
>>> qvalue 2.7.0 2016-10-23 Bioconductor
>>> R6 2.2.0 2016-10-05 CRAN (R 3.4.0)
>>> RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0)
>>> Rcpp 0.12.10 2017-03-19 CRAN (R 3.4.0)
>>> RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.0)
>>> registry 0.3 2015-07-08 CRAN (R 3.4.0)
>>> reshape2 1.4.2 2016-10-22 CRAN (R 3.4.0)
>>> rngtools 1.2.4 2014-03-06 CRAN (R 3.4.0)
>>> rpart 4.1-10 2015-06-29 CRAN (R 3.4.0)
>>> Rsamtools 1.27.13 2017-03-14 cran (@1.27.13)
>>> RSQLite 1.1-2 2017-01-08 CRAN (R 3.4.0)
>>> rtracklayer 1.35.9 2017-03-19 cran (@1.35.9)
>>> S4Vectors * 0.13.15 2017-02-14 cran (@0.13.15)
>>> scales 0.4.1 2016-11-09 CRAN (R 3.4.0)
>>> stringi 1.1.2 2016-10-01 CRAN (R 3.4.0)
>>> stringr 1.2.0 2017-02-18 CRAN (R 3.4.0)
>>> SummarizedExperiment 1.5.7 2017-02-23 Bioconductor
>>> survival 2.41-2 2017-03-16 CRAN (R 3.4.0)
>>> testthat * 1.0.2 2016-04-23 CRAN (R 3.4.0)
>>> tibble 1.2 2016-08-26 CRAN (R 3.4.0)
>>> VariantAnnotation 1.21.17 2017-02-12 Bioconductor
>>> withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
>>> XML 3.98-1.5 2016-11-10 CRAN (R 3.4.0)
>>> xtable 1.8-2 2016-02-05 CRAN (R 3.4.0)
>>> XVector 0.15.2 2017-02-02 Bioconductor
>>> zlibbioc 1.21.0 2016-10-23 Bioconductor
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