Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

eWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI=q-0nEguTQCQNv04U4nju5HMBn6l8GmC_yCd7KSemIU8= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Sea

Re: [Rd] unlink() on "~" removes the home directory

es or files, please let me know. I would be happy to submit a patch for the new unlink("~") behavior. Thanks, Gabor __ R-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddev

Re: [Bioc-devel] TIMEOUT error in building vignette in package scruff

fqt84VtBcfhQ=BK7q3X eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=stHSi8EN5PUgMEVus6KdL2z7-DfGz ikck8btNROFUx0=dSXLn6y8wJtjg6ukcpOpGbSHfXqqsH97r9fuSJkakGo= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

be a reasonable substitute, especially if it can spit out a VRanges somehow --t On Thu, Oct 11, 2018 at 10:14 AM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote: Sounds good. I should also mention that Rsamtools has pileup() that is available on all platforms. Don't know how easy

Re: [Bioc-devel] Bioconductor package build fails

iZvSXAJJKaaPhzWA=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw=5WZzTZGK1jX2QI5fKn_INmjLYyv876INVFqftwFxlT4= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

, platform agnostic. This should work. --t On Oct 11, 2018, at 1:41 AM, Hervé Pagès wrote: And of course: the whole trick I described below only makes sense if MTseeker doesn't rely on gmapR for its core functionality, that is, if not having gmapR installed still allows the user to accomplish

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

on Windows but Windows users won't be able to accomplish anything meaningful with it. In that case, marking the package as unsupported on Windows would be preferable. Hope this makes sense, H. On 10/10/2018 10:26 PM, Hervé Pagès wrote: Hi Tim, No platform-specific dontrun capabilities AFAIK

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

WYiZvSXAJJKaaPhzWA=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hp

Re: [Bioc-devel] Problem with setClassUnion and DelayedArray

my function for the slot definition. And I don’t think the user sees this generally. But given that we’re coming up on a release I thought I would ask if there’s anything I can do to get rid of this warning! Or can I go with my first instinct and safely ignore it? Thanks, Elizabeth Purdom

Re: [Bioc-devel] a pattern to be avoided? mcols(x)$y <- z

0.058 0.006 0.065 Presumably the mcols()$<- copies/rewrites a lot of data needlessly? -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: h

Re: [Bioc-devel] GenomeInfoDB SeqInfo function error

___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-DK9eRRfECV1yPP6ZtcqI5wTDmAcAznmepaSA1e4lRE=sYIOe-2EKFxkXyKVQFowbNaXORn4F0Q

[Rd] Bug in printing array of type "list"

<- array(NA, 2:0) typeof(a2) # [1] "logical" a2 # <2 x 1 x 0 array of logical> # [,1] # [1,] # [2,] Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N,

Re: [Rd] as.vector() broken on a matrix or array of type "list"

Hi Martin, On 09/26/2018 12:41 AM, Martin Maechler wrote: Hervé Pagès on Tue, 25 Sep 2018 23:27:19 -0700 writes: > Hi, Unlike on an atomic matrix, as.vector() doesn't drop > the "dim" attribute of matrix or array of type "list": m <- matrix(

[Rd] as.vector() broken on a matrix or array of type "list"

# [1,] NULL NULL NULL # [2,] NULL NULL NULL is.vector(as.vector(m)) # [1] FALSE Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa

Re: [Rd] Bias in R's random integers?

rldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=tVt5ARiRzaOYr7BgOc0nC_hDq80BUkAUKNwcowN5W1k=WOx4NyeYmWxpDG3tBRQ9-_Y3_7YAlKUKOP6gZLs0BrQ= -- Hervé Pagès Program in Computational Biology Division of Public

Re: [Bioc-devel] Errors in Building AssessORF

__ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=tS_aEsUJun1qA9WO0HWeyiqKt8zalnNiL3cp0BZVtKQ=oWrN9I53U5I1BDWdLuzccCO_u

Re: [Bioc-devel] proteoQC

. On 09/07/2018 10:25 AM, Bo Wen wrote: Yes. Bo On Fri, Sep 7, 2018 at 12:24 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote: Hi Bo, Are you saying you cannot push changes to your package? H. On 09/07/2018 09:55 AM, Bo Wen wrote: > Hi, > I'

Re: [Bioc-devel] proteoQC

=-qRky554yTDVN2u7XQ0xlXDcnNdMzg93wm5J1Z0dAd8=8KSj7P_s3AiHvIUqkGETwbJeuTqxb0ptt1zRCEzYMbE= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667

Re: [Bioc-devel] BSGenome submission Annotation pckg

=k4gMuekxpPsqOqqUSi0uHUPWOMOjAVWbvHVFbq-rMYA= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax

Re: [Bioc-devel] Web hook push error

___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Asx6gaOwY0Z5CgT-ST6S6E1x3niqMsE76PJRThTxe6M=Or_DF3OO0pZW-21R4n_QqIqrQIrOhGssX9bm0EuLQyQ=

Re: [Rd] Argument 'dim' misspelled in error message

Thanks! On 09/01/2018 05:42 AM, Kurt Hornik wrote: Hervé Pagès writes: Thanks: fixed in the trunk with c75223. Best -k Hi, The following error message misspells the name of the 'dim' argument: array(integer(0), dim=integer(0)) Error in array(integer(0), dim = integer(0

[Rd] Argument 'dim' misspelled in error message

length(data), dimnames = NULL) NULL Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:

Re: [Bioc-devel] Help with class lost after subsetting.

On 08/28/2018 11:46 AM, Hervé Pagès wrote: On 08/27/2018 11:01 PM, Martin Morgan wrote: On 08/28/2018 12:19 AM, Charles Plessy wrote: Dear Bioconductor developers, In the CAGEr package, I created a "CAGEexp" class that extends "MultiAssayExperiment" without adding

Re: [Bioc-devel] Help with class lost after subsetting.

ject.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=BFHgkPpGkkRZx_me9V6pN2aTIxXYDgkUBG5jJTKLugc=Xa6tx2WwH603kmeR7WiV1PLMBM3myI5fUfjLL6WkMmU= -- Hervé Pagès Program in Computati

Re: [Rd] Where does L come from?

On 08/25/2018 04:33 PM, Duncan Murdoch wrote: On 25/08/2018 4:49 PM, Hervé Pagès wrote: The choice of the L suffix in R to mean "R integer type", which is mapped to the "int" type at the C level, and NOT to the "long int" type, is really unfortunate as it seems

Re: [Rd] Where does L come from?

On 08/25/2018 02:23 PM, Dirk Eddelbuettel wrote: On 25 August 2018 at 13:49, Hervé Pagès wrote: | The choice of the L suffix in R to mean "R integer type", which | is mapped to the "int" type at the C level, and NOT to the "long int" | type, is really unfortunat

Re: [Rd] Where does L come from?

he size is an implementation detail and later "essentially everybody" moved to 32 bit integers and 64 bit longs as the 64 bit architectures became prevalent. Which is why when it matters one should really use more explicit types like int32_t or int64_t.) Dirk -- Hervé Pagès Program

Re: [Rd] longint

On 08/16/2018 11:30 AM, Prof Brian Ripley wrote: On 16/08/2018 18:33, Hervé Pagès wrote: ... Only on Intel platforms int is 32 bits. Strictly speaking int is only required to be >= 16 bits. Who knows what the size of an int is on the Sunway TaihuLight for example ;-) R's configure che

Re: [Rd] longint

ide data.table. We use it for 64-bit integers as nanosecond timestamps in our nanotime package (which has some converters). Dirk -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19

Re: [Rd] longint

list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ERck0y30d00Np6hqTNYfjusx1beZim0OrKe9O4vkUxU=x1gI9ACZol7WbaWQ7Ocv60csJFJClZotWkJIMwUdjIc= -- Hervé Pagès Program in Computational Biolog

Re: [Bioc-devel] Block bootstrap for GenomicRanges

nterest that y' may have more or less features than y. I will explore a bit using the solutions you've laid out. Now that I think about it, the start-position based solution that I was thinking about will break if two features in y share the same start position, so that's not good. On Mon, Aug 13,

Re: [Bioc-devel] Block bootstrap for GenomicRanges

start(y.boot.1)[runValue(y.boot.1) == 1], width=runLength(y.boot.1)[runValue(y.boot.1) == 1]) I'm interested in building a function that takes in IRanges and outputs these shuffled set of IRanges. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Ca

Re: [Bioc-devel] Block bootstrap for GenomicRanges

.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=58qAk0b5MsXbsLCIUZP84lVgqb3DywZToIUQoX2WpTc=kaZA6WamwApoWQOGryaxzaB3GgxiLFgfd1YRK4w0O7U= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchins

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=YRPQuTB5uy8tiE-k-5akRFXnJhoNwjhnS3ooygAEUQU= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...

Re: [Bioc-devel] as.data.frame for GRanges when one meta column is a data frame

the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt8

[Rd] MARGIN in base::unique.matrix() and base::unique.array()

.) : arguments cannot be recycled to the same length > unique(matrix(1:10, ncol=2), MARGIN=3) Error in unique.matrix(matrix(1:10, ncol = 2), MARGIN = 3) : c("MARGIN = 3 is invalid for dim = 5", "MARGIN = 3 is invalid for dim = 2") Thanks, H. -- Hervé Pagès Program in

Re: [Bioc-devel] reverting to older version

PM, Samsiddhi Bhattacharjee wrote: OK...1.98.0 and 1.99.0 sounds good. Shall do that. Is it necessary to convey the reasons for the change e.g. NEWS file ? That's my last question...I hope ! On Tuesday, June 12, 2018, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote: Ah ok. Y

Re: [Bioc-devel] reverting to older version

? It should probably have been 1.19.1 ? On Monday, June 11, 2018, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote: Hi, Having a package that is known to be broken in release is not really an option. How about replacing all the files in the RELEASE_3_7 branch wi

Re: [Bioc-devel] reverting to older version

dGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=fgBGvYIMbW3NwrKMVPVed43z9LsMyZhyprB7VIWmzRQ=mkxJZC0R8tmJDvJ5e5BD4q_sni2JIJB-sCIAkpGut9c= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-ma

Re: [Rd] Subsetting the "ROW"s of an object

at's a good one. Need to change this in S4Vectors::default_extractROWS() and other places. Thanks! H. Hadley -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-102

Re: [Rd] Subsetting the "ROW"s of an object

an max #> #> 1 arr[i, TRUE, TRUE, TRUE] 41.8ms 43.6ms 46.5ms #> 2 arr[i, , , ] 41.7ms 43.1ms 46.3ms On Fri, Jun 8, 2018 at 12:31 PM, Berry, Charles wrote: On Jun 8, 2018, at 11:52 AM, Hadley Wickham wrote: On Fri, Jun 8, 2018 at

Re: [Rd] Subsetting the "ROW"s of an object

kham wrote: On Fri, Jun 8, 2018 at 11:38 AM, Berry, Charles wrote: On Jun 8, 2018, at 10:37 AM, Hervé Pagès wrote: Also the TRUEs cause problems if some dimensions are 0: > matrix(raw(0), nrow=5, ncol=0)[1:3 , TRUE] Error in matrix(raw(0), nrow = 5, ncol = 0)[1:3, TRUE] : (subsc

Re: [Rd] Subsetting the "ROW"s of an object

] 2 3 4 subset_ROW(data.frame(x = 1:10, y = 10:1), 2:4) #> x y #> 2 2 9 #> 3 3 8 #> 4 4 7 HTH, Chuck -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Sea

Re: [Rd] Subsetting the "ROW"s of an object

On 06/08/2018 10:32 AM, Hervé Pagès wrote: On 06/08/2018 10:15 AM, Michael Lawrence wrote: There probably should be an abstraction for this. In S4Vectors, we have extractROWS(). FWIW the code in S4Vectors that does what your subset_ROW() does is: https://urldefense.proofpoint.com/v2/url?u

Re: [Rd] Subsetting the "ROW"s of an object

YtcFXIyQwpQKs9lVbLNvdBBUubTv7BVAfM=HsEbNAT5IElAUS-W2VVSeJs4tfQc77heV7BbQxru518= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.

Re: [Bioc-devel] build cache on bioconductor build system?

sage in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seat

Re: [Bioc-devel] How best to remap S4Vectors::Hits indices?

18k--I=axfJINFZYMTUgAtiTpF1FfjKAHOgjHrsbge0ANjtCrE= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 66

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

hz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=lfZWGGarfZUEkLuLxuYCQktiBKaASsMbNpCwLMzfFrM=8onp29q_vGi-gvujeRnxw0EL-gvcJNBKB7_FPrP4zYg= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Researc

Re: [Bioc-devel] Batch Package Submission

provide links to the other packages (as a comment in the issue tracker) after you submit the first package. This will provide some context to the review. Thanks, H. Thanks a lot -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research

Re: [Rd] Dispatch mechanism seems to alter object before calling method on it

On 05/16/2018 01:24 PM, Michael Lawrence wrote: On Wed, May 16, 2018 at 12:23 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: On 05/16/2018 10:22 AM, Michael Lawrence wrote: Factors and data.frames are not structures, because they must have a class attribute. Just call them &q

Re: [Rd] Dispatch mechanism seems to alter object before calling method on it

me(), "vector") # [1] FALSE is(data.frame(), "factor") # [1] FALSE is(data.frame(), "vector_OR_factor") # [1] TRUE etc... Many people stay away from S4 because of these incomprehensible behaviors. Finally note that even pure S3 operations can produce ou

Re: [Rd] Dispatch mechanism seems to alter object before calling method on it

) # [1] TRUE Couldn't we recognize these problems as real, even if they are by design? Hopefully we can all agree that: - the dispatch mechanism should only dispatch, not alter objects; - is() and selectMethod() should not contradict each other. Thanks, H. Michael On Tue, May 15, 2018 at 5:

Re: [Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

tat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=09DDSYiwyEgMDuRBEXo2G8cd-Yse5xe8Z_k_aT3ciew=zcOg_EezEKrtpGE_7wyqZHWJPaVh4cYJd739M3rPjqA= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchi

Re: [Bioc-devel] BSGenome submission.

Yes the .tar.gz file. Thanks! H. On 05/14/2018 11:37 AM, Jose Die wrote: Hi Hervé, You mean the .tar.gz file? Sorry, first time I’m doing this. Jose El 14/5/2018, a las 1:33, Hervé Pagès <hpa...@fredhutch.org> escribió: Hi Jose, Contributed BSgenome packages get added to the repo

Re: [Bioc-devel] GenomicRanges List subclass and apply

vel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=k5vpJVkh58WH_4jBoE8Hcz_bmop9lW6D_bqF-tDiDm8=s_wv4S9c-aOZ3KFs8bcPcZL8UJUz0xC6cOi4LMqmkRc= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave.

Re: [Bioc-devel] BSGenome submission.

=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DwkzuTPwUOhQjGp3ABzxFdKpIIE-QUyp-aib_k9yLhM=UIIcIndBybo3SSq8zvAkZbz76A466wWBbc0ks5vIauM= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

HVfED9YMwnudCUfe0s= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

ailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iR0SNBpjI6zR3P2WDdOLGY07wOto6iaQWjT91Sn6ln8=IIGlY5oxZoalMA00eVotN8FxahrYeGHBN8kPlQ9hQ_k= -- Hervé Pagès P

Re: [Rd] length of `...`

Thanks Martin for the clarifications. H. On 05/04/2018 06:02 AM, Martin Maechler wrote: Hervé Pagès <hpa...@fredhutch.org> on Thu, 3 May 2018 08:55:20 -0700 writes: > Hi, > It would be great if one of the experts could comment on the > difference b

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

3dPT3MzP89-SrXj7WE68ASStRykpsAASpDJU=l2WFtbtf4nCVcoygg5Eob_wu-Q4qfETzWYAA_f9-mKc= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 66

Re: [Rd] length of `...`

ut evaluating the rest using ..1, but I don't know a way to do this for general n in pre-3.5.0 base R. If you don't mind using a package: # works with R 3.1 and up library(rlang) x <- "global" f <- function(...) { x <- "f" g(...) } g <- function(...) { do

Re: [Bioc-devel] Suggested edits to support site posting guide

__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=S5D7QD263pcF-j96zEV-sY0v_ulBJ_ZpI9JMXcbAEOI=chTCvAJdVNlm_YsDjNRIrvNNptfOmOK0yc5mLpWzIkQ= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fre

Re: [Bioc-devel] Error: node stack overflow

er fix can be hard to figure out even if it's simple. BTW, before the fix, the 'envir' argument was ignored so I wonder if a static code analysis tool couldn't have detected this... H. On 04/30/2018 03:26 PM, Michael Lawrence wrote: I just pushed it to the 3.5 branch. On Mon, Apr 30, 2018

Re: [Bioc-devel] Error: node stack overflow

is thread. I will look into this and hopefully fix it. On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: Hi, I made progress on this. This has actually nothing to do with Java. You get the same thing with the flexmix package. What rJava and flexmix have in common is tha

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

kage and potentially other things. So you could define a parent class of 'matrix' using setClassUnion() and then use setIs() to establish further derivations: setClassUnion("MatrixLike", "matrix") setIs("DelayedMatrix", "MatrixLike") Michael On Mon, Apr 30

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

__ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Rhy4i6H9xaY8HzWv9v_jhOnp5OyEpJcG52RP3nHorU8=Pc

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

tinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=WCuDvGWmDrT5ZoYylftzjbrlaEu-lOxIIJaNJgn6itQ=_3ZIrKjXNYWYMKKDBvbn1aNtGMB6rfqfhs-zU_P5_ug= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100

Re: [Bioc-devel] Last minute error in the build

you get when running the code in scmeth vignette. The build system will pick-up the latest version of HDF5Array so scmeth should go green again on the build report tomorrow. H. On 04/30/2018 10:21 AM, Hervé Pagès wrote: Hi Divy, I will take care of this. You don't need to do anything. Cheers, H

Re: [Bioc-devel] Last minute error in the build

84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=RBt9k3A-vxuVohDsl55aCS2e531MTyn_iu2qGRh2-qI=OO19dRaLUk9SvbPL7BTpB_uWkqIJk-_78VSX_p_SznQ= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-102

Re: [Bioc-devel] Error: node stack overflow

ils datasets [8] methods base other attached packages: [1] IRanges_2.13.29 S4Vectors_0.17.44 BiocGenerics_0.25.3 [4] rJava_0.9-9 loaded via a namespace (and not attached): [1] compiler_3.5.0 On 04/14/2018 03:11 AM, Hervé Pagès wrote: Hi Zheng, I can totally reproduce this on my Ubuntu lap

Re: [Bioc-devel] DMRcaller build error

x' derives from GRangesList. Doing class(x) == "CompressedGRangesList" will be FALSE if 'x' is another GRangesList derivative and that is probably not what you want. Cheers, H. Radu On Fri, Apr 27, 2018 at 8:11 PM, Hervé Pagès <hpa...@fredhutch.org <mailto:hpa...@fredhutch.

Re: [Bioc-devel] build machines

-- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kasper Daniel Hansen <kasperdanielhan...@gmail.com> Sent: Friday, April 27, 2018 10:29 AM To: Hervé Pagès Cc: bioc-devel@r-proje

Re: [Bioc-devel] How to update R version in terminal?

roject.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=HqvexBcWB-xz8MjS_TwC_bBhQlHytyjCHlOhaJf4nb8=TeoqGt6tumKLFdxpQcB4ys07vuqVmLjW-5n8OBCEkzo= -- Hervé Pagè

Re: [Bioc-devel] build machines

fo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=JwiMI-3BEUJlonlihLD_mDkPuEIalQbkrQPSGahzfsg=R1DGN1kNpBZ4ZRBCTQzDPQlNYapuBNSYB4JTM6tO60w= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Cente

Re: [Bioc-devel] git push confusion

this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

artin On Sat, Apr 14, 2018 at 4:05 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: How about renaming Annotated? Isn't having 2 classes around with the same name fundamentally a bad situation? No amount of workarounds will change that. H. On 04/12/2018 04:06 PM, Michael Lawrence wrot

Re: [Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MeyA9WrkJOQDYGySOlgR8QARzH-hSAPwc5-b4mJ5E9A=njLygKe4nxHzP911sM3TIgYMkMHsNWR97p3ZFIr0Voc= -- Hervé Pagès Program

Re: [Bioc-devel] Error: node stack overflow

aphicsgrDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5 IRanges_2.13.28 [4] S4Vectors_0.17.38 BiocGenerics_0.25.3 rJava_0.9-9 [7] rmarkdown_1.9 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 digest_0.6.15rprojroot_1.3-2 [4] bitops_1

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=fol6oIBKr5fVzLGchc4RvlrsYKehauLVF5_G-LWRaXM=UovEzK2nsWLv9tn6_XmxsASzSfuAFOLSHTrOousDJOY= -- Hervé Pagès Program in Computational B

Re: [Bioc-devel] AAString - Amino acid code enforced?

Hi Felix, Please see my answer in the issue you opened on GitHub: https://github.com/Bioconductor/Biostrings/issues/10 Cheers, H. On 04/02/2018 06:07 AM, Felix Ernst wrote: Dear all, probably this is for Hervé Pagès: I tried the following code, which should according to ?AAString

Re: [Bioc-devel] update schedule of packages

-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Xihpoy1_6CIsMRaulXn9QucRVEAhRMGoi5grnm_DGSw=6AdKUYeJMBHCnEqKX2fADWWvyIV5o-ICqyRff0pqS9A= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer

Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class

man_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qpgk0XNxCYLZKHMRS-PnHD2znDDwj1P-Eiu7P4aUSuI=qjwH7TgvfYKGtMDCI77_VVUw8S-5PA6ctju8Jb3erUQ= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Ce

Re: [Bioc-devel] Error: node stack overflow

Hi Zheng, Thanks for the report. I will look into this and will let you know. H. On 04/01/2018 02:38 AM, Zheng Wei wrote: Dear all, I find this error if calling library(rJava) before using BiocGenerics::unique The code is pasted below. Thanks, Zheng > library(rJava) >

[Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

deprecate the old mechanism (workflowInstall()) at some point in the future. Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this migration. Let us know if you have any question about this. H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred

Re: [Bioc-devel] No Windows binary for GenomicRanges

Hi Gordon, The TIMEOUT that was preventing the Windows binary of GenomicRanges from propagating has been addressed. The latest version of the package (1.31.23) is now available for BioC devel users on all platforms via biocLite(). Cheers, H. On 03/19/2018 10:01 AM, Hervé Pagès wrote: Hi

Re: [Bioc-devel] Tensorflow support for bioconductor packages

On 03/28/2018 02:41 PM, Hervé Pagès wrote: Hi Kieran, Note that you can execute arbitrary code at load time by defining an .onLoad() hook in your package. So you *could* put something like this in your package:   .onUnload <- function(libpath)   {     if (!reticulate::py_module_availa

Re: [Bioc-devel] Tensorflow support for bioconductor packages

Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=w2p-VnxwECq9u90RNv_B6yCOpXxDkcIPAjcgcpbEeBE=RS0haeXXw_GuGbzVJJuh_ZJ

Re: [Bioc-devel] Error during CHECK on Windows (tokay1)

the error and some days we won't. Since openPrimeR has not changed between release and devel, it's possible that we'll sometimes see this error in devel too. H. On 03/22/2018 11:02 AM, Hervé Pagès wrote: The build system captures the output of the 'R CMD check' command and displays it. If you look

Re: [Bioc-devel] Error during CHECK on Windows (tokay1)

e parallel execution would be a permanent fix that would ensure that all Bioconductor packages pass the checks smoothly on Windows. Maybe Martin could comment on this as well? Kind regards  Matthias On 03/22/2018 05:08 PM, Hervé Pagès wrote: Hi Matthias, Not sure what's causing this but I j

Re: [Bioc-devel] Error during CHECK on Windows (tokay1)

nPrimeR_tokay2-2Dchecksrc.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=HjFin7ZZwuYWdlO8wvE3KmoPwjRiq-bV_UKHWdKLLP4=SZhlV-e7h7S6Ndf9G2qUGp37kMZHgjDPmkvI7cCtGDA=zAWDhUHJG5jAGFu2WUc1K_uSBXN1daXMN5VVObIUjEk=). Should I just ignore this problem? Any pointers? Best  Matthias -- Hervé Pagès Program in

Re: [Bioc-devel] Update existing packages and change name

the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. -

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=p2zu7G8IjcYJfFGXTvJAlITWCwrBG0zBH72Htgm6go8=Rs9gi9iOQtOG4zUXSOO07D7t_smZ_h6OPyISr1DHf8c= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer R

Re: [Bioc-devel] No Windows binary for GenomicRanges

=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=NrBBRFv3CReEoWizyQHKlkyTU3dgJ1g0EEVfrBK3-Io=QlSpRQkMeHpZXcbywJfyWc5ehC8aLRdx5oHlJsyVGDA= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O

Re: [Bioc-devel] mcols Function Not Found for Windows Build

uuGL4PsURm-OztXlZm4Ux1RRClPhKwg= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206

Re: [Bioc-devel] Best practice on commit

=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_Es-Y9BxNNAd6d09znWColNeE9BpwvW9oXOWFQ5AYGA=ldTZV-PR3E4FQclCT1hSz7Y761vz8xv4Fc_1EPYxEvc= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E

Re: [Bioc-devel] as.list fails on IRanges inside of lapply(, blah)

ot working in release, that is a bug in the rentrez (which is on CRAN, not Bioc). I've submitted a PR to fix that, and we'll see what the response is as to whether I need to remove that integration or not. ~G On Tue, Feb 20, 2018 at 10:48 AM, Hervé Pagès <hpa...@fredhutch.org

Re: [Bioc-devel] as.list fails on IRanges inside of lapply(, blah)

3 BiocGenerics_0.25.3* loaded via a namespace (and not attached): [1] compiler_3.5.0 tools_3.5.0 Best, ~G -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA

Re: [Bioc-devel] as.list of a GRanges

=http-3A__www.germanstrias.org_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=u-uKbpvH_T_qRONe44P6puvfV2kgFjcrH7YBeLoAyOg=Jq9kJoc872fO0LkbqV1pjIvd522K7WQXmvwvgfOsNLw=> El 02/15/2018 a las 11:19 PM, Hervé Pagès escribió: On 02/15/2018 01:57 PM, Michael Lawre

Re: [Bioc-devel] as.list of a GRanges

5gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=yfkWiY-f8hZ6C9aR8HdZEQurWS_HnLMEGwRYr5dTJCo=U2fT0SvLZq-JipogjNgeAMproXB4yH_oBQgNjS8HWsA=>> El 02/17/2018 a las 04:19 AM, Hervé Pagès escribió: Hi Bernat, On 02/15/2018 11:57 PM, Bernat Gel wrote: Hi Hervé and ot

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