[Bioc-devel] core dump in MotifDb build
Paul Shannon
p@u|@thurmond@@h@nnon @end|ng |rom gm@||@com
Fri Mar 27 15:14:01 CET 2020
Thanks, Herve. Thanks, Martin.
In the devel version, I added a method to MotifDb for matching motif to sequence - a small, useful addition I thought.
The core dump (thanks for the analysis, Martin) seems to come in the call to motifmatchr::matchMotifs, which wraps the C++ MOODS library, and forms the core of my new method. See below.
MotifDb acquired other new dependencies as well, which needed to transform MotifDb native matrices into the form motifmatchr expects.
This capability -seemed- like a sensible addition to the package. But not so much any more. I will remove it, and whittle the dependencies down to a minimum.
Which leads to this broader question: should I eliminate every dependency I can?
For instance, two long-standing dependencies in MotifDb are seqlogo and MotIV. Neither are needed by the package. They appear only in the vignette to illustrate some the things that MotifDb enables. Is there an approved Bioc documentation style for describing these related uses without incurring the dependencies that comes with executable code? If so, I could use that approach to explain motifmatchr as well.
- Paul
setMethod('matchMotif', signature='MotifList',
function(object, motifs, genomeName, regions, pval.cutoff, fimoDataFrameStyle=FALSE){
motifs.pfmatrix <- lapply(motifs, function(motif) convert_motifs(motif, "TFBSTools-PFMatrix"))
motifs.pfmList <- do.call(PFMatrixList, motifs.pfmatrix)
gr.list <- motifmatchr::matchMotifs(motifs.pfmList, regions, genome=genomeName,
out="positions", p.cutoff=pval.cutoff)
result <- gr.list
if(fimoDataFrameStyle){
gr <- unlist(gr.list)
motif.names <- names(gr)
names(gr) <- NULL
tbl <- as.data.frame(gr)
tbl$motif_id <- motif.names
colnames(tbl)[1] <- "chrom"
tbl$chrom <- as.character(tbl$chrom)
colnames(tbl)[grep("score", colnames(tbl))] <- "mood.score"
new.order <- order(tbl$start, decreasing=FALSE)
tbl <- tbl[new.order,]
result <- tbl
}
return(result)
})
> On Mar 27, 2020, at 2:29 AM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>
> I was also able to reproduce this using the bioconductor/bioconductor_docker:devel image.
>
> 1. (first time) pull the docker image
>
> docker pull bioconductor/bioconductor_docker:devel
>
> 2. run the image (I want to work at the command line, but could have launched RStudio instead...)
>
> docker run -it bioconductor/bioconductor_docker:devel bash
>
> 3. In the docker image, clone MotifDb, since the segfault isn't available in the publicly available tarball (yeah it seems wrong to do things as root, but that's life in the docker world; one could have used docker run with --user rstudio...)
>
> # git clone --depth 1 https://git.bioconductor.org/packages/MotifDb
>
> 4. Update pre-installed packages
>
> # R -e "BiocManager::install(ask=FALSE)"
>
> 5. Install MotifDb dependencies, culled from the DESCRIPTION file (the image doesn't have the system command `less`, but it does have `cat` and `more`) and also MotIV, which as Hervé mentions is used in the vignette and should be in the Suggests: field
>
> # R -e "BiocManager::install(c('splitstackshape', 'TFBSTools', 'universalmotif', 'motifmatchr', 'MotIV'))"
>
> 6. Install MotifDb from the git clone
>
> # R CMD INSTALL MotifDb
>
> 7. Stangle the vignette
>
> # cd MotifDb/vignettes
> # R CMD Stangle MotifDb.Rnw
>
> 8. Crash!
>
> # R -f MotifDb.R
> ...
>> ###################################################
>> ### code chunk number 24: motifmatch
>> ###################################################
>> egr1.hits <- motifMatch (as.list (egr1.motif) [1], as.list (MotifDb), top=11)
>
> Ungapped Alignment
> Scores read
> Database read
> Motif matches : 11
> double free or corruption (out)
> Aborted
>
> 9. As an added bonus, run under gdb
>
> # R -d gdb
> ...
> (gdb) run
>> source("MotifDb.R", echo = TRUE)
> ...
> double free or corruption (out)
>
> Thread 1 "R" received signal SIGABRT, Aborted.
> 0x00007fbe727247bb in raise () from /lib/x86_64-linux-gnu/libc.so.6
> (gdb) where
> ...
> #5 0x00007fbe52e2cf8f in PlatformSupport::~PlatformSupport (
> this=0x5567b1ec11c0, __in_chrg=<optimized out>) at PlatformSupport.cpp:705
> #6 0x00007fbe52e2a7ea in motifMatch (CC=0x55678c162780, ALIGN=0x556782505850,
> top=<optimized out>, go=<optimized out>, ge=<optimized out>,
> inputPWM=0x5567ab3ff030, inputDB=0x5567b1310a70,
> inputScores=0x5567b305bcc0) at MotifMatch.cpp:123
> ...
>
> one could go further in debugging at the C level by editing /usr/local/lib/R/etc/Makeconf so that CXXFLAGS='-g -O0' (generate debugging symbols, don't optimize) before (re)installing MotIV.
>
> For what it's worth, a recent developer forum (see the 2020‑02‑20 entry for Robert Castelo, slides and video) talked about dependencies and the pros and cons of adding packages. There has been very fruitful work / discussion on the developer-forum slack channel culminating in the link https://community-bioc.slack.com/archives/CLUJWDQF4/p1584286306073500 ; see https://bioc-community.herokuapp.com/ to sign up). MotifDb in the current release has 41 dependencies
>
>> db = available.packages(repos=BiocManager::repositories())
>> deps = tools::package_dependencies("MotifDb", db, recursive=TRUE)
>> length(unique(unlist(deps)))
> [1] 41
>
> whereas in devel there are 142
>
>> dcf = read.dcf("DESCRIPTION", fields=c("Depends", "Imports", "Suggests"))
>> pkgs = sub(" .*", "", trimws(unlist(strsplit(dcf, ","))))
>> pkgs = setdiff(pkgs, "R")
>> deps1 = tools::package_dependencies(pkgs, db, recursive=TRUE)
>> length(unique(unlist(deps1)))
> [1] 142
>
> and I think it's worth asking whether the new features are worth the 3.5x increase in dependencies
>
> Martin
>
> On 3/26/20, 10:20 PM, "Bioc-devel on behalf of Hervé Pagès" <bioc-devel-bounces using r-project.org on behalf of hpages using fredhutch.org> wrote:
>
> Hi Paul,
>
> I can reproduce this on my laptop. See full output below (it's big!).
> Make sure to use a recent version of R devel (I updated mine 3 days
> ago). The error seems to occur in MotIV's C/C++ code (in
> /home/hpages/R/R-4.0.r78037/library/MotIV/libs/MotIV.so on my machine).
>
> 2 unrelated things:
> - Please add MotIV and seqLogo to your Suggests field (they're used in
> the vignette and/or the unit tests).
> - Make sure to remove vignettes/MotifDb.tex
>
> Best,
> H.
>
> ----------------------------------------------------------------------
>
> hpages using spectre:~/MotifDb/vignettes$ R-4.0 CMD Stangle MotifDb.Rnw
> Output file: MotifDb.R
>
> hpages using spectre:~/MotifDb/vignettes$ R-4.0
>
> R Under development (unstable) (2020-03-23 r78037) -- "Unsuffered
> Consequences"
> Copyright (C) 2020 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> source("MotifDb.R", echo=TRUE)
>
>> ### R code from vignette source
> '/home/hpages/git.bioconductor.org/software/MotifDb/vignettes/MotifDb.Rnw'
>>
>> #################################### .... [TRUNCATED]
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, sd, var, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, basename, cbind, colnames,
> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
> union, unique, unsplit, which, which.max, which.min
>
> Loading required package: S4Vectors
> Loading required package: stats4
>
> Attaching package: ‘S4Vectors’
>
> The following object is masked from ‘package:base’:
>
> expand.grid
>
> Loading required package: IRanges
> Loading required package: GenomicRanges
> Loading required package: GenomeInfoDb
> Loading required package: Biostrings
> Loading required package: XVector
>
> Attaching package: ‘Biostrings’
>
> The following object is masked from ‘package:base’:
>
> strsplit
>
>
> Registered S3 method overwritten by 'treeio':
> method from
> root.phylo ape
> See system.file("LICENSE", package="MotifDb") for use restrictions.
>
>> library (MotIV)
>
> Attaching package: ‘MotIV’
>
> The following object is masked from ‘package:stats’:
>
> filter
>
>
>> library (seqLogo)
> Loading required package: grid
>
> Attaching package: ‘seqLogo’
>
> The following object is masked from ‘package:MotIV’:
>
> makePWM
>
>
>> ###################################################
>> ### code chunk number 2: MotifDb.Rnw:71-90
>> ################################################# .... [TRUNCATED]
>
>> ###################################################
>> ### code chunk number 3: sources
>> ###################################################
>> lengt .... [TRUNCATED]
> [1] 10701
>
>> sort (table (values (MotifDb)$dataSource), decreasing=TRUE)
>
> jaspar2018 jaspar2016 HOCOMOCOv10
> 1564 1209 1066
> cisbp_1.02 jolma2013 SwissRegulon
> 874 843 684
> stamlab FlyFactorSurvey JASPAR_2014
> 683 614 592
> JASPAR_CORE hPDI UniPROBE
> 459 437 380
> HOMER HOCOMOCOv11-secondary-D ScerTF
> 332 290 196
> HOCOMOCOv11-core-A HOCOMOCOv11-core-C HOCOMOCOv11-core-B
> 181 135 84
> HOCOMOCOv11-secondary-A HOCOMOCOv11-secondary-B HOCOMOCOv11-secondary-C
> 46 19 13
>
>> ###################################################
>> ### code chunk number 4: organisms
>> ###################################################
>> sor .... [TRUNCATED]
>
>
> Hsapiens
>
> 5384
>
> Mmusculus
>
> 1411
>
> Dmelanogaster
>
> 1287
>
> Scerevisiae
>
> 1051
>
> Athaliana
>
> 803
>
> Celegans
>
> 90
>
> NA
>
> 40
>
> Rnorvegicus
>
> 35
>
> Pfalciparum
>
> 28
>
> Zmays
>
> 27
>
> Vertebrata
>
> 18
>
> Ncrassa
>
> 15
>
> Psativum
>
> 13
>
> Amajus
>
> 12
>
> Ddiscoideum
>
> 9
>
> Anidulans
>
> 8
>
> Ggallus
>
> 8
>
> Ppatens
>
> 7
>
> Xlaevis
>
> 7
>
> Mmusculus;Rnorvegicus;Hsapiens
>
> 6
>
> Osativa
>
> 5
>
> Hroretzi
>
> 4
>
> Hvulgare
>
> 4
>
> Ocuniculus
>
> 4
>
> Phybrida
>
> 4
>
> Rrattus
>
> 4
>
> Taestivam
>
> 4
>
> Drerio
>
> 3
>
> Gallus
>
> 3
>
> Mmusculus;Hsapiens
>
> 3
>
> Bdistachyon
>
> 2
>
> Cparvum
>
> 2
>
> Csativa
>
> 2
>
> Mmusculus;Rnorvegicus
>
> 2
> Mmusculus;Rnorvegicus;Xlaevis;Stropicalis;Ggallus;Hsapiens;Btaurus;Ocuniculus
>
>
> 2
>
> Nsp.
>
> 2
>
> Nsylvestris
>
> 2
>
> Otauri
>
> 2
>
> Acarolinensis
>
> 1
>
> Apisum
>
> 1
>
> Aterreus
>
> 1
>
> Gaculeatus
>
> 1
>
> Hcapsulatum
>
> 1
>
> Mdomestica
>
> 1
>
> Mgallopavo
>
> 1
>
> Mmurinus
>
> 1
>
> Mmusculus;Rnorvegicus;Hsapiens;Ocuniculus
>
> 1
>
> Mmusculus;Rnorvegicus;Omykiss;Ggallus;Hsapiens
>
> 1
>
> Mmusculus;Rrattus;Hsapiens;Ocuniculus
>
> 1
>
> Mtruncatula
>
> 1
>
> Ngruberi
>
> 1
>
> Nhaematococca
>
> 1
>
> Nvectensis
>
> 1
>
> Pcapensis
>
> 1
>
> Ppygmaeus
>
> 1
>
> Ptetraurelia
>
> 1
>
> Rnorvegicus;Hsapiens
>
> 1
>
> Tthermophila
>
> 1
>
> Vvinifera
>
> 1
>
> Xtropicalis
>
> 1
>
>> ###################################################
>> ### code chunk number 5: metadata
>> ###################################################
>> coln .... [TRUNCATED]
> [1] "providerName" "providerId" "dataSource" "geneSymbol"
>
> [5] "geneId" "geneIdType" "proteinId"
> "proteinIdType"
> [9] "organism" "sequenceCount" "bindingSequence"
> "bindingDomain"
> [13] "tfFamily" "experimentType" "pubmedID"
>
>> ###################################################
>> ### code chunk number 6: queryHuman
>> ###################################################
>> qu .... [TRUNCATED]
> MotifDb object of length 5399
> | Created from downloaded public sources: 2013-Aug-30
> | 5399 position frequency matrices from 18 sources:
> | cisbp_1.02: 313
> | HOCOMOCOv10: 640
> | HOCOMOCOv11-core-A: 181
> | HOCOMOCOv11-core-B: 84
> | HOCOMOCOv11-core-C: 135
> | HOCOMOCOv11-secondary-A: 46
> | HOCOMOCOv11-secondary-B: 19
> | HOCOMOCOv11-secondary-C: 13
> | HOCOMOCOv11-secondary-D: 290
> | hPDI: 437
> | JASPAR_2014: 117
> | JASPAR_CORE: 66
> | jaspar2016: 442
> | jaspar2018: 537
> | jolma2013: 710
> | stamlab: 683
> | SwissRegulon: 684
> | UniPROBE: 2
> | 8 organism/s
> | Hsapiens: 5384
> | Mmusculus;Rnorvegicus;Hsapiens: 6
> | Mmusculus;Hsapiens: 3
> |
> Mmusculus;Rnorvegicus;Xlaevis;Stropicalis;Ggallus;Hsapiens;Btaurus;Ocuniculus:
> 2
> | Mmusculus;Rnorvegicus;Hsapiens;Ocuniculus: 1
> | Mmusculus;Rnorvegicus;Omykiss;Ggallus;Hsapiens: 1
> | other: 2
> Hsapiens-cisbp_1.02-M1838_1.02
> Hsapiens-cisbp_1.02-M1857_1.02
> Hsapiens-cisbp_1.02-M1875_1.02
> Hsapiens-cisbp_1.02-M1880_1.02
> Hsapiens-cisbp_1.02-M1889_1.02
> ...
> Hsapiens-SwissRegulon-ZNF784.SwissRegulon
> Hsapiens-SwissRegulon-ZNF8.SwissRegulon
> Hsapiens-SwissRegulon-ZSCAN4.SwissRegulon
> Hsapiens-UniPROBE-Sox4.UP00401
> Hsapiens-UniPROBE-Oct_1.UP00399
>
>> ###################################################
>> ### code chunk number 7: querySox
>> ###################################################
>> quer .... [TRUNCATED]
> MotifDb object of length 196
> | Created from downloaded public sources: 2013-Aug-30
> | 196 position frequency matrices from 17 sources:
> | FlyFactorSurvey: 2
> | HOCOMOCOv10: 25
> | HOCOMOCOv11-core-A: 1
> | HOCOMOCOv11-core-B: 5
> | HOCOMOCOv11-core-C: 2
> | HOCOMOCOv11-secondary-A: 2
> | HOCOMOCOv11-secondary-B: 1
> | HOCOMOCOv11-secondary-D: 9
> | HOMER: 9
> | hPDI: 2
> | JASPAR_2014: 8
> | JASPAR_CORE: 5
> | jaspar2016: 16
> | jaspar2018: 19
> | jolma2013: 56
> | SwissRegulon: 19
> | UniPROBE: 15
> | 7 organism/s
> | Hsapiens: 115
> | Mmusculus: 67
> | Dmelanogaster: 2
> | Mmusculus;Rnorvegicus;Hsapiens: 1
> | Rnorvegicus: 1
> | Vertebrata: 1
> | other: 9
> Dmelanogaster-FlyFactorSurvey-Sox14_SANGER_10_FBgn0005612
> Dmelanogaster-FlyFactorSurvey-Sox15_SANGER_5_FBgn0005613
> Hsapiens-HOCOMOCOv10-SOX10_HUMAN.H10MO.D
> Hsapiens-HOCOMOCOv10-SOX11_HUMAN.H10MO.D
> Hsapiens-HOCOMOCOv10-SOX13_HUMAN.H10MO.D
> ...
> Mmusculus-UniPROBE-Sox30.UP00023
> Mmusculus-UniPROBE-Sox4.UP00062
> Mmusculus-UniPROBE-Sox5.UP00091
> Mmusculus-UniPROBE-Sox7.UP00034
> Mmusculus-UniPROBE-Sox8.UP00051
>
>> ###################################################
>> ### code chunk number 8: queryYeastHomeo
>> ################################################### .... [TRUNCATED]
> MotifDb object of length 32
> | Created from downloaded public sources: 2013-Aug-30
> | 32 position frequency matrices from 5 sources:
> | JASPAR_2014: 10
> | JASPAR_CORE: 10
> | jaspar2016: 4
> | jaspar2018: 4
> | UniPROBE: 4
> | 1 organism/s
> | Scerevisiae: 32
> Scerevisiae-JASPAR_CORE-CUP9-MA0288.1
> Scerevisiae-JASPAR_CORE-HMRA2-MA0318.1
> Scerevisiae-JASPAR_CORE-MATA1-MA0327.1
> Scerevisiae-JASPAR_CORE-MATALPHA2-MA0328.1
> Scerevisiae-JASPAR_CORE-PHO2-MA0356.1
> ...
> Scerevisiae-jaspar2018-TOS8-MA0408.1
> Scerevisiae-UniPROBE-Cup9.UP00308
> Scerevisiae-UniPROBE-Matalpha2.UP00307
> Scerevisiae-UniPROBE-Pho2.UP00268
> Scerevisiae-UniPROBE-Yox1.UP00274
>
>> ###################################################
>> ### code chunk number 9: homeoVariety
>> ###################################################
>> .... [TRUNCATED]
> [1] "Homeobox" "Hox9_act;Homeobox"
>
> [3] "LIM;Homeobox" "PAX;Homeobox"
>
> [5] "OAR;Homeobox" "Pou;Homeobox"
>
> [7] "Distant similarity to homeodomain" "Homeo"
>
> [9] "Homeo, PAX" "Homeo, POU"
>
>
>> unique (grep ('homeo', values(MotifDb)$tfFamily, ignore.case=T, v=T))
> [1] "HOX-related factors{3.1.1}: CDX (Caudal type homeobox){3.1.1.9}"
>
> [2] "HOX-related factors{3.1.1}: GBX (Gastrulation brain
> homeobox){3.1.1.11}"
> [3] "TALE-type homeo domain factors{3.1.4}: IRX (Iroquois){3.1.4.1}"
>
> [4] "TALE-type homeo domain factors{3.1.4}: MEIS{3.1.4.2}"
>
> [5] "Paired domain only{3.2.2}: PAX-1/9 (no homeo remnant){3.2.2.1}"
>
> [6] "Paired domain only{3.2.2}: PAX-2-like factors (partial
> homeobox){3.2.2.2}"
> [7] "Paired plus homeo domain{3.2.1}: PAX-3/7{3.2.1.1}"
>
> [8] "Paired plus homeo domain{3.2.1}: PAX-4/6{3.2.1.2}"
>
> [9] "TALE-type homeo domain factors{3.1.4}: PBX{3.1.4.4}"
>
> [10] "TALE-type homeo domain factors{3.1.4}: PKNOX{3.1.4.5}"
>
> [11] "TALE-type homeo domain factors{3.1.4}: TGIF{3.1.4.6}"
>
> [12] "Homeo"
>
> [13] "Homeo::Nuclear Factor I-CCAAT-binding"
>
> [14] "Homeodomain"
>
> [15] "Paired plus homeo domain"
>
> [16] "TALE-type homeo domain factors"
>
> [17] "homeodomain"
>
>
>> ###################################################
>> ### code chunk number 10: grepHuman
>> ###################################################
>> md .... [TRUNCATED]
>
>> mdb.sox <- MotifDb [grep ('sox', values (MotifDb)$geneSymbol,
> ignore.case=TRUE)]
>
>> yeast.indices = grepl ('scere', values (MotifDb)$organism,
> ignore.case=TRUE)
>
>> homeo.indices.domain = grepl ('homeo', values
> (MotifDb)$bindingDomain, ignore.case=TRUE)
>
>> homeo.indices.family = grepl ('homeo', values (MotifDb)$tfFamily,
> ignore.case=TRUE)
>
>> yeast.homeo.indices = yeast.indices & (homeo.indices.domain |
> homeo.indices.family)
>
>> yeast.homeoDb = MotifDb [yeast.homeo.indices]
>
>> ###################################################
>> ### code chunk number 11: withHomeo
>> ###################################################
>> ye .... [TRUNCATED]
>
>> ###################################################
>> ### code chunk number 12: subsetHuman
>> ###################################################
>> .... [TRUNCATED]
> MotifDb object of length 5384
> | Created from downloaded public sources: 2013-Aug-30
> | 5384 position frequency matrices from 18 sources:
> | cisbp_1.02: 313
> | HOCOMOCOv10: 640
> | HOCOMOCOv11-core-A: 181
> | HOCOMOCOv11-core-B: 84
> | HOCOMOCOv11-core-C: 135
> | HOCOMOCOv11-secondary-A: 46
> | HOCOMOCOv11-secondary-B: 19
> | HOCOMOCOv11-secondary-C: 13
> | HOCOMOCOv11-secondary-D: 290
> | hPDI: 437
> | JASPAR_2014: 117
> | JASPAR_CORE: 66
> | jaspar2016: 442
> | jaspar2018: 522
> | jolma2013: 710
> | stamlab: 683
> | SwissRegulon: 684
> | UniPROBE: 2
> | 1 organism/s
> | Hsapiens: 5384
> Hsapiens-cisbp_1.02-M1838_1.02
> Hsapiens-cisbp_1.02-M1857_1.02
> Hsapiens-cisbp_1.02-M1875_1.02
> Hsapiens-cisbp_1.02-M1880_1.02
> Hsapiens-cisbp_1.02-M1889_1.02
> ...
> Hsapiens-SwissRegulon-ZNF784.SwissRegulon
> Hsapiens-SwissRegulon-ZNF8.SwissRegulon
> Hsapiens-SwissRegulon-ZSCAN4.SwissRegulon
> Hsapiens-UniPROBE-Sox4.UP00401
> Hsapiens-UniPROBE-Oct_1.UP00399
>
>> ###################################################
>> ### code chunk number 13: subsetSox
>> ###################################################
>> if .... [TRUNCATED]
> MotifDb object of length 10
> | Created from downloaded public sources: 2013-Aug-30
> | 10 position frequency matrices from 8 sources:
> | HOCOMOCOv10: 2
> | HOCOMOCOv11-core-B: 1
> | HOMER: 1
> | jaspar2016: 1
> | jaspar2018: 1
> | jolma2013: 1
> | SwissRegulon: 1
> | UniPROBE: 2
> | 3 organism/s
> | Hsapiens: 7
> | Mmusculus: 2
> | other: 1
> Hsapiens-HOCOMOCOv10-SOX4_HUMAN.H10MO.C
> Mmusculus-HOCOMOCOv10-SOX4_MOUSE.H10MO.C
> Hsapiens-HOCOMOCOv11-core-B-SOX4_HUMAN.H11MO.0.B
> NA-HOMER-Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer
> Hsapiens-jaspar2016-SOX4-MA0867.1
> Hsapiens-jaspar2018-SOX4-MA0867.1
> Hsapiens-jolma2013-SOX4
> Hsapiens-SwissRegulon-SOX4.SwissRegulon
> Hsapiens-UniPROBE-Sox4.UP00401
> Mmusculus-UniPROBE-Sox4.UP00062
>
>> ###################################################
>> ### code chunk number 14: subsetYeastHomeo
>> ################################################# .... [TRUNCATED]
> MotifDb object of length 4
> | Created from downloaded public sources: 2013-Aug-30
> | 4 position frequency matrices from 1 source:
> | UniPROBE: 4
> | 1 organism/s
> | Scerevisiae: 4
> Scerevisiae-UniPROBE-Cup9.UP00308
> Scerevisiae-UniPROBE-Matalpha2.UP00307
> Scerevisiae-UniPROBE-Pho2.UP00268
> Scerevisiae-UniPROBE-Yox1.UP00274
>
>> ###################################################
>> ### code chunk number 15: findEgr1
>> ###################################################
>> # .... [TRUNCATED]
> $`Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.A`
> 1 2 3 4 5 6 7 8 9 10 11
> 12 13
> A 0.190 0.208 0.212 0.270 0.222 0.116 0.168 0.042 0.034 0.160 0.008
> 0.032 0.262
> C 0.192 0.206 0.144 0.140 0.074 0.082 0.484 0.042 0.008 0.006 0.000
> 0.038 0.452
> G 0.438 0.446 0.452 0.468 0.380 0.756 0.050 0.808 0.452 0.804 0.976
> 0.914 0.006
> T 0.180 0.140 0.192 0.122 0.324 0.046 0.298 0.108 0.506 0.030 0.016
> 0.016 0.280
> 14 15 16 17 18
> A 0.180 0.072 0.236 0.278 0.218
> C 0.012 0.012 0.092 0.098 0.184
> G 0.750 0.774 0.534 0.458 0.490
> T 0.058 0.142 0.138 0.166 0.108
>
> $`Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.S`
> 1 2 3 4 5 6
> A 0.1515633 0.04398516 0.05988341 0.003709592 0.009538951 0.07578166
> C 0.1886592 0.06041335 0.82829889 0.001059883 0.013248543 0.01907790
> G 0.3184950 0.88288288 0.01854796 0.993640700 0.490726020 0.90196078
> T 0.3412825 0.01271860 0.09326974 0.001589825 0.486486486 0.00317965
> 7 8 9 10 11
> A 0.025437202 0.01218866 0.089030207 0.021727610 0.09062003
> C 0.065712772 0.01006889 0.748277689 0.007419184 0.06518283
> G 0.900900901 0.97774245 0.007419184 0.955484897 0.60943296
> T 0.007949126 0.00000000 0.155272920 0.015368309 0.23476418
>
> $`Mmusculus-HOCOMOCOv10-EGR1_MOUSE.H10MO.A`
> 1 2 3 4 5 6
> A 0.1515633 0.04398516 0.05988341 0.003709592 0.009538951 0.07578166
> C 0.1886592 0.06041335 0.82829889 0.001059883 0.013248543 0.01907790
> G 0.3184950 0.88288288 0.01854796 0.993640700 0.490726020 0.90196078
> T 0.3412825 0.01271860 0.09326974 0.001589825 0.486486486 0.00317965
> 7 8 9 10 11
> A 0.025437202 0.01218866 0.089030207 0.021727610 0.09062003
> C 0.065712772 0.01006889 0.748277689 0.007419184 0.06518283
> G 0.900900901 0.97774245 0.007419184 0.955484897 0.60943296
> T 0.007949126 0.00000000 0.155272920 0.015368309 0.23476418
>
> $`Hsapiens-HOCOMOCOv11-core-A-EGR1_HUMAN.H11MO.0.A`
> 1 2 3 4 5 6 7 8 9 10 11
> 12 13
> A 0.232 0.320 0.278 0.236 0.112 0.236 0.056 0.032 0.092 0.016 0.024
> 0.220 0.088
> C 0.248 0.128 0.180 0.112 0.030 0.506 0.034 0.004 0.002 0.004 0.032
> 0.476 0.010
> G 0.410 0.318 0.460 0.354 0.808 0.046 0.870 0.410 0.892 0.958 0.930
> 0.004 0.842
> T 0.110 0.234 0.082 0.298 0.050 0.212 0.040 0.554 0.014 0.022 0.014
> 0.300 0.060
> 14 15 16 17
> A 0.110 0.338 0.312 0.264
> C 0.022 0.128 0.082 0.182
> G 0.696 0.406 0.456 0.436
> T 0.172 0.128 0.150 0.118
>
> $`NA-HOMER-Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer`
> 1 2 3 4 5 6 7 8 9 10
> A 0.128 0.078 0.154 0.001 0.001 0.027 0.001 0.001 0.153 0.034
> C 0.072 0.036 0.523 0.001 0.001 0.001 0.002 0.001 0.415 0.002
> G 0.142 0.882 0.023 0.997 0.282 0.971 0.973 0.997 0.010 0.940
> T 0.658 0.004 0.300 0.001 0.716 0.001 0.024 0.001 0.422 0.024
>
> $`Mmusculus-JASPAR_CORE-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-JASPAR_2014-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Mmusculus-jaspar2016-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-jaspar2016-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Mmusculus-jaspar2018-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-jaspar2018-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Hsapiens-jaspar2018-EGR1-MA0162.3`
> 1 2 3 4 5 6 7
> A 0.2722977 0.737507906 0.006723716 0.01834431 0 0.000000000 0.0000000
> C 0.2309510 0.249209361 0.987775061 0.00000000 1 0.992159228 0.9797136
> G 0.1139988 0.001897533 0.001833741 0.98165569 0 0.000000000 0.0000000
> T 0.3827525 0.011385199 0.003667482 0.00000000 0 0.007840772 0.0202864
> 8 9 10 11 12 13
> A 0.795439739 0.0000000000 0.0000000000 0.00000000 0.86166008 0.29390244
> C 0.200000000 0.9993943065 0.0000000000 0.99220156 0.01317523 0.27926829
> G 0.004560261 0.0000000000 0.9990732159 0.00000000 0.10540184 0.06341463
> T 0.000000000 0.0006056935 0.0009267841 0.00779844 0.01976285 0.36341463
> 14
> A 0.3035714
> C 0.1255952
> G 0.1077381
> T 0.4630952
>
> $`Hsapiens-jolma2013-EGR1`
> 1 2 3 4 5 6
> A 0.2494781 0.51390568 0.003223727 0.105202754 0.000000000 0.002604167
> C 0.2411273 0.39540508 0.969696970 0.005355777 0.980025773 0.992838542
> G 0.1539666 0.03627570 0.007736944 0.854246366 0.007731959 0.000000000
> T 0.3554280 0.05441354 0.019342360 0.035195103 0.012242268 0.004557292
> 7 8 9 10 11 12
> 13
> A 0.000000000 0.652638191 0.003253090 0.01906158 0.010000 0.68089431
> 0.2790573
> C 0.928214732 0.343592965 0.995445673 0.01136364 0.938125 0.06910569
> 0.2485270
> G 0.009363296 0.000000000 0.000000000 0.93181818 0.011875 0.14227642
> 0.1253348
> T 0.062421973 0.003768844 0.001301236 0.03775660 0.040000 0.10772358
> 0.3470809
> 14
> A 0.2673936
> C 0.1905504
> G 0.1396677
> T 0.4023884
>
> $`Hsapiens-jolma2013-EGR1-2`
> 1 2 3 4 5 6 7
> A 0.2722977 0.737507906 0.006723716 0.01834431 0 0.000000000 0.0000000
> C 0.2309510 0.249209361 0.987775061 0.00000000 1 0.992159228 0.9797136
> G 0.1139988 0.001897533 0.001833741 0.98165569 0 0.000000000 0.0000000
> T 0.3827525 0.011385199 0.003667482 0.00000000 0 0.007840772 0.0202864
> 8 9 10 11 12 13
> A 0.795439739 0.0000000000 0.0000000000 0.00000000 0.86166008 0.29390244
> C 0.200000000 0.9993943065 0.0000000000 0.99220156 0.01317523 0.27926829
> G 0.004560261 0.0000000000 0.9990732159 0.00000000 0.10540184 0.06341463
> T 0.000000000 0.0006056935 0.0009267841 0.00779844 0.01976285 0.36341463
> 14
> A 0.3035714
> C 0.1255952
> G 0.1077381
> T 0.4630952
>
> $`Mmusculus-jolma2013-Egr1`
> 1 2 3 4 5 6
> A 0.3231418 0.32278481 0.618181818 0.0000000000 0.075444498 0.0000000000
> C 0.3241961 0.30907173 0.366753247 0.9968454259 0.004324844 0.9994728519
> G 0.1133368 0.03691983 0.003636364 0.0005257624 0.911100432 0.0005271481
> T 0.2393253 0.33122363 0.011428571 0.0026288118 0.009130226 0.0000000000
> 7 8 9 10 11 12 13
> A 0.001578117 0 0.517114271 0.003149606 0.00422833 0.001579779 0.89181562
> C 0.997369805 1 0.481305951 0.995275591 0.16732105 0.998420221 0.05738476
> G 0.001052078 0 0.001579779 0.000000000 0.25581395 0.000000000 0.03621825
> T 0.000000000 0 0.000000000 0.001574803 0.57263667 0.000000000 0.01458137
> 14 15 16
> A 0.44251055 0.31170886 0.26213080
> C 0.32278481 0.19778481 0.31012658
> G 0.04957806 0.04272152 0.09651899
> T 0.18512658 0.44778481 0.33122363
>
> $`Hsapiens-SwissRegulon-EGR1.SwissRegulon`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Mmusculus-UniPROBE-Egr1.UP00007`
> 1 2 3 4 5 6
> A 0.2115466 0.14198757 0.03260499 0.11512588 0.003516173 0.004715059
> C 0.2827083 0.72243721 0.87717185 0.07060553 0.990021152 0.982482238
> G 0.2034722 0.05485440 0.01243161 0.78128969 0.002264928 0.009896878
> T 0.3022730 0.08072082 0.07779155 0.03297890 0.004197748 0.002905824
> 7 8 9 10 11 12
> A 0.001626612 0.262351637 0.005889514 0.02289301 0.02303758 0.56763334
> C 0.975937323 0.731731673 0.985755764 0.09046006 0.85994854 0.05739392
> G 0.001661635 0.002729558 0.002081402 0.64932246 0.03791264 0.16679165
> T 0.020774430 0.003187133 0.006273319 0.23732447 0.07910124 0.20818108
> 13 14
> A 0.1765973 0.1830489
> C 0.3312648 0.1837744
> G 0.1253083 0.2267928
> T 0.3668295 0.4063840
>
>
>> # grep returns indices which allow for more flexibility
>> indices = grep ('egr1', values (MotifDb)$geneSymbol, ignore.case=TRUE)
>
>> length (indices)
> [1] 17
>
>> ###################################################
>> ### code chunk number 16: MotifDbViews
>> ###################################################
>> .... [TRUNCATED]
> MotifDb object of length 17
> | Created from downloaded public sources: 2013-Aug-30
> | 17 position frequency matrices from 10 sources:
> | HOCOMOCOv10: 3
> | HOCOMOCOv11-core-A: 1
> | HOMER: 1
> | JASPAR_2014: 1
> | JASPAR_CORE: 1
> | jaspar2016: 2
> | jaspar2018: 3
> | jolma2013: 3
> | SwissRegulon: 1
> | UniPROBE: 1
> | 3 organism/s
> | Hsapiens: 10
> | Mmusculus: 6
> | other: 1
> Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.A
> Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.S
> Mmusculus-HOCOMOCOv10-EGR1_MOUSE.H10MO.A
> Hsapiens-HOCOMOCOv11-core-A-EGR1_HUMAN.H11MO.0.A
> NA-HOMER-Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer
> ...
> Hsapiens-jolma2013-EGR1
> Hsapiens-jolma2013-EGR1-2
> Mmusculus-jolma2013-Egr1
> Hsapiens-SwissRegulon-EGR1.SwissRegulon
> Mmusculus-UniPROBE-Egr1.UP00007
>
>> ###################################################
>> ### code chunk number 17: as.list
>> ###################################################
>> as.l .... [TRUNCATED]
> $`Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.A`
> 1 2 3 4 5 6 7 8 9 10 11
> 12 13
> A 0.190 0.208 0.212 0.270 0.222 0.116 0.168 0.042 0.034 0.160 0.008
> 0.032 0.262
> C 0.192 0.206 0.144 0.140 0.074 0.082 0.484 0.042 0.008 0.006 0.000
> 0.038 0.452
> G 0.438 0.446 0.452 0.468 0.380 0.756 0.050 0.808 0.452 0.804 0.976
> 0.914 0.006
> T 0.180 0.140 0.192 0.122 0.324 0.046 0.298 0.108 0.506 0.030 0.016
> 0.016 0.280
> 14 15 16 17 18
> A 0.180 0.072 0.236 0.278 0.218
> C 0.012 0.012 0.092 0.098 0.184
> G 0.750 0.774 0.534 0.458 0.490
> T 0.058 0.142 0.138 0.166 0.108
>
> $`Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.S`
> 1 2 3 4 5 6
> A 0.1515633 0.04398516 0.05988341 0.003709592 0.009538951 0.07578166
> C 0.1886592 0.06041335 0.82829889 0.001059883 0.013248543 0.01907790
> G 0.3184950 0.88288288 0.01854796 0.993640700 0.490726020 0.90196078
> T 0.3412825 0.01271860 0.09326974 0.001589825 0.486486486 0.00317965
> 7 8 9 10 11
> A 0.025437202 0.01218866 0.089030207 0.021727610 0.09062003
> C 0.065712772 0.01006889 0.748277689 0.007419184 0.06518283
> G 0.900900901 0.97774245 0.007419184 0.955484897 0.60943296
> T 0.007949126 0.00000000 0.155272920 0.015368309 0.23476418
>
> $`Mmusculus-HOCOMOCOv10-EGR1_MOUSE.H10MO.A`
> 1 2 3 4 5 6
> A 0.1515633 0.04398516 0.05988341 0.003709592 0.009538951 0.07578166
> C 0.1886592 0.06041335 0.82829889 0.001059883 0.013248543 0.01907790
> G 0.3184950 0.88288288 0.01854796 0.993640700 0.490726020 0.90196078
> T 0.3412825 0.01271860 0.09326974 0.001589825 0.486486486 0.00317965
> 7 8 9 10 11
> A 0.025437202 0.01218866 0.089030207 0.021727610 0.09062003
> C 0.065712772 0.01006889 0.748277689 0.007419184 0.06518283
> G 0.900900901 0.97774245 0.007419184 0.955484897 0.60943296
> T 0.007949126 0.00000000 0.155272920 0.015368309 0.23476418
>
> $`Hsapiens-HOCOMOCOv11-core-A-EGR1_HUMAN.H11MO.0.A`
> 1 2 3 4 5 6 7 8 9 10 11
> 12 13
> A 0.232 0.320 0.278 0.236 0.112 0.236 0.056 0.032 0.092 0.016 0.024
> 0.220 0.088
> C 0.248 0.128 0.180 0.112 0.030 0.506 0.034 0.004 0.002 0.004 0.032
> 0.476 0.010
> G 0.410 0.318 0.460 0.354 0.808 0.046 0.870 0.410 0.892 0.958 0.930
> 0.004 0.842
> T 0.110 0.234 0.082 0.298 0.050 0.212 0.040 0.554 0.014 0.022 0.014
> 0.300 0.060
> 14 15 16 17
> A 0.110 0.338 0.312 0.264
> C 0.022 0.128 0.082 0.182
> G 0.696 0.406 0.456 0.436
> T 0.172 0.128 0.150 0.118
>
> $`NA-HOMER-Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer`
> 1 2 3 4 5 6 7 8 9 10
> A 0.128 0.078 0.154 0.001 0.001 0.027 0.001 0.001 0.153 0.034
> C 0.072 0.036 0.523 0.001 0.001 0.001 0.002 0.001 0.415 0.002
> G 0.142 0.882 0.023 0.997 0.282 0.971 0.973 0.997 0.010 0.940
> T 0.658 0.004 0.300 0.001 0.716 0.001 0.024 0.001 0.422 0.024
>
> $`Mmusculus-JASPAR_CORE-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-JASPAR_2014-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Mmusculus-jaspar2016-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-jaspar2016-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Mmusculus-jaspar2018-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Hsapiens-jaspar2018-EGR1-MA0162.2`
> 1 2 3 4 5 6 7
> 8
> A 0.08958877 0.1228786 0.09464752 0.10892624 0.01901110 0.2375163 0
> 0.00000000
> C 0.46736292 0.5586651 0.49355418 0.85109334 0.94435379 0.0000000 1
> 0.96703655
> G 0.25155026 0.1108845 0.18358355 0.00000000 0.00000000 0.5580940 0
> 0.00000000
> T 0.19149804 0.2075718 0.22821475 0.03998042 0.03663512 0.2043897 0
> 0.03296345
> 9 10 11 12 13 14
> A 0.00000000 0.29797650 0.00000000 0.1932115 0.00000000 0.2468995
> C 0.82849217 0.68219648 0.97519582 0.0000000 0.80360640 0.4565111
> G 0.04985313 0.00000000 0.00000000 0.5384302 0.11586162 0.1560868
> T 0.12165470 0.01982702 0.02480418 0.2683584 0.08053198 0.1405026
>
> $`Hsapiens-jaspar2018-EGR1-MA0162.3`
> 1 2 3 4 5 6 7
> A 0.2722977 0.737507906 0.006723716 0.01834431 0 0.000000000 0.0000000
> C 0.2309510 0.249209361 0.987775061 0.00000000 1 0.992159228 0.9797136
> G 0.1139988 0.001897533 0.001833741 0.98165569 0 0.000000000 0.0000000
> T 0.3827525 0.011385199 0.003667482 0.00000000 0 0.007840772 0.0202864
> 8 9 10 11 12 13
> A 0.795439739 0.0000000000 0.0000000000 0.00000000 0.86166008 0.29390244
> C 0.200000000 0.9993943065 0.0000000000 0.99220156 0.01317523 0.27926829
> G 0.004560261 0.0000000000 0.9990732159 0.00000000 0.10540184 0.06341463
> T 0.000000000 0.0006056935 0.0009267841 0.00779844 0.01976285 0.36341463
> 14
> A 0.3035714
> C 0.1255952
> G 0.1077381
> T 0.4630952
>
> $`Hsapiens-jolma2013-EGR1`
> 1 2 3 4 5 6
> A 0.2494781 0.51390568 0.003223727 0.105202754 0.000000000 0.002604167
> C 0.2411273 0.39540508 0.969696970 0.005355777 0.980025773 0.992838542
> G 0.1539666 0.03627570 0.007736944 0.854246366 0.007731959 0.000000000
> T 0.3554280 0.05441354 0.019342360 0.035195103 0.012242268 0.004557292
> 7 8 9 10 11 12
> 13
> A 0.000000000 0.652638191 0.003253090 0.01906158 0.010000 0.68089431
> 0.2790573
> C 0.928214732 0.343592965 0.995445673 0.01136364 0.938125 0.06910569
> 0.2485270
> G 0.009363296 0.000000000 0.000000000 0.93181818 0.011875 0.14227642
> 0.1253348
> T 0.062421973 0.003768844 0.001301236 0.03775660 0.040000 0.10772358
> 0.3470809
> 14
> A 0.2673936
> C 0.1905504
> G 0.1396677
> T 0.4023884
>
> $`Hsapiens-jolma2013-EGR1-2`
> 1 2 3 4 5 6 7
> A 0.2722977 0.737507906 0.006723716 0.01834431 0 0.000000000 0.0000000
> C 0.2309510 0.249209361 0.987775061 0.00000000 1 0.992159228 0.9797136
> G 0.1139988 0.001897533 0.001833741 0.98165569 0 0.000000000 0.0000000
> T 0.3827525 0.011385199 0.003667482 0.00000000 0 0.007840772 0.0202864
> 8 9 10 11 12 13
> A 0.795439739 0.0000000000 0.0000000000 0.00000000 0.86166008 0.29390244
> C 0.200000000 0.9993943065 0.0000000000 0.99220156 0.01317523 0.27926829
> G 0.004560261 0.0000000000 0.9990732159 0.00000000 0.10540184 0.06341463
> T 0.000000000 0.0006056935 0.0009267841 0.00779844 0.01976285 0.36341463
> 14
> A 0.3035714
> C 0.1255952
> G 0.1077381
> T 0.4630952
>
> $`Mmusculus-jolma2013-Egr1`
> 1 2 3 4 5 6
> A 0.3231418 0.32278481 0.618181818 0.0000000000 0.075444498 0.0000000000
> C 0.3241961 0.30907173 0.366753247 0.9968454259 0.004324844 0.9994728519
> G 0.1133368 0.03691983 0.003636364 0.0005257624 0.911100432 0.0005271481
> T 0.2393253 0.33122363 0.011428571 0.0026288118 0.009130226 0.0000000000
> 7 8 9 10 11 12 13
> A 0.001578117 0 0.517114271 0.003149606 0.00422833 0.001579779 0.89181562
> C 0.997369805 1 0.481305951 0.995275591 0.16732105 0.998420221 0.05738476
> G 0.001052078 0 0.001579779 0.000000000 0.25581395 0.000000000 0.03621825
> T 0.000000000 0 0.000000000 0.001574803 0.57263667 0.000000000 0.01458137
> 14 15 16
> A 0.44251055 0.31170886 0.26213080
> C 0.32278481 0.19778481 0.31012658
> G 0.04957806 0.04272152 0.09651899
> T 0.18512658 0.44778481 0.33122363
>
> $`Hsapiens-SwissRegulon-EGR1.SwissRegulon`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
> $`Mmusculus-UniPROBE-Egr1.UP00007`
> 1 2 3 4 5 6
> A 0.2115466 0.14198757 0.03260499 0.11512588 0.003516173 0.004715059
> C 0.2827083 0.72243721 0.87717185 0.07060553 0.990021152 0.982482238
> G 0.2034722 0.05485440 0.01243161 0.78128969 0.002264928 0.009896878
> T 0.3022730 0.08072082 0.07779155 0.03297890 0.004197748 0.002905824
> 7 8 9 10 11 12
> A 0.001626612 0.262351637 0.005889514 0.02289301 0.02303758 0.56763334
> C 0.975937323 0.731731673 0.985755764 0.09046006 0.85994854 0.05739392
> G 0.001661635 0.002729558 0.002081402 0.64932246 0.03791264 0.16679165
> T 0.020774430 0.003187133 0.006273319 0.23732447 0.07910124 0.20818108
> 13 14
> A 0.1765973 0.1830489
> C 0.3312648 0.1837744
> G 0.1253083 0.2267928
> T 0.3668295 0.4063840
>
>
>> ###################################################
>> ### code chunk number 18: as.metadata
>> ###################################################
>> .... [TRUNCATED]
> Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.A
> providerName EGR1_HUMAN.H10MO.A
> providerId EGR1_HUMAN.H10MO.A
> dataSource HOCOMOCOv10
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 500
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily <NA>
> experimentType low- and high-throughput methods
> pubmedID 26586801
> Hsapiens-HOCOMOCOv10-EGR1_HUMAN.H10MO.S
> providerName EGR1_HUMAN.H10MO.S
> providerId EGR1_HUMAN.H10MO.S
> dataSource HOCOMOCOv10
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 1887
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily <NA>
> experimentType low- and high-throughput methods
> pubmedID 26586801
> Mmusculus-HOCOMOCOv10-EGR1_MOUSE.H10MO.A
> providerName EGR1_MOUSE.H10MO.A
> providerId EGR1_MOUSE.H10MO.A
> dataSource HOCOMOCOv10
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount 1887
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily <NA>
> experimentType low- and high-throughput methods
> pubmedID 26586801
> Hsapiens-HOCOMOCOv11-core-A-EGR1_HUMAN.H11MO.0.A
>
> providerName EGR1_HUMAN.H11MO.0.A
>
> providerId EGR1_HUMAN.H11MO.0.A
>
> dataSource HOCOMOCOv11-core-A
>
> geneSymbol EGR1
>
> geneId 1958
>
> geneIdType ENTREZ
>
> proteinId EGR1_HUMAN
>
> proteinIdType UNIPROT
>
> organism Hsapiens
>
> sequenceCount 500
>
> bindingSequence <NA>
>
> bindingDomain <NA>
>
> tfFamily Three-zinc finger Krüppel-related factors{2.3.1}: EGR
> factors{2.3.1.3}
> experimentType ChIP-Seq
>
> pubmedID 23175603
>
> NA-HOMER-Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer
> providerName Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer
> providerId Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer
> dataSource HOMER
> geneSymbol Egr1
> geneId <NA>
> geneIdType <NA>
> proteinId ?query=Egr1(Zf)_K562-Egr1-ChIP-Seq(GSE32465)
> proteinIdType UNIPROT
> organism <NA>
> sequenceCount 1
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily <NA>
> experimentType low- and high-throughput methods
> pubmedID 26586801
> Mmusculus-JASPAR_CORE-Egr1-MA0162.1
> providerName Egr1
> providerId MA0162.1
> dataSource JASPAR_CORE
> geneSymbol Egr1
> geneId 13653
> geneIdType ENTREZ
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount 15
> bindingSequence <NA>
> bindingDomain Zinc-coordinating
> tfFamily BetaBetaAlpha-zinc finger
> experimentType bacterial 1-hybrid
> pubmedID 16041365
> Hsapiens-JASPAR_2014-EGR1-MA0162.2
> providerName EGR1
> providerId MA0162.2
> dataSource JASPAR_2014
> geneSymbol EGR1
> geneId 1958
> geneIdType ENTREZ
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 12256
> bindingSequence <NA>
> bindingDomain Zinc-coordinating
> tfFamily BetaBetaAlpha-zinc finger
> experimentType ChIP-seq
> pubmedID 16041365
> Mmusculus-jaspar2016-Egr1-MA0162.1
> providerName MA0162.1
> providerId MA0162.1
> dataSource jaspar2016
> geneSymbol Egr1
> geneId <NA>
> geneIdType <NA>
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount 15
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily BetaBetaAlpha-zinc finger
> experimentType bacterial 1-hybrid
> pubmedID 24194598
> Hsapiens-jaspar2016-EGR1-MA0162.2
> providerName MA0162.2
> providerId MA0162.2
> dataSource jaspar2016
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 12256
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily Three-zinc finger Krüppel-related factors
> experimentType ChIP-seq
> pubmedID 24194598
> Mmusculus-jaspar2018-Egr1-MA0162.1
> providerName MA0162.1
> providerId MA0162.1
> dataSource jaspar2018
> geneSymbol Egr1
> geneId <NA>
> geneIdType <NA>
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount 15
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily Three-zinc finger Kruppel-related factors
> experimentType bacterial 1-hybrid
> pubmedID 16041365
> Hsapiens-jaspar2018-EGR1-MA0162.2
> providerName MA0162.2
> providerId MA0162.2
> dataSource jaspar2018
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 12256
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily Three-zinc finger Kruppel-related factors
> experimentType ChIP-seq
> pubmedID 16041365
> Hsapiens-jaspar2018-EGR1-MA0162.3
> providerName MA0162.3
> providerId MA0162.3
> dataSource jaspar2018
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId P18146
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 2158
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily Three-zinc finger Kruppel-related factors
> experimentType HT-SELEX
> pubmedID 16041365
> Hsapiens-jolma2013-EGR1 Hsapiens-jolma2013-EGR1-2
> providerName Hsapiens-jolma2013-EGR1 Hsapiens-jolma2013-EGR1-2
> providerId EGR1 EGR1
> dataSource jolma2013 jolma2013
> geneSymbol EGR1 EGR1
> geneId 1958 1958
> geneIdType ENTREZ ENTREZ
> proteinId <NA> <NA>
> proteinIdType <NA> <NA>
> organism Hsapiens Hsapiens
> sequenceCount 1831 1703
> bindingSequence NMCGCCCMCGCANN NACGCCCACGCANN
> bindingDomain <NA> <NA>
> tfFamily C2H2 C2H2
> experimentType SELEX SELEX
> pubmedID 23332764 23332764
> Mmusculus-jolma2013-Egr1
> providerName Mmusculus-jolma2013-Egr1
> providerId Egr1
> dataSource jolma2013
> geneSymbol Egr1
> geneId 1958
> geneIdType ENTREZ
> proteinId <NA>
> proteinIdType <NA>
> organism Mmusculus
> sequenceCount 2013
> bindingSequence NNMCGCCCMCTCANNN
> bindingDomain <NA>
> tfFamily C2H2
> experimentType SELEX
> pubmedID 23332764
> Hsapiens-SwissRegulon-EGR1.SwissRegulon
> providerName EGR1.SwissRegulon
> providerId EGR1.SwissRegulon
> dataSource SwissRegulon
> geneSymbol EGR1
> geneId <NA>
> geneIdType <NA>
> proteinId <NA>
> proteinIdType UNIPROT
> organism Hsapiens
> sequenceCount 15
> bindingSequence <NA>
> bindingDomain <NA>
> tfFamily <NA>
> experimentType low- and high-throughput methods
> pubmedID 19377474
> Mmusculus-UniPROBE-Egr1.UP00007
> providerName SCI09/Egr1_pwm_primary.txt
> providerId UP00007
> dataSource UniPROBE
> geneSymbol Egr1
> geneId 13653
> geneIdType ENTREZ
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount <NA>
> bindingSequence <NA>
> bindingDomain ZnF_C2H2
> tfFamily <NA>
> experimentType protein binding microarray
> pubmedID 19443739
>
>> ###################################################
>> ### code chunk number 19: egr1-multi-grep
>> ################################################## .... [TRUNCATED]
>
>> organism.rows = grep ('Mmusculus', values (MotifDb)$organism,
> ignore.case=TRUE)
>
>> source.rows = grep ('JASPAR', values (MotifDb)$dataSource,
> ignore.case=TRUE)
>
>> egr1.mouse.jaspar.rows = intersect (geneSymbol.rows,
> + intersect (organism.rows, source.rows))
>
>> print (egr1.mouse.jaspar.rows)
> [1] 4246 5400 6521
>
>> egr1.motif <- MotifDb [egr1.mouse.jaspar.rows]
>
>> ###################################################
>> ### code chunk number 20: MotifDbViews
>> ###################################################
>> .... [TRUNCATED]
>
>> ###################################################
>> ### code chunk number 22: examine-egr1
>> ###################################################
>> .... [TRUNCATED]
> MotifDb object of length 1
> | Created from downloaded public sources: 2013-Aug-30
> | 1 position frequency matrices from 1 source:
> | JASPAR_CORE: 1
> | 1 organism/s
> | Mmusculus: 1
> Mmusculus-JASPAR_CORE-Egr1-MA0162.1
>
>> as.list (egr1.motif)
> $`Mmusculus-JASPAR_CORE-Egr1-MA0162.1`
> 1 2 3 4 5 6 7 8 9 10
> A 0.20000000 0.13333333 0.0000000 0 0.0 0.2 0.06666667 0 0.1333333 0
> C 0.26666667 0.06666667 0.8666667 0 0.0 0.0 0.00000000 0 0.6666667 0
> G 0.06666667 0.80000000 0.0000000 1 0.2 0.8 0.93333333 1 0.0000000 1
> T 0.46666667 0.00000000 0.1333333 0 0.8 0.0 0.00000000 0 0.2000000 0
> 11
> A 0.06666667
> C 0.00000000
> G 0.46666667
> T 0.46666667
>
>
>> noquote (t (as.data.frame (values (egr1.motif))))
> Mmusculus-JASPAR_CORE-Egr1-MA0162.1
> providerName Egr1
> providerId MA0162.1
> dataSource JASPAR_CORE
> geneSymbol Egr1
> geneId 13653
> geneIdType ENTREZ
> proteinId P08046
> proteinIdType UNIPROT
> organism Mmusculus
> sequenceCount 15
> bindingSequence <NA>
> bindingDomain Zinc-coordinating
> tfFamily BetaBetaAlpha-zinc finger
> experimentType bacterial 1-hybrid
> pubmedID 16041365
>
>> ###################################################
>> ### code chunk number 23: egr1
>> ###################################################
>> seqLogo .... [TRUNCATED]
>
>> ###################################################
>> ### code chunk number 24: motifmatch
>> ###################################################
>> e .... [TRUNCATED]
>
> Ungapped Alignment
> Scores read
> Database read
> Motif matches : 11
> *** Error in `/home/hpages/R/R-4.0.r78037/bin/exec/R': double free or
> corruption (out): 0x00000000437ffa80 ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f8738f287e5]
> /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f8738f3137a]
> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f8738f3553c]
> /home/hpages/R/R-4.0.r78037/library/MotIV/libs/MotIV.so(_ZN15PlatformSupportD1Ev+0x8c)[0x7f871cc28c2c]
> /home/hpages/R/R-4.0.r78037/library/MotIV/libs/MotIV.so(_Z10motifMatchP7SEXPRECS0_S0_S0_S0_S0_S0_S0_+0x31e)[0x7f871cc2623e]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0xfc9d2)[0x7f87395949d2]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0xfceed)[0x7f8739594eed]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x134601)[0x7f87395cc601]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f87395dbfd0]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f87395ddd91]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f87395deb34]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x2ce)[0x7f87395dc0fe]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1490e9)[0x7f87395e10e9]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x53d)[0x7f87395dc36d]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x14a8e3)[0x7f87395e28e3]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x134601)[0x7f87395cc601]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f87395dbfd0]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f87395ddd91]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f87395deb34]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f87395d64f7]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f87395dbfd0]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1449c9)[0x7f87395dc9c9]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x818)[0x7f87395dc648]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x14abec)[0x7f87395e2bec]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x18682f)[0x7f873961e82f]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x136175)[0x7f87395ce175]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f87395dbfd0]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f87395ddd91]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f87395deb34]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13e4f7)[0x7f87395d64f7]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f87395dbfd0]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f87395ddd91]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f87395deb34]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x2ce)[0x7f87395dc0fe]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_ReplIteration+0x242)[0x7f873960f662]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1779f1)[0x7f873960f9f1]
> /home/hpages/R/R-4.0.r78037/lib/libR.so(run_Rmainloop+0x48)[0x7f873960faa8]
> /home/hpages/R/R-4.0.r78037/bin/exec/R(main+0x1b)[0x4007cb]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f8738ed1830]
> /home/hpages/R/R-4.0.r78037/bin/exec/R(_start+0x29)[0x400809]
> ======= Memory map: ========
> 00400000-00401000 r-xp 00000000 00:33 23419198
> /home/hpages/R/R-4.0.r78037/bin/exec/R
> 00600000-00601000 r--p 00000000 00:33 23419198
> /home/hpages/R/R-4.0.r78037/bin/exec/R
> 00601000-00602000 rw-p 00001000 00:33 23419198
> /home/hpages/R/R-4.0.r78037/bin/exec/R
> 01334000-49409000 rw-p 00000000 00:00 0
> [heap]
> 7f8710000000-7f8710021000 rw-p 00000000 00:00 0
> 7f8710021000-7f8714000000 ---p 00000000 00:00 0
> 7f871709e000-7f871709f000 rw-p 00000000 00:00 0
> 7f871709f000-7f87170c0000 r--p 00000000 103:02 9972832
> /usr/share/texmf/fonts/opentype/public/tex-gyre/texgyreheros-regular.otf
> 7f87170c0000-7f87170c7000 r--s 00000000 103:02 29494673
> /var/cache/fontconfig/4be9850f182b35c1350b6bbf2e42601c-le64.cache-6
> 7f87170c7000-7f87170c9000 r--s 00000000 103:02 29495045
> /var/cache/fontconfig/30a99c4256905863f7aa12b5e873c27c-le64.cache-6
> 7f87170c9000-7f87170ca000 r--s 00000000 103:02 29495044
> /var/cache/fontconfig/087e1975ba9a574b140bb1df193bf770-le64.cache-6
> 7f87170ca000-7f87170ce000 r--s 00000000 103:02 29494827
> /var/cache/fontconfig/6aa41aa22e18b8fa06a12da28ea9c28b-le64.cache-6
> 7f87170ce000-7f87170d9000 r--s 00000000 103:02 29491544
> /var/cache/fontconfig/945677eb7aeaf62f1d50efc3fb3ec7d8-le64.cache-6
> 7f87170d9000-7f87170db000 r--s 00000000 103:02 29494713
> /var/cache/fontconfig/99e8ed0e538f840c565b6ed5dad60d56-le64.cache-6
> 7f87170db000-7f87170e1000 r--s 00000000 103:02 29491526
> /var/cache/fontconfig/2cd17615ca594fa2959ae173292e504c-le64.cache-6
> 7f87170e1000-7f87170f6000 r--s 00000000 103:02 29491520
> /var/cache/fontconfig/04aabc0a78ac019cf9454389977116d2-le64.cache-6
> 7f87170f6000-7f8717131000 r--s 00000000 103:02 29491555
> /var/cache/fontconfig/365b55f210c0a22e9a19e35191240f32-le64.cache-6
> 7f8717131000-7f8718131000 rw-s 00000000 00:05 7897109
> /SYSV00000000 (deleted)
> 7f8718131000-7f8718136000 r-xp 00000000 103:02 9969348
> /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
> 7f8718136000-7f8718335000 ---p 00005000 103:02 9969348
> /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
> 7f8718335000-7f8718336000 r--p 00004000 103:02 9969348
> /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
> 7f8718336000-7f8718337000 rw-p 00005000 103:02 9969348
> /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
> 7f8718337000-7f8718340000 r-xp 00000000 103:02 9968387
> /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
> 7f8718340000-7f871853f000 ---p 00009000 103:02 9968387
> /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
> 7f871853f000-7f8718540000 r--p 00008000 103:02 9968387
> /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
> 7f8718540000-7f8718541000 rw-p 00009000 103:02 9968387
> /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
> 7f8718541000-7f8718565000 r-xp 00000000 103:02 9962891
> /usr/lib/x86_64-linux-gnu/libgraphite2.so.3.0.1
> 7f8718565000-7f8718764000 ---p 00024000 103:02 9962891
> /usr/lib/x86_64-linux-gnu/libgraphite2.so.3.0.1
> 7f8718764000-7f8718766000 r--p 00023000 103:02 9962891
> /usr/lib/x86_64-linux-gnu/libgraphite2.so.3.0.1
> 7f8718766000-7f8718767000 rw-p 00025000 103:02 9962891
> /usr/lib/x86_64-linux-gnu/libgraphite2.so.3.0.1
> 7f8718767000-7f871876b000 r-xp 00000000 103:02 393297
> /lib/x86_64-linux-gnu/libuuid.so.1.3.0
> 7f871876b000-7f871896a000 ---p 00004000 103:02 393297
> /lib/x86_64-linux-gnu/libuuid.so.1.3.0
> 7f871896a000-7f871896b000 r--p 00003000 103:02 393297
> /lib/x86_64-linux-gnu/libuuid.so.1.3.0
> 7f871896b000-7f871896c000 rw-p 00004000 103:02 393297
> /lib/x86_64-linux-gnu/libuuid.so.1.3.0
> 7f871896c000-7f8718971000 r-xp 00000000 103:02 9969344
> /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
> 7f8718971000-7f8718b70000 ---p 00005000 103:02 9969344
> /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
> 7f8718b70000-7f8718b71000 r--p 00004000 103:02 9969344
> /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
> 7f8718b71000-7f8718b72000 rw-p 00005000 103:02 9969344
> /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
> 7f8718b72000-7f8718b74000 r-xp 00000000 103:02 9969333
> /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
> 7f8718b74000-7f8718d74000 ---p 00002000 103:02 9969333
> /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
> 7f8718d74000-7f8718d75000 r--p 00002000 103:02 9969333
> /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
> 7f8718d75000-7f8718d76000 rw-p 00003000 103:02 9969333
> /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
> 7f8718d76000-7f8718d7c000 r-xp 00000000 103:02 9969594
> /usr/lib/x86_64-linux-gnu/libdatrie.so.1.3.3
> 7f8718d7c000-7f8718f7c000 ---p 00006000 103:02 9969594
> /usr/lib/x86_64-linux-gnu/libdatrie.so.1.3.3
> 7f8718f7c000-7f8718f7d000 r--p 00006000 103:02 9969594
> /usr/lib/x86_64-linux-gnu/libdatrie.so.1.3.3
> 7f8718f7d000-7f8718f7e000 rw-p 00007000 103:02 9969594
> /usr/lib/x86_64-linux-gnu/libdatrie.so.1.3.3
> 7f8718f7e000-7f8718fda000 r-xp 00000000 103:02 9969986
> /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0.10000.1
> 7f8718fda000-7f87191da000 ---p 0005c000 103:02 9969986
> /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0.10000.1
> 7f87191da000-7f87191db000 r--p 0005c000 103:02 9969986
> /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0.10000.1
> 7f87191db000-7f87191dc000 rw-p 0005d000 103:02 9969986
> /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0.10000.1
> 7f87191dc000-7f8719202000 r-xp 00000000 103:02 404901
> /lib/x86_64-linux-gnu/libexpat.so.1.6.0
> 7f8719202000-7f8719402000 ---p 00026000 103:02 404901
> /lib/x86_64-linux-gnu/libexpat.so.1.6.0
> 7f8719402000-7f8719404000 r--p 00026000 103:02 404901
> /lib/x86_64-linux-gnu/libexpat.so.1.6.0
> 7f8719404000-7f8719405000 rw-p 00028000 103:02 404901
> /lib/x86_64-linux-gnu/libexpat.so.1.6.0
> 7f8719405000-7f8719473000 r-xp 00000000 103:02 397882
> /lib/x86_64-linux-gnu/libpcre.so.3.13.2
> 7f8719473000-7f8719673000 ---p 0006e000 103:02 397882
> /lib/x86_64-linux-gnu/libpcre.so.3.13.2
> 7f8719673000-7f8719674000 r--p 0006e000 103:02 397882
> /lib/x86_64-linux-gnu/libpcre.so.3.13.2
> 7f8719674000-7f8719675000 rw-p 0006f000 103:02 397882
> /lib/x86_64-linux-gnu/libpcre.so.3.13.2
> 7f8719675000-7f871968b000 r-xp 00000000 103:02 9969197
> /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
> 7f871968b000-7f871988a000 ---p 00016000 103:02 9969197
> /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
> 7f871988a000-7f871988b000 r--p 00015000 103:02 9969197
> /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
> 7f871988b000-7f871988c000 rw-p 00016000 103:02 9969197
> /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
> 7f871988c000-7f871988f000 rw-p 00000000 00:00 0
> 7f871988f000-7f8719896000 r-xp 00000000 103:02 9969319
> /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
> 7f8719896000-7f8719a95000 ---p 00007000 103:02 9969319
> /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
> 7f8719a95000-7f8719a96000 r--p 00006000 103:02 9969319
> /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
> 7f8719a96000-7f8719a97000 rw-p 00007000 103:02 9969319
> /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
> 7f8719a97000-7f8719aa8000 r-xp 00000000 103:02 9969346
> /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
> 7f8719aa8000-7f8719ca7000 ---p 00011000 103:02 9969346
> /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
> 7f8719ca7000-7f8719ca8000 r--p 00010000 103:02 9969346
> /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
> 7f8719ca8000-7f8719ca9000 rw-p 00011000 103:02 9969346
> /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
> 7f8719ca9000-7f8719cb2000 r-xp 00000000 103:02 9969368
> /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
> 7f8719cb2000-7f8719eb1000 ---p 00009000 103:02 9969368
> /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
> 7f8719eb1000-7f8719eb2000 r--p 00008000 103:02 9969368
> /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
> 7f8719eb2000-7f8719eb3000 rw-p 00009000 103:02 9969368
> /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
> 7f8719eb3000-7f8719ed4000 r-xp 00000000 103:02 9970751
> /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
> 7f8719ed4000-7f871a0d3000 ---p 00021000 103:02 9970751
> /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
> 7f871a0d3000-7f871a0d4000 r--p 00020000 103:02 9970751
> /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
> 7f871a0d4000-7f871a0d5000 rw-p 00021000 103:02 9970751
> /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
> 7f871a0d5000-7f871a0dd000 r-xp 00000000 103:02 9970737
> /usr/lib/x86_64-linux-gnu/libxcb-render.so.0.0.0
> 7f871a0dd000-7f871a2dd000 ---p 00008000 103:02 9970737
> /usr/lib/x86_64-linux-gnu/libxcb-render.so.0.0.0
> 7f871a2dd000-7f871a2de000 r--p 00008000 103:02 9970737
> /usr/lib/x86_64-linux-gnu/libxcb-render.so.0.0.0
> 7f871a2de000-7f871a2df000 rw-p 00009000 103:02 9970737
> /usr/lib/x86_64-linux-gnu/libxcb-render.so.0.0.0
> 7f871a2df000-7f871a2e1000 r-xp 00000000 103:02 9970741
> /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0.0.0
> 7f871a2e1000-7f871a4e1000 ---p 00002000 103:02 9970741
> /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0.0.0
> 7f871a4e1000-7f871a4e2000 r--p 00002000 103:02 9970741
> /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0.0.0
> 7f871a4e2000-7f871a4e3000 rw-p 00003000 103:02 9970741
> /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0.0.0
> 7f871a4e3000-7f871a582000 r-xp 00000000 103:02 9970322
> /usr/lib/x86_64-linux-gnu/libpixman-1.so.0.33.6
> 7f871a582000-7f871a782000 ---p 0009f000 103:02 9970322
> /usr/lib/x86_64-linux-gnu/libpixman-1.so.0.33.6
> 7f871a782000-7f871a78a000 r--p 0009f000 103:02 9970322
> /usr/lib/x86_64-linux-gnu/libpixman-1.so.0.33.6
> 7f871a78a000-7f871a78b000 rw-p 000a7000 103:02 9970322
> /usr/lib/x86_64-linux-gnu/libpixman-1.so.0.33.6
> 7f871a78b000-7f871a793000 r-xp 00000000 103:02 9970523
> /usr/lib/x86_64-linux-gnu/libthai.so.0.2.4
> 7f871a793000-7f871a992000 ---p 00008000 103:02 9970523
> /usr/lib/x86_64-linux-gnu/libthai.so.0.2.4
> 7f871a992000-7f871a993000 r--p 00007000 103:02 9970523
> /usr/lib/x86_64-linux-gnu/libthai.so.0.2.4
> 7f871a993000-7f871a994000 rw-p 00008000 103:02 9970523
> /usr/lib/x86_64-linux-gnu/libthai.so.0.2.4
> 7f871a994000-7f871aa38000 r-xp 00000000 103:02 9964379
> /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
> 7f871aa38000-7f871ac37000 ---p 000a4000 103:02 9964379
> /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
> 7f871ac37000-7f871ac3d000 r--p 000a3000 103:02 9964379
> /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
> 7f871ac3d000-7f871ac3e000 rw-p 000a9000 103:02 9964379
> /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
> 7f871ac3e000-7f871ac52000 r-xp 00000000 103:02 9970296
> /usr/lib/x86_64-linux-gnu/libpangoft2-1.0.so.0.3800.1
> 7f871ac52000-7f871ae52000 ---p 00014000 103:02 9970296
> /usr/lib/x86_64-linux-gnu/libpangoft2-1.0.so.0.3800.1
> 7f871ae52000-7f871ae53000 r--p 00014000 103:02 9970296
> /usr/lib/x86_64-linux-gnu/libpangoft2-1.0.so.0.3800.1
> 7f871ae53000-7f871ae54000 rw-p 00015000 103:02 9970296
> /usr/lib/x86_64-linux-gnu/libpangoft2-1.0.so.0.3800.1
> 7f871ae54000-7f871ae91000 r-xp 00000000 103:02 9969737
> /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
> 7f871ae91000-7f871b090000 ---p 0003d000 103:02 9969737
> /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
> 7f871b090000-7f871b092000 r--p 0003c000 103:02 9969737
> /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
> 7f871b092000-7f871b097000 rw-p 0003e000 103:02 9969737
> /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
> 7f871b097000-7f871b1a6000 r-xp 00000000 103:02 393581
> /lib/x86_64-linux-gnu/libglib-2.0.so.0.4800.2
> 7f871b1a6000-7f871b3a5000 ---p 0010f000 103:02 393581
> /lib/x86_64-linux-gnu/libglib-2.0.so.0.4800.2
> 7f871b3a5000-7f871b3a6000 r--p 0010e000 103:02 393581
> /lib/x86_64-linux-gnu/libglib-2.0.so.0.4800.2
> 7f871b3a6000-7f871b3a7000 rw-p 0010f000 103:02 393581
> /lib/x86_64-linux-gnu/libglib-2.0.so.0.4800.2
> 7f871b3a7000-7f871b3a8000 rw-p 00000000 00:00 0
> 7f871b3a8000-7f871b3b3000 r-xp 00000000 103:02 9970081
> /usr/lib/x86_64-linux-gnu/libjbig.so.0
> 7f871b3b3000-7f871b5b2000 ---p 0000b000 103:02 9970081
> /usr/lib/x86_64-linux-gnu/libjbig.so.0
> 7f871b5b2000-7f871b5b3000 r--p 0000a000 103:02 9970081
> /usr/lib/x86_64-linux-gnu/libjbig.so.0
> 7f871b5b3000-7f871b5b6000 rw-p 0000b000 103:02 9970081
> /usr/lib/x86_64-linux-gnu/libjbig.so.0
> 7f871b5b6000-7f871b618000 r-xp 00000000 103:02 9969372
> /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
> 7f871b618000-7f871b818000 ---p 00062000 103:02 9969372
> /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
> 7f871b818000-7f871b819000 r--p 00062000 103:02 9969372
> /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
> 7f871b819000-7f871b81e000 rw-p 00063000 103:02 9969372
> /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
> 7f871b81e000-7f871b81f000 rw-p 00000000 00:00 0
> 7f871b81f000-7f871b954000 r-xp 00000000 103:02 9967427
> /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
> 7f871b954000-7f871bb54000 ---p 00135000 103:02 9967427
> /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
> 7f871bb54000-7f871bb55000 r--p 00135000 103:02 9967427
> /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
> 7f871bb55000-7f871bb59000 rw-p 00136000 103:02 9967427
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> /home/hpages/R/R-4.0.r78037/library/Biostrings/libs/Biostrings.so
> 7f8725b41000-7f8725b42000 r--p 00035000 00:33 23471641
> /home/hpages/R/R-4.0.r78037/library/Biostrings/libs/Biostrings.so
> 7f8725b42000-7f8725b43000 rw-p 00036000 00:33 23471641
> /home/hpages/R/R-4.0.r78037/library/Biostrings/libs/Biostrings.so
> 7f8725b43000-7f87281ad000 rw-p 00000000 00:00 0
> 7f87281ad000-7f87281b7000 r-xp 00000000 00:33 23473101
> /home/hpages/R/R-4.0.r78037/library/GenomicRanges/libs/GenomicRanges.so
> 7f87281b7000-7f87283b6000 ---p 0000a000 00:33 23473101
> /home/hpages/R/R-4.0.r78037/library/GenomicRanges/libs/GenomicRanges.so
> 7f87283b6000-7f87283b7000 r--p 00009000 00:33 23473101
> /home/hpages/R/R-4.0.r78037/library/GenomicRanges/libs/GenomicRanges.so
> 7f87283b7000-7f87283b8000 rw-p 0000a000 00:33 23473101
> /home/hpages/R/R-4.0.r78037/library/GenomicRanges/libs/GenomicRanges.so
> 7f87283b8000-7f87283d4000 r-xp 00000000 00:33 23470820
> /home/hpages/R/R-4.0.r78037/library/XVector/libs/XVector.so
> 7f87283d4000-7f87285d4000 ---p 0001c000 00:33 23470820
> /home/hpages/R/R-4.0.r78037/library/XVector/libs/XVector.so
> 7f87285d4000-7f87285d5000 r--p 0001c000 00:33 23470820
> /home/hpages/R/R-4.0.r78037/library/XVector/libs/XVector.so
> 7f87285d5000-7f87285d6000 rw-p 0001d000 00:33 23470820
> /home/hpages/R/R-4.0.r78037/library/XVector/libs/XVector.so
> 7f87285d6000-7f87285df000 r-xp 00000000 103:02 394745
> /lib/x86_64-linux-gnu/libcrypt-2.23.so
> 7f87285df000-7f87287de000 ---p 00009000 103:02 394745
> /lib/x86_64-linux-gnu/libcrypt-2.23.so
> 7f87287de000-7f87287df000 r--p 00008000 103:02 394745
> /lib/x86_64-linux-gnu/libcrypt-2.23.so
> 7f87287df000-7f87287e0000 rw-p 00009000 103:02 394745
> /lib/x86_64-linux-gnu/libcrypt-2.23.so
> 7f87287e0000-7f872880e000 rw-p 00000000 00:00 0
> 7f872880e000-7f87288de000 r-xp 00000000 103:02 9964072
> /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
> 7f87288de000-7f8728add000 ---p 000d0000 103:02 9964072
> /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
> 7f8728add000-7f8728ae0000 r--p 000cf000 103:02 9964072
> /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
> 7f8728ae0000-7f8728ae2000 rw-p 000d2000 103:02 9964072
> /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
> 7f8728ae2000-7f8728ae3000 rw-p 00000000 00:00 0
> 7f8728ae3000-7f8728b2a000 r-xp 00000000 103:02 9970008
> /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
> 7f8728b2a000-7f8728d29000 ---p 00047000 103:02 9970008
> /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
> 7f8728d29000-7f8728d2b000 r--p 00046000 103:02 9970008
> /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
> 7f8728d2b000-7f8728d2d000 rw-p 00048000 103:02 9970008
> /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
> 7f8728d2d000-7f8728d2e000 rw-p 00000000 00:00 0
> 7f8728d2e000-7f8728d3c000 r-xp 00000000 103:02 9969990
> /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
> 7f8728d3c000-7f8728f3b000 ---p 0000e000 103:02 9969990
> /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
> 7f8728f3b000-7f8728f3c000 r--p 0000d000 103:02 9969990
> /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
> 7f8728f3c000-7f8728f3d000 rw-p 0000e000 103:02 9969990
> /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
> 7f8728f3d000-7f8728f64000 r-xp 00000000 103:02 9970665
> /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
> 7f8728f64000-7f8729164000 ---p 00027000 103:02 9970665
> /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
> 7f8729164000-7f8729165000 r--p 00027000 103:02 9970665
> /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
> 7f8729165000-7f8729166000 rw-p 00028000 103:02 9970665
> /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
> 7f8729166000-7f872916d000 r-xp 00000000 103:02 9969723
> /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
> 7f872916d000-7f872936c000 ---p 00007000 103:02 9969723
> /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
> 7f872936c000-7f872936d000 r--p 00006000 103:02 9969723
> /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
> 7f872936d000-7f872936e000 rw-p 00007000 103:02 9969723
> /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
> 7f872936e000-7f8729383000 r-xp 00000000 103:02 9970406
> /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
> 7f8729383000-7f8729582000 ---p 00015000 103:02 9970406
> /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
> 7f8729582000-7f8729583000 r--p 00014000 103:02 9970406
> /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
> 7f8729583000-7f8729584000 rw-p 00015000 103:02 9970406
> /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
> 7f8729584000-7f87295b4000 r-xp 00000000 103:02 9969988
> /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
> 7f87295b4000-7f87297b4000 ---p 00030000 103:02 9969988
> /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
> 7f87297b4000-7f87297b5000 r--p 00030000 103:02 9969988
> /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
> 7f87297b5000-7f87297b6000 rw-p 00031000 103:02 9969988
> /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
> 7f87297b6000-7f87297b7000 rw-p 00000000 00:00 0
> 7f87297b7000-7f8729856000 r-xp 00000000 103:02 9969425
> /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
> 7f8729856000-7f8729a55000 ---p 0009f000 103:02 9969425
> /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
> 7f8729a55000-7f8729a56000 r--p 0009e000 103:02 9969425
> /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
> 7f8729a56000-7f8729a59000 rw-p 0009f000 103:02 9969425
> /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
> 7f8729a59000-7f8729add000 r-xp 00000000 103:02 9970095
> /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
> 7f8729add000-7f8729cdc000 ---p 00084000 103:02 9970095
> /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
> 7f8729cdc000-7f8729cdf000 r--p 00083000 103:02 9970095
> /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
> 7f8729cdf000-7f8729ce2000 rw-p 00086000 103:02 9970095
> /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
> 7f8729ce2000-7f8729ce3000 rw-p 00000000 00:00 0
> 7f8729ce3000-7f8729ceb000 r-xp 00000000 103:02 9969992
> /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
> 7f8729ceb000-7f8729eea000 ---p 00008000 103:02 9969992
> /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
> 7f8729eea000-7f8729eeb000 r--p 00007000 103:02 9969992
> /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
> 7f8729eeb000-7f8729eec000 rw-p 00008000 103:02 9969992
> /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
> 7f8729eec000-7f8729eef000 r-xp 00000000 103:02 397814
> /lib/x86_64-linux-gnu/libkeyutils.so.1.5
> 7f8729eef000-7f872a0ee000 ---p 00003000 103:02 397814
> /lib/x86_64-linux-gnu/libkeyutils.so.1.5
> 7f872a0ee000-7f872a0ef000 r--p 00002000 103:02 397814
> /lib/x86_64-linux-gnu/libkeyutils.so.1.5
> 7f872a0ef000-7f872a0f0000 rw-p 00003000 103:02 397814
> /lib/x86_64-linux-gnu/libkeyutils.so.1.5
> 7f872a0f0000-7f872a101000 r-xp 00000000 103:02 9966496
> /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
> 7f872a101000-7f872a301000 ---p 00011000 103:02 9966496
> /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
> 7f872a301000-7f872a302000 r--p 00011000 103:02 9966496
> /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
> 7f872a302000-7f872a303000 rw-p 00012000 103:02 9966496
> /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
> 7f872a303000-7f872a35c000 r-xp 00000000 103:02 9970282
> /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
> 7f872a35c000-7f872a55b000 ---p 00059000 103:02 9970282
> /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
> 7f872a55b000-7f872a565000 r--p 00058000 103:02 9970282
> /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
> 7f872a565000-7f872a567000 rw-p 00062000 103:02 9970282
> /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
> 7f872a567000-7f872a5a4000 r-xp 00000000 103:02 9969911
> /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
> 7f872a5a4000-7f872a7a4000 ---p 0003d000 103:02 9969911
> /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
> 7f872a7a4000-7f872a7a5000 r--p 0003d000 103:02 9969911
> /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
> 7f872a7a5000-7f872a7a7000 rw-p 0003e000 103:02 9969911
> /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
> 7f872a7a7000-7f872a7a8000 rw-p 00000000 00:00 0
> 7f872a7a8000-7f872a7c1000 r-xp 00000000 103:02 9962902
> /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
> 7f872a7c1000-7f872a9c1000 ---p 00019000 103:02 9962902
> /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
> 7f872a9c1000-7f872a9c2000 r--p 00019000 103:02 9962902
> /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
> 7f872a9c2000-7f872a9c3000 rw-p 0001a000 103:02 9962902
> /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
> 7f872a9c3000-7f872a9da000 r-xp 00000000 103:02 394744
> /lib/x86_64-linux-gnu/libresolv-2.23.so
> 7f872a9da000-7f872abda000 ---p 00017000 103:02 394744
> /lib/x86_64-linux-gnu/libresolv-2.23.so
> 7f872abda000-7f872abdb000 r--p 00017000 103:02 394744
> /lib/x86_64-linux-gnu/libresolv-2.23.so
> 7f872abdb000-7f872abdc000 rw-p 00018000 103:02 394744
> /lib/x86_64-linux-gnu/libresolv-2.23.so
> 7f872abdc000-7f872abde000 rw-p 00000000 00:00 0
> 7f872abde000-7f872abe8000 r-xp 00000000 103:02 9970088
> /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
> 7f872abe8000-7f872ade7000 ---p 0000a000 103:02 9970088
> /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
> 7f872ade7000-7f872ade8000 r--p 00009000 103:02 9970088
> /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
> 7f872ade8000-7f872ade9000 rw-p 0000a000 103:02 9970088
> /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
> 7f872ade9000-7f872adec000 r-xp 00000000 103:02 393421
> /lib/x86_64-linux-gnu/libcom_err.so.2.1
> 7f872adec000-7f872afeb000 ---p 00003000 103:02 393421
> /lib/x86_64-linux-gnu/libcom_err.so.2.1
> 7f872afeb000-7f872afec000 r--p 00002000 103:02 393421
> /lib/x86_64-linux-gnu/libcom_err.so.2.1
> 7f872afec000-7f872afed000 rw-p 00003000 103:02 393421
> /lib/x86_64-linux-gnu/libcom_err.so.2.1
> 7f872afed000-7f872b019000 r-xp 00000000 103:02 9968219
> /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
> 7f872b019000-7f872b218000 ---p 0002c000 103:02 9968219
> /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
> 7f872b218000-7f872b21a000 r--p 0002b000 103:02 9968219
> /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
> 7f872b21a000-7f872b21b000 rw-p 0002d000 103:02 9968219
> /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
> 7f872b21b000-7f872b21c000 rw-p 00000000 00:00 0
> 7f872b21c000-7f872b2df000 r-xp 00000000 103:02 9968224
> /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
> 7f872b2df000-7f872b4df000 ---p 000c3000 103:02 9968224
> /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
> 7f872b4df000-7f872b4ec000 r--p 000c3000 103:02 9968224
> /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
> 7f872b4ec000-7f872b4ee000 rw-p 000d0000 103:02 9968224
> /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
> 7f872b4ee000-7f872b56d000 r-xp 00000000 103:02 9969856
> /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
> 7f872b56d000-7f872b76c000 ---p 0007f000 103:02 9969856
> /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
> 7f872b76c000-7f872b76d000 r--p 0007e000 103:02 9969856
> /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
> 7f872b76d000-7f872b76e000 rw-p 0007f000 103:02 9969856
> /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
> 7f872b76e000-7f872b7a2000 r-xp 00000000 103:02 9970219
> /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
> 7f872b7a2000-7f872b9a1000 ---p 00034000 103:02 9970219
> /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
> 7f872b9a1000-7f872b9a3000 r--p 00033000 103:02 9970219
> /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
> 7f872b9a3000-7f872b9a4000 rw-p 00035000 103:02 9970219
> /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
> 7f872b9a4000-7f872b9d6000 r-xp 00000000 103:02 9969994
> /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
> 7f872b9d6000-7f872bbd5000 ---p 00032000 103:02 9969994
> /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
> 7f872bbd5000-7f872bbd6000 r--p 00031000 103:02 9969994
> /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
> 7f872bbd6000-7f872bbd7000 rw-p 00032000 103:02 9969994
> /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
> 7f872bbd7000-7f872bcfa000 r-xp 00000000 103:02 9962162
> /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
> 7f872bcfa000-7f872bef9000 ---p 00123000 103:02 9962162
> /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
> 7f872bef9000-7f872bf04000 r--p 00122000 103:02 9962162
> /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
> 7f872bf04000-7f872bf06000 rw-p 0012d000 103:02 9962162
> /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
> 7f872bf06000-7f872bf07000 rw-p 00000000 00:00 0
> 7f872bf07000-7f872bf54000 r-xp 00000000 103:02 9962195
> /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
> 7f872bf54000-7f872c153000 ---p 0004d000 103:02 9962195
> /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
> 7f872c153000-7f872c155000 r--p 0004c000 103:02 9962195
> /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
> 7f872c155000-7f872c156000 rw-p 0004e000 103:02 9962195
> /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
> 7f872c156000-7f872c158000 rw-p 00000000 00:00 0
> 7f872c158000-7f872c165000 r-xp 00000000 103:02 9962171
> /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
> 7f872c165000-7f872c365000 ---p 0000d000 103:02 9962171
> /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
> 7f872c365000-7f872c366000 r--p 0000d000 103:02 9962171
> /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
> 7f872c366000-7f872c367000 rw-p 0000e000 103:02 9962171
> /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
> 7f872c367000-7f872c3ae000 r-xp 00000000 103:02 9968221
> /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
> 7f872c3ae000-7f872c5ad000 ---p 00047000 103:02 9968221
> /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
> 7f872c5ad000-7f872c5af000 r--p 00046000 103:02 9968221
> /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
> 7f872c5af000-7f872c5b1000 rw-p 00048000 103:02 9968221
> /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
> 7f872c5b1000-7f872c7cc000 r-xp 00000000 103:02 393427
> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
> 7f872c7cc000-7f872c9cb000 ---p 0021b000 103:02 393427
> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
> 7f872c9cb000-7f872c9e7000 r--p 0021a000 103:02 393427
> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
> 7f872c9e7000-7f872c9f3000 rw-p 00236000 103:02 393427
> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
> 7f872c9f3000-7f872c9f6000 rw-p 00000000 00:00 0
> 7f872c9f6000-7f872ca54000 r-xp 00000000 103:02 393439
> /lib/x86_64-linux-gnu/libssl.so.1.0.0
> 7f872ca54000-7f872cc54000 ---p 0005e000 103:02 393439
> /lib/x86_64-linux-gnu/libssl.so.1.0.0
> 7f872cc54000-7f872cc58000 r--p 0005e000 103:02 393439
> /lib/x86_64-linux-gnu/libssl.so.1.0.0
> 7f872cc58000-7f872cc5f000 rw-p 00062000 103:02 393439
> /lib/x86_64-linux-gnu/libssl.so.1.0.0
> 7f872cc5f000-7f872cc7a000 r-xp 00000000 103:02 9970414
> /usr/lib/x86_64-linux-gnu/librtmp.so.1
> 7f872cc7a000-7f872ce79000 ---p 0001b000 103:02 9970414
> /usr/lib/x86_64-linux-gnu/librtmp.so.1
> 7f872ce79000-7f872ce7a000 r--p 0001a000 103:02 9970414
> /usr/lib/x86_64-linux-gnu/librtmp.so.1
> 7f872ce7a000-7f872ce7b000 rw-p 0001b000 103:02 9970414
> /usr/lib/x86_64-linux-gnu/librtmp.so.1
> 7f872ce7b000-7f872ceac000 r-xp 00000000 103:02 9961783
> /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
> 7f872ceac000-7f872d0ac000 ---p 00031000 103:02 9961783
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> 7f87376cf000-7f87376d0000 rw-p 00261000 103:02 9965694
> /usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
> 7f87376d0000-7f873784f000 r-xp 00000000 103:02 9965692
> /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
> 7f873784f000-7f8737a4f000 ---p 0017f000 103:02 9965692
> /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
> 7f8737a4f000-7f8737a5f000 r--p 0017f000 103:02 9965692
> /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
> 7f8737a5f000-7f8737a60000 rw-p 0018f000 103:02 9965692
> /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
> 7f8737a60000-7f8737a64000 rw-p 00000000 00:00 0
> 7f8737a64000-7f8737a67000 r-xp 00000000 103:02 394736
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f8737a67000-7f8737c66000 ---p 00003000 103:02 394736
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f8737c66000-7f8737c67000 r--p 00002000 103:02 394736
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f8737c67000-7f8737c68000 rw-p 00003000 103:02 394736
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f8737c68000-7f8737c6f000 r-xp 00000000 103:02 394731
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f8737c6f000-7f8737e6e000 ---p 00007000 103:02 394731
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f8737e6e000-7f8737e6f000 r--p 00006000 103:02 394731
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f8737e6f000-7f8737e70000 rw-p 00007000 103:02 394731
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f8737e70000-7f8737e89000 r-xp 00000000 103:02 393404
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f8737e89000-7f8738088000 ---p 00019000 103:02 393404
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f8738088000-7f8738089000 r--p 00018000 103:02 393404
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f8738089000-7f873808a000 rw-p 00019000 103:02 393404
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f873808a000-7f8738099000 r-xp 00000000 103:02 393588
> /lib/x86_64-linux-gnu/libbz2.so.1.0.4
> 7f8738099000-7f8738298000 ---p 0000f000 103:02 393588
> /lib/x86_64-linux-gnu/libbz2.so.1.0.4
> 7f8738298000-7f8738299000 r--p 0000e000 103:02 393588
> /lib/x86_64-linux-gnu/libbz2.so.1.0.4
> 7f8738299000-7f873829a000 rw-p 0000f000 103:02 393588
> /lib/x86_64-linux-gnu/libbz2.so.1.0.4
> 7f873829a000-7f87382bb000 r-xp 00000000 103:02 397820
> /lib/x86_64-linux-gnu/liblzma.so.5.0.0
> 7f87382bb000-7f87384ba000 ---p 00021000 103:02 397820
> /lib/x86_64-linux-gnu/liblzma.so.5.0.0
> 7f87384ba000-7f87384bb000 r--p 00020000 103:02 397820
> /lib/x86_64-linux-gnu/liblzma.so.5.0.0
> 7f87384bb000-7f87384bc000 rw-p 00021000 103:02 397820
> /lib/x86_64-linux-gnu/liblzma.so.5.0.0
> 7f87384bc000-7f8738534000 r-xp 00000000 103:02 9971004
> /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
> 7f8738534000-7f8738733000 ---p 00078000 103:02 9971004
> /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
> 7f8738733000-7f8738734000 r--p 00077000 103:02 9971004
> /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
> 7f8738734000-7f8738735000 rw-p 00078000 103:02 9971004
> /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
> 7f8738735000-7f8738772000 r-xp 00000000 103:02 397904
> /lib/x86_64-linux-gnu/libreadline.so.6.3
> 7f8738772000-7f8738972000 ---p 0003d000 103:02 397904
> /lib/x86_64-linux-gnu/libreadline.so.6.3
> 7f8738972000-7f8738974000 r--p 0003d000 103:02 397904
> /lib/x86_64-linux-gnu/libreadline.so.6.3
> 7f8738974000-7f873897a000 rw-p 0003f000 103:02 397904
> /lib/x86_64-linux-gnu/libreadline.so.6.3
> 7f873897a000-7f873897b000 rw-p 00000000 00:00 0
> 7f873897b000-7f8738a83000 r-xp 00000000 103:02 394777
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f8738a83000-7f8738c82000 ---p 00108000 103:02 394777
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f8738c82000-7f8738c83000 r--p 00107000 103:02 394777
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f8738c83000-7f8738c84000 rw-p 00108000 103:02 394777
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f8738c84000-7f8738cb0000 r-xp 00000000 00:33 23418713
> /home/hpages/R/R-4.0.r78037/lib/libRblas.so
> 7f8738cb0000-7f8738eaf000 ---p 0002c000 00:33 23418713
> /home/hpages/R/R-4.0.r78037/lib/libRblas.so
> 7f8738eaf000-7f8738eb0000 r--p 0002b000 00:33 23418713
> /home/hpages/R/R-4.0.r78037/lib/libRblas.so
> 7f8738eb0000-7f8738eb1000 rw-p 0002c000 00:33 23418713
> /home/hpages/R/R-4.0.r78037/lib/libRblas.so
> 7f8738eb1000-7f8739071000 r-xp 00000000 103:02 394763
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f8739071000-7f8739271000 ---p 001c0000 103:02 394763
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f8739271000-7f8739275000 r--p 001c0000 103:02 394763
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f8739275000-7f8739277000 rw-p 001c4000 103:02 394763
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f8739277000-7f873927b000 rw-p 00000000 00:00 0
> 7f873927b000-7f8739293000 r-xp 00000000 103:02 394738
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f8739293000-7f8739492000 ---p 00018000 103:02 394738
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f8739492000-7f8739493000 r--p 00017000 103:02 394738
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f8739493000-7f8739494000 rw-p 00018000 103:02 394738
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f8739494000-7f8739498000 rw-p 00000000 00:00 0
> 7f8739498000-7f87397b5000 r-xp 00000000 00:33 23419195
> /home/hpages/R/R-4.0.r78037/lib/libR.so
> 7f87397b5000-7f87399b5000 ---p 0031d000 00:33 23419195
> /home/hpages/R/R-4.0.r78037/lib/libR.so
> 7f87399b5000-7f87399d3000 r--p 0031d000 00:33 23419195
> /home/hpages/R/R-4.0.r78037/lib/libR.so
> 7f87399d3000-7f87399e1000 rw-p 0033b000 00:33 23419195
> /home/hpages/R/R-4.0.r78037/lib/libR.so
> 7f87399e1000-7f8739b31000 rw-p 00000000 00:00 0
> 7f8739b31000-7f8739b57000 r-xp 00000000 103:02 394737
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f8739b57000-7f8739b58000 r--s 00000000 103:02 29495028
> /var/cache/fontconfig/406a1d2d2bf3ed7664fbadefac0b2f66-le64.cache-6
> 7f8739b58000-7f8739b59000 r--s 00000000 103:02 29491528
> /var/cache/fontconfig/30829fa25452a46451e813d634d7f916-le64.cache-6
> 7f8739b59000-7f8739b67000 r--s 00000000 103:02 29495026
> /var/cache/fontconfig/198d8fcf01c96d0cf813f74fd759bdb7-le64.cache-6
> 7f8739b67000-7f8739b68000 r--s 00000000 103:02 29491522
> /var/cache/fontconfig/0c9eb80ebd1c36541ebe2852d3bb0c49-le64.cache-6
> 7f8739b68000-7f8739b69000 r--s 00000000 103:02 29494695
> /var/cache/fontconfig/4b2eda6bb976bda485cb2176619421d5-le64.cache-6
> 7f8739b69000-7f8739b6c000 r--s 00000000 103:02 29491539
> /var/cache/fontconfig/75114ca45c98e8a441da0ff356701271-le64.cache-6
> 7f8739b6c000-7f8739b77000 r--s 00000000 103:02 29491542
> /var/cache/fontconfig/83bf95040141907cd45bb53cf7c1c148-le64.cache-6
> 7f8739b77000-7f8739b89000 r--s 00000000 103:02 29491546
> /var/cache/fontconfig/9b89f8e3dae116d678bbf48e5f21f69b-le64.cache-6
> 7f8739b89000-7f8739b8b000 r--s 00000000 103:02 29495024
> /var/cache/fontconfig/6e6b34ae150a7ad95e82fb4a522f0bda-le64.cache-6
> 7f8739b8b000-7f8739b92000 r--s 00000000 103:02 29495022
> /var/cache/fontconfig/53d14c92082a93e67d5078324eb314ca-le64.cache-6
> 7f8739b92000-7f8739b94000 r--s 00000000 103:02 29495021
> /var/cache/fontconfig/43bfe21a9e1edebcf703d79ee2950b06-le64.cache-6
> 7f8739b94000-7f8739ba7000 r--s 00000000 103:02 29495020
> /var/cache/fontconfig/4ac51e5cfbc76fc3f983e470323a16d3-le64.cache-6
> 7f8739ba7000-7f8739bbd000 r--s 00000000 103:02 29494737
> /var/cache/fontconfig/e13b20fdb08344e0e664864cc2ede53d-le64.cache-6
> 7f8739bbd000-7f8739bde000 r--s 00000000 103:02 29494932
> /var/cache/fontconfig/467c019e582ee353435ea5c21d137ef6-le64.cache-6
> 7f8739bde000-7f8739d30000 rw-p 00000000 00:00 0
> 7f8739d30000-7f8739d31000 r--s 00000000 103:02 29495023
> /var/cache/fontconfig/3334a778d104e76d188e9df399bc24d2-le64.cache-6
> 7f8739d31000-7f8739d32000 r--s 00000000 103:02 29495019
> /var/cache/fontconfig/c277e94e32b20404286a1ddafa5a80f0-le64.cache-6
> 7f8739d32000-7f8739d36000 r--s 00000000 103:02 29495018
> /var/cache/fontconfig/3629f2adf904f9a612908891fae71ceb-le64.cache-6
> 7f8739d36000-7f8739d39000 r--s 00000000 103:02 29495017
> /var/cache/fontconfig/de83a0a961185c8bd1f159015d56c039-le64.cache-6
> 7f8739d39000-7f8739d3d000 r--s 00000000 103:02 29491649
> /var/cache/fontconfig/7ef2298fde41cc6eeb7af42e48b7d293-le64.cache-6
> 7f8739d3d000-7f8739d3f000 r--s 00000000 103:02 29494943
> /var/cache/fontconfig/16326683038b281783a0ef8c680e3a10-le64.cache-6
> 7f8739d3f000-7f8739d4c000 r--s 00000000 103:02 29494941
> /var/cache/fontconfig/8f02d4cb045bd6ce15663e43f347c9f8-le64.cache-6
> 7f8739d4c000-7f8739d4d000 r--s 00000000 103:02 29494940
> /var/cache/fontconfig/e0aa53bcfa504e64f87823c16bc01eb6-le64.cache-6
> 7f8739d4d000-7f8739d4e000 r--p 00000000 00:33 23419290
> /home/hpages/R/R-4.0.r78037/library/translations/en/LC_MESSAGES/R.mo
> 7f8739d4e000-7f8739d55000 r--s 00000000 103:02 10235479
> /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
> 7f8739d55000-7f8739d56000 rw-p 00000000 00:00 0
> 7f8739d56000-7f8739d57000 r--p 00025000 103:02 394737
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f8739d57000-7f8739d58000 rw-p 00026000 103:02 394737
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f8739d58000-7f8739d59000 rw-p 00000000 00:00 0
> 7ffd424ab000-7ffd42500000 rw-p 00000000 00:00 0
> [stack]
> 7ffd425c4000-7ffd425c7000 r--p 00000000 00:00 0
> [vvar]
> 7ffd425c7000-7ffd425c9000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
> Aborted (core dumped)
> hpages using spectre:~/MotifDb/vignettes$
>
> ----------------------------------------------------------------------
>
> On 3/26/20 16:31, Paul Shannon wrote:
>> Dear Bioc,
>>
>> I have added the lasted HOCOMOCO motifs to MotifDb but changed no code. The package 1.29.6 dumps core during in the bioc devel linux build, and fails perhaps similarly on windows.
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_MotifDb_malbec2-2Dbuildsrc.html&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=3nyFO44fKEjL0UQgr9v3rdH5xN5N0L-oPwJKqCde-KA&s=39WsjZfDBDIfFAUX64qytpa9HhMcXAg5hSs9bnZWf4A&e=
>>
>> Any suggestions on how I can track this down? The package builds and checks clean on my macOS and linux systems.
>>
>> - Paul
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=3nyFO44fKEjL0UQgr9v3rdH5xN5N0L-oPwJKqCde-KA&s=R3gXyvG3OC_JFgAHmeE67RR_NRUmDjW7YGAJb7dIdsA&e=
>>
>
> --
> 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: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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