[Bioc-devel] core dump in MotifDb build
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Fri Mar 27 03:19:15 CET 2020
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]
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/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]
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/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]
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/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]
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/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
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/home/hpages/R/R-4.0.r78037/library/methods/libs/methods.so
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7f8734dd4000-7f8734dea000 r-xp 00000000 103:02 397791
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7f8734fe9000-7f8734fea000 rw-p 00015000 103:02 397791
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7f8734fea000-7f873515c000 r-xp 00000000 103:02 9961864
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f873515c000-7f873535c000 ---p 00172000 103:02 9961864
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f873535c000-7f8735366000 r--p 00172000 103:02 9961864
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f8735366000-7f8735368000 rw-p 0017c000 103:02 9961864
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7f8735368000-7f873536c000 rw-p 00000000 00:00 0
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7f8736c22000-7f8736e21000 ---p 018b6000 103:02 9965696
/usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f8736e21000-7f8736e22000 r--p 018b5000 103:02 9965696
/usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f8736e22000-7f8736e23000 rw-p 018b6000 103:02 9965696
/usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f8736e23000-7f8736e48000 r-xp 00000000 103:02 397925
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7f8736e48000-7f8737047000 ---p 00025000 103:02 397925
/lib/x86_64-linux-gnu/libtinfo.so.5.9
7f8737047000-7f873704b000 r--p 00024000 103:02 397925
/lib/x86_64-linux-gnu/libtinfo.so.5.9
7f873704b000-7f873704c000 rw-p 00028000 103:02 397925
/lib/x86_64-linux-gnu/libtinfo.so.5.9
7f873704c000-7f873706d000 r-xp 00000000 103:02 9969010
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7f873706d000-7f873726c000 ---p 00021000 103:02 9969010
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f873726c000-7f873726d000 r--p 00020000 103:02 9969010
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7f873726d000-7f873726e000 rw-p 00021000 103:02 9969010
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f873726e000-7f87374c0000 r-xp 00000000 103:02 9965694
/usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f87374c0000-7f87376c0000 ---p 00252000 103:02 9965694
/usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f87376c0000-7f87376cf000 r--p 00252000 103:02 9965694
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7f87376cf000-7f87376d0000 rw-p 00261000 103:02 9965694
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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
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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
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