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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HD2013SGI
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* checking for file ‘HD2013SGI/DESCRIPTION’ ... OK
* preparing ‘HD2013SGI’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HD2013SGI.Rnw’ using Sweave
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:gplots’:
space
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: XML
Loading required package: splots
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:geneplotter’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: vcd
Loading required package: grid
Attaching package: ‘vcd’
The following object is masked from ‘package:IRanges’:
tile
Loading required package: LSD
Loading required package: EBImage
Attaching package: ‘EBImage’
The following object is masked from ‘package:vcd’:
tile
The following objects are masked from ‘package:IRanges’:
resize, tile
The following object is masked from ‘package:Biobase’:
channel
--- finished re-building ‘HD2013SGI.Rnw’
echo 'Stangle(file.path("src","sec02_dataAccess.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec02_dataAccess.R
echo 'Stangle(file.path("src","sec03_figures.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec03_figures.R
echo 'Stangle(file.path("src","sec04_imageProcessing.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec04_imageProcessing.R
echo 'Stangle(file.path("src","sec05_convertData.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec05_convertData.R
echo 'Stangle(file.path("src","sec06_rawDataProcessing.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec06_rawDataProcessing.R
echo 'Stangle(file.path("src","sec07_exampleInteractions.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec07_exampleInteractions.R
echo 'Stangle(file.path("src","sec08_siRNAcorrelation.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec08_siRNAcorrelation.R
echo 'Stangle(file.path("src","sec09_heatmaps.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec09_heatmaps.R
echo 'Stangle(file.path("src","sec10_smallCellNumber.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec10_smallCellNumber.R
echo 'Stangle(file.path("src","sec11_distributionOfInteractions.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec11_distributionOfInteractions.R
echo 'Stangle(file.path("src","sec12_scatterplots.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec12_scatterplots.R
echo 'Stangle(file.path("src","sec13_screenplots.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec13_screenplots.R
echo 'Stangle(file.path("src","sec14_table.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec14_table.R
echo 'Stangle("HD2013SGI.Rnw")' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file HD2013SGI.R
echo 'Sweave(file.path("src","sec02_dataAccess.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec02_dataAccess.tex
Processing code chunks with options ...
1 : echo keep.source term hide (label = dataAcceess1, sec02_dataAccess.Rnw:6)
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:gplots’:
space
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: XML
Loading required package: splots
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:geneplotter’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: vcd
Loading required package: grid
Attaching package: ‘vcd’
The following object is masked from ‘package:IRanges’:
tile
Loading required package: LSD
Loading required package: EBImage
Attaching package: ‘EBImage’
The following object is masked from ‘package:vcd’:
tile
The following objects are masked from ‘package:IRanges’:
resize, tile
The following object is masked from ‘package:Biobase’:
channel
2 : echo keep.source (label = dataAccess2, sec02_dataAccess.Rnw:16)
You can now run (pdf)latex on ‘sec02_dataAccess.tex’
echo 'Sweave(file.path("src","sec03_figures.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec03_figures.tex
Processing code chunks with options ...
1 : echo keep.source term verbatim (label = VennDiagram, sec03_figures.Rnw:63)
You can now run (pdf)latex on ‘sec03_figures.tex’
echo 'Sweave(file.path("src","sec04_imageProcessing.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec04_imageProcessing.tex
Processing code chunks with options ...
1 : echo keep.source term verbatim (label = imageProcessing1, sec04_imageProcessing.Rnw:7)
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:gplots’:
space
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: XML
Loading required package: splots
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:geneplotter’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: vcd
Loading required package: grid
Attaching package: ‘vcd’
The following object is masked from ‘package:IRanges’:
tile
Loading required package: LSD
Loading required package: EBImage
Attaching package: ‘EBImage’
The following object is masked from ‘package:vcd’:
tile
The following objects are masked from ‘package:IRanges’:
resize, tile
The following object is masked from ‘package:Biobase’:
channel
2 : echo keep.source term verbatim (label = imageProcessing2, sec04_imageProcessing.Rnw:26)
3 : echo keep.source term verbatim (label = imageProcessing3, sec04_imageProcessing.Rnw:41)
4 : echo keep.source (label = imageProcessing3, sec04_imageProcessing.Rnw:46)
5 : keep.source term verbatim (label = imageProcessing4, sec04_imageProcessing.Rnw:53)
6 : echo keep.source term verbatim (label = imageProcessing5, sec04_imageProcessing.Rnw:87)
7 : echo keep.source (label = imageProcessing6, sec04_imageProcessing.Rnw:90)
8 : keep.source term verbatim (label = imageProcessing7, sec04_imageProcessing.Rnw:93)
9 : echo keep.source term verbatim (label = imageProcessing8, sec04_imageProcessing.Rnw:118)
10 : echo keep.source term verbatim (label = imageProcessing9, sec04_imageProcessing.Rnw:132)
11 : echo keep.source (label = imageProcessing10, sec04_imageProcessing.Rnw:137)
12 : keep.source term verbatim (label = imageProcessing11, sec04_imageProcessing.Rnw:140)
13 : echo keep.source term verbatim (label = imageProcessing12, sec04_imageProcessing.Rnw:174)
14 : echo keep.source term verbatim (label = imageProcessing13, sec04_imageProcessing.Rnw:179)
15 : echo keep.source term verbatim (label = imageProcessing14, sec04_imageProcessing.Rnw:183)
16 : echo keep.source term verbatim (label = imageProcessing15, sec04_imageProcessing.Rnw:195)
17 : echo keep.source term verbatim (label = imageProcessing16, sec04_imageProcessing.Rnw:206)
18 : echo keep.source (label = imageProcessing17, sec04_imageProcessing.Rnw:210)
19 : keep.source term verbatim (label = imageProcessing18, sec04_imageProcessing.Rnw:217)
20 : echo keep.source term verbatim (label = imageProcessing19, sec04_imageProcessing.Rnw:268)
21 : echo keep.source term verbatim (label = imageProcessing20, sec04_imageProcessing.Rnw:277)
22 : echo keep.source term verbatim (label = imageProcessing21, sec04_imageProcessing.Rnw:286)
23 : echo keep.source term verbatim (label = imageProcessing22, sec04_imageProcessing.Rnw:297)
24 : echo keep.source (label = imageProcessing23, sec04_imageProcessing.Rnw:304)
25 : keep.source term verbatim (label = imageProcessing24, sec04_imageProcessing.Rnw:311)
26 : echo keep.source term verbatim (label = imageProcessing25, sec04_imageProcessing.Rnw:360)
27 : keep.source term verbatim (label = imageProcessing26, sec04_imageProcessing.Rnw:377)
28 : echo keep.source term verbatim (label = imageProcessing27, sec04_imageProcessing.Rnw:434)
29 : echo keep.source term verbatim (label = imageProcessing28, sec04_imageProcessing.Rnw:443)
30 : keep.source term hide (label = imageProcessing29, sec04_imageProcessing.Rnw:451)
31 : echo keep.source term verbatim (label = imageProcessing29, sec04_imageProcessing.Rnw:537)
You can now run (pdf)latex on ‘sec04_imageProcessing.tex’
echo 'Sweave(file.path("src","sec05_convertData.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec05_convertData.tex
Processing code chunks with options ...
1 : echo keep.source term verbatim (label = convertData2, sec05_convertData.Rnw:7)
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:gplots’:
space
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: XML
Loading required package: splots
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:geneplotter’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: vcd
Loading required package: grid
Attaching package: ‘vcd’
The following object is masked from ‘package:IRanges’:
tile
Loading required package: LSD
Loading required package: EBImage
Attaching package: ‘EBImage’
The following object is masked from ‘package:vcd’:
tile
The following objects are masked from ‘package:IRanges’:
resize, tile
The following object is masked from ‘package:Biobase’:
channel
2 : echo keep.source term verbatim (label = convertData3, sec05_convertData.Rnw:12)
3 : echo keep.source term verbatim (label = convertData1, sec05_convertData.Rnw:24)
4 : echo keep.source term verbatim (label = convertData4, sec05_convertData.Rnw:34)
5 : echo keep.source term verbatim (label = convertData3, sec05_convertData.Rnw:42)
6 : echo keep.source term verbatim (label = convertData4, sec05_convertData.Rnw:50)
7 : echo keep.source term verbatim (label = convertData9, sec05_convertData.Rnw:63)
8 : echo keep.source term verbatim (label = convertData10, sec05_convertData.Rnw:101)
You can now run (pdf)latex on ‘sec05_convertData.tex’
echo 'Sweave(file.path("src","sec06_rawDataProcessing.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec06_rawDataProcessing.tex
Processing code chunks with options ...
1 : echo keep.source term verbatim (label = RawDataProcessing1, sec06_rawDataProcessing.Rnw:7)
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:gplots’:
space
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: XML
Loading required package: splots
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:geneplotter’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: vcd
Loading required package: grid
Attaching package: ‘vcd’
The following object is masked from ‘package:IRanges’:
tile
Loading required package: LSD
Loading required package: EBImage
Attaching package: ‘EBImage’
The following object is masked from ‘package:vcd’:
tile
The following objects are masked from ‘package:IRanges’:
resize, tile
The following object is masked from ‘package:Biobase’:
channel
2 : echo keep.source term verbatim (label = RawDataProcessing2, sec06_rawDataProcessing.Rnw:12)
3 : echo keep.source term verbatim (label = RawDataProcessing3, sec06_rawDataProcessing.Rnw:20)
4 : echo keep.source term verbatim (label = RawDataProcessing4, sec06_rawDataProcessing.Rnw:28)
5 : echo keep.source term verbatim (label = RawDataProcessing5, sec06_rawDataProcessing.Rnw:36)
6 : keep.source term verbatim (label = TransformationAndNormalization1, sec06_rawDataProcessing.Rnw:57)
7 : keep.source term hide (label = TransformationAndNormalization1, sec06_rawDataProcessing.Rnw:68)
8 : echo keep.source term verbatim (label = TransformationAndNormalization2, sec06_rawDataProcessing.Rnw:85)
9 : echo keep.source term verbatim (label = TransformationAndNormalization3, sec06_rawDataProcessing.Rnw:98)
10 : echo keep.source term verbatim (label = TransformationAndNormalization4, sec06_rawDataProcessing.Rnw:114)
11 : echo keep.source term verbatim (label = qualityControlFeatures1, sec06_rawDataProcessing.Rnw:153)
12 : keep.source term hide (label = qualityControlFeatures2, sec06_rawDataProcessing.Rnw:162)
13 : echo keep.source term hide (label = qualityControlFeatures2, sec06_rawDataProcessing.Rnw:165)
14 : keep.source term hide (label = qualityControlFeatures2, sec06_rawDataProcessing.Rnw:170)
15 : keep.source term hide (label = qualityControlFeatures3, sec06_rawDataProcessing.Rnw:178)
16 : echo keep.source term hide (label = qualityControlFeatures3, sec06_rawDataProcessing.Rnw:181)
17 : keep.source term hide (label = qualityControlFeatures3, sec06_rawDataProcessing.Rnw:192)
18 : keep.source term verbatim (label = qualityControlFeatures4, sec06_rawDataProcessing.Rnw:199)
19 : echo keep.source term verbatim (label = qualityControlFeatures5, sec06_rawDataProcessing.Rnw:208)
20 : echo keep.source term verbatim (label = qualityControlsiRNA2, sec06_rawDataProcessing.Rnw:243)
21 : keep.source term hide (label = qualityControlsiRNA3, sec06_rawDataProcessing.Rnw:260)
22 : echo keep.source term hide (label = qualityControlsiRNA3, sec06_rawDataProcessing.Rnw:263)
23 : keep.source term hide (label = qualityControlsiRNA3, sec06_rawDataProcessing.Rnw:269)
24 : keep.source term hide (label = qualityControlsiRNA4, sec06_rawDataProcessing.Rnw:280)
25 : echo keep.source term hide (label = qualityControlsiRNA4, sec06_rawDataProcessing.Rnw:284)
26 : keep.source term hide (label = qualityControlsiRNA4, sec06_rawDataProcessing.Rnw:292)
27 : echo keep.source term verbatim (label = qualityControlsiRNA4, sec06_rawDataProcessing.Rnw:305)
28 : echo keep.source term verbatim (label = featureSelection1, sec06_rawDataProcessing.Rnw:332)
29 : echo keep.source term verbatim (label = featureSelection2, sec06_rawDataProcessing.Rnw:339)
30 : echo keep.source term verbatim (label = featureSelection3, sec06_rawDataProcessing.Rnw:369)
k=1 selected = count cor = 0.922237814494435 r = 1
k=2 selected = cell.act.m.majoraxis cor = 0.97170506215823 r = 1
k=3 selected = nuc.nuc.b.q001 cor = 0.933252141870726 r = 0.946666666666667
k=4 selected = nuc.0.s.radius.min cor = 0.913405018230971 r = 0.928571428571429
k=5 selected = cell.Bact.h.f12.s2 cor = 0.886418300395878 r = 0.928251121076233
k=6 selected = nuc.nuc.b.sd cor = 0.875879935466446 r = 0.761261261261261
k=7 selected = nuc.0.m.majoraxis cor = 0.857395413484588 r = 0.719457013574661
k=8 selected = cell.Btub.h.sen.s2 cor = 0.788150926412458 r = 0.686363636363636
k=9 selected = cell.tub.b.mad cor = 0.707278833263634 r = 0.598173515981735
k=10 selected = nuc.0.m.eccentricity cor = 0.705475153486411 r = 0.477064220183486
k=11 selected = cell.Bnuctub.m.eccentricity cor = 0.648855565739401 r = 0.465437788018433
k=12 selected = cell.Bact.m.eccentricity cor = 0.587343348032663 r = 0.430555555555556
k=13 selected = cell.Bact.b.q05 cor = 0.50076214089337 r = 0.423255813953488
k=14 selected = nuc.Bnuc.b.q05 cor = 0.46303702505399 r = 0.406542056074766
k=15 selected = cell.Bnuctub.b.q05 cor = 0.457491292687548 r = 0.347417840375587
k=16 selected = cell.Bact.h.sva.s2 cor = 0.391290706442435 r = 0.334905660377358
k=17 selected = cell.nuctub.m.eccentricity cor = 0.359293447849131 r = 0.28436018957346
k=18 selected = nuc.nuc.h.con.s2 cor = 0.285356708043695 r = 0.266666666666667
k=19 selected = cell.0.m.eccentricity cor = 0.243069538773204 r = 0.162679425837321
k=20 selected = cell.tub.b.q001 cor = 0.237314433435067 r = 0.116504854368932
k=21 selected = cell.tub.h.f12.s2 cor = 0.232104117337946 r = 0.0926829268292683
k=22 selected = cell.act.h.asm.s1 cor = 0.218025677580057 r = 0.0294117647058824
k=23 selected = nuc.Bnuc.h.sva.s2 cor = 0.00550093294362163 r = 0.00492610837438424
k=24 selected = cell.nuctub.m.majoraxis cor = -0.0825840501254408 r = 0
k=25 selected = cell.Btub.b.q001 cor = -0.102559472280825 r = 0
31 : echo keep.source term verbatim (label = featureSelection4, sec06_rawDataProcessing.Rnw:386)
32 : keep.source term hide (label = featureSelection5, sec06_rawDataProcessing.Rnw:395)
33 : echo keep.source term hide (label = featureSelection5, sec06_rawDataProcessing.Rnw:400)
34 : keep.source term hide (label = featureSelection5, sec06_rawDataProcessing.Rnw:406)
35 : keep.source term hide (label = featureSelection6, sec06_rawDataProcessing.Rnw:415)
36 : echo keep.source term hide (label = featureSelection6, sec06_rawDataProcessing.Rnw:419)
37 : keep.source term hide (label = featureSelection6, sec06_rawDataProcessing.Rnw:425)
38 : echo keep.source term verbatim (label = featureSelection7, sec06_rawDataProcessing.Rnw:433)
39 : echo keep.source term verbatim (label = featureSelection8, sec06_rawDataProcessing.Rnw:455)
40 : echo keep.source term verbatim (label = pairwiseInteractionScores1, sec06_rawDataProcessing.Rnw:470)
41 : echo keep.source term verbatim (label = callingInteractions1, sec06_rawDataProcessing.Rnw:504)
42 : echo keep.source term verbatim (label = callingInteractions2, sec06_rawDataProcessing.Rnw:531)
You can now run (pdf)latex on ‘sec06_rawDataProcessing.tex’
Warning messages:
1: Zero sample variances detected, have been offset away from zero
2: Zero sample variances detected, have been offset away from zero
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echo 'Sweave(file.path("src","sec07_exampleInteractions.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec07_exampleInteractions.tex
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Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
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2 : echo keep.source term hide (label = exampleSingleKnockDownEffects2, sec07_exampleInteractions.Rnw:24)
3 : keep.source term hide (label = exampleSingleKnockDownEffects3, sec07_exampleInteractions.Rnw:29)
4 : echo keep.source term hide (label = exampleSingleKnockDownEffects4, sec07_exampleInteractions.Rnw:32)
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11 : echo keep.source term hide (label = exampleInteractions3, sec07_exampleInteractions.Rnw:65)
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13 : echo keep.source term verbatim (label = overlapOfInteractions1, sec07_exampleInteractions.Rnw:85)
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You can now run (pdf)latex on ‘sec07_exampleInteractions.tex’
echo 'Sweave(file.path("src","sec08_siRNAcorrelation.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
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2 : echo keep.source term verbatim (label = siRNAcorrelation2, sec08_siRNAcorrelation.Rnw:21)
3 : echo keep.source term verbatim (label = siRNAcorrelation3, sec08_siRNAcorrelation.Rnw:36)
4 : echo keep.source term verbatim (label = siRNAcorrelation4, sec08_siRNAcorrelation.Rnw:46)
5 : echo keep.source term hide (label = siRNAcorrelation5, sec08_siRNAcorrelation.Rnw:57)
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8 : keep.source term hide (label = siRNAcorrelation8, sec08_siRNAcorrelation.Rnw:77)
9 : echo keep.source term verbatim (label = siRNAcorrelation9, sec08_siRNAcorrelation.Rnw:85)
You can now run (pdf)latex on ‘sec08_siRNAcorrelation.tex’
Warning messages:
1: In dir.create(file.path("result", "Figures"), recursive = TRUE) :
'result/Figures' already exists
2: In dir.create(file.path("result", "data"), recursive = TRUE) :
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echo 'Sweave(file.path("src","sec09_heatmaps.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec09_heatmaps.tex
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
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2 : echo keep.source term verbatim (label = heatmap2, sec09_heatmaps.Rnw:19)
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10 : echo keep.source term verbatim (label = heatmap10, sec09_heatmaps.Rnw:96)
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You can now run (pdf)latex on ‘sec09_heatmaps.tex’
Warning message:
In dir.create(file.path("result", "Figures"), recursive = TRUE) :
'result/Figures' already exists
echo 'Sweave(file.path("src","sec10_smallCellNumber.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec10_smallCellNumber.tex
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
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8 : echo keep.source term verbatim (label = smallCellNumber4, sec10_smallCellNumber.Rnw:116)
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15 : echo keep.source term verbatim (label = SCNqualityControlsiRNA1, sec10_smallCellNumber.Rnw:214)
16 : echo keep.source term verbatim (label = SCNqualityControlsiRNA2, sec10_smallCellNumber.Rnw:221)
17 : echo keep.source term verbatim (label = SCNqualityControlsiRNA4, sec10_smallCellNumber.Rnw:244)
18 : echo keep.source term hide (label = SCNfeatureSelection3, sec10_smallCellNumber.Rnw:257)
19 : echo keep.source term verbatim (label = SCNfeatureSelection7, sec10_smallCellNumber.Rnw:266)
20 : echo keep.source term verbatim (label = SCNpairwiseInteractionScores1, sec10_smallCellNumber.Rnw:280)
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You can now run (pdf)latex on ‘sec10_smallCellNumber.tex’
There were 12 warnings (use warnings() to see them)
echo 'Sweave(file.path("src","sec11_distributionOfInteractions.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec11_distributionOfInteractions.tex
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
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2 : echo keep.source term hide (label = distributionOfInteractions2, sec11_distributionOfInteractions.Rnw:17)
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You can now run (pdf)latex on ‘sec11_distributionOfInteractions.tex’
echo 'Sweave(file.path("src","sec12_scatterplots.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec12_scatterplots.tex
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
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2 : echo keep.source term hide (label = distributionOfInteractions1, sec12_scatterplots.Rnw:16)
3 : echo keep.source term hide (label = distributionOfInteractions2, sec12_scatterplots.Rnw:24)
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5 : echo keep.source term hide (label = distributionOfInteractions4, sec12_scatterplots.Rnw:31)
6 : keep.source term hide (label = distributionOfInteractions5, sec12_scatterplots.Rnw:34)
You can now run (pdf)latex on ‘sec12_scatterplots.tex’
echo 'Sweave(file.path("src","sec13_screenplots.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
Writing to file sec13_screenplots.tex
Processing code chunks with options ...
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as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
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2 : echo keep.source term hide (label = screenplots2, sec13_screenplots.Rnw:19)
3 : keep.source term hide (label = screenplots2, sec13_screenplots.Rnw:40)
4 : echo keep.source term hide (label = screenplots2, sec13_screenplots.Rnw:42)
5 : keep.source term hide (label = screenplots2, sec13_screenplots.Rnw:46)
You can now run (pdf)latex on ‘sec13_screenplots.tex’
Warning messages:
1: In plotScreen(z[1:2], ncol = 2L, na.fill = "gray90", main = "pi-score (cell.act.m.majoraxis)", :
The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
2: In plotScreen(z[1:2], ncol = 2L, na.fill = "gray90", main = "pi-score (cell.act.m.majoraxis)", :
The function splots::plotScreen is obsolete, please use ggplot with geom_raster and facet_wrap instead, as described in the vignette of the splots package
echo 'Sweave(file.path("src","sec14_table.Rnw"))' | /home/biocbuild/bbs-3.20-bioc/R/bin/R --slave --vanilla
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