Aaron Lun
| Snapshot Date: 2018-05-18 07:35:07 -0400 (Fri, 18 May 2018) |
| URL: https://git.bioconductor.org/packages/chipseqDB |
| Branch: master |
| Last Commit: 78bb70e |
| Last Changed Date: 2018-04-30 10:10:33 -0400 (Mon, 30 Apr 2018) |
| Back to Workflows build report for BioC 3.8 |
This page was generated on 2018-05-18 09:51:44 -0400 (Fri, 18 May 2018).
| Package 4/21 | Hostname | OS / Arch | INSTALL | BUILD | ||||||
| chipseqDB 1.3.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | |
| Package: chipseqDB |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")' |
| StartedAt: 2018-05-18 08:43:42 -0400 (Fri, 18 May 2018) |
| EndedAt: 2018-05-18 09:15:19 -0400 (Fri, 18 May 2018) |
| EllapsedTime: 1897.5 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")'
###
##############################################################################
##############################################################################
> rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")
processing file: work-1-intro.Rmd
|
| | 0%
|
|....................... | 33%
inline R code fragments
|
|............................................... | 67%
label: style (with options)
List of 3
$ echo : logi FALSE
$ results: chr "hide"
$ message: logi FALSE
|
|......................................................................| 100%
inline R code fragments
output file: work-1-intro.knit.md
/usr/bin/pandoc +RTS -K512m -RTS work-1-intro.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-1-intro.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.8-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc
Output created: work-1-intro.html
>
>
> knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")
processing file: .buildwebvig/chipseqDB/work-1-intro.Rmd
|
| | 0%
|
|...................... | 33%
|
|........................................... | 67%
|
|.................................................................| 100%
output file: .buildwebvig/chipseqDB/work-1-intro.R
[1] ".buildwebvig/chipseqDB/work-1-intro.R"
>
>
> rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")
processing file: work-3-h3k9ac.Rmd
|
| | 0%
|
|. | 1%
inline R code fragments
|
|. | 2%
label: style (with options)
List of 3
$ echo : logi FALSE
$ results: chr "hide"
$ message: logi FALSE
|
|.. | 3%
ordinary text without R code
label: unnamed-chunk-1
|
|... | 4%
ordinary text without R code
|
|.... | 5%
label: unnamed-chunk-2 (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
|
|.... | 6%
ordinary text without R code
|
|..... | 7%
label: unnamed-chunk-3 (with options)
List of 1
$ eval: symbol remap
|
|..... | 8%
ordinary text without R code
|
|...... | 8%
label: unnamed-chunk-4 (with options)
List of 1
$ eval: symbol remap
|
|...... | 9%
inline R code fragments
|
|....... | 10%
label: unnamed-chunk-5 (with options)
List of 3
$ results: chr "hide"
$ eval : symbol remap
$ message: logi FALSE
|
|........ | 11%
inline R code fragments
|
|........ | 12%
label: unnamed-chunk-6 (with options)
List of 3
$ message: logi FALSE
$ results: chr "hide"
$ eval : symbol remap
|
|......... | 13%
ordinary text without R code
label: killindex (with options)
List of 4
$ echo : logi FALSE
$ results: chr "hide"
$ message: logi FALSE
$ eval : symbol remap
|
|.......... | 14%
ordinary text without R code
|
|........... | 15%
label: unnamed-chunk-7 (with options)
List of 1
$ eval: symbol remap
|
|........... | 16%
inline R code fragments
|
|............ | 17%
label: unnamed-chunk-8 (with options)
List of 4
$ eval : language !remap
$ results: chr "hide"
$ echo : logi FALSE
$ message: logi FALSE
Loading required package: GenomeInfoDb
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, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, 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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
|
|............ | 18%
ordinary text without R code
|
|............. | 18%
label: unnamed-chunk-9 (with options)
List of 4
$ eval : symbol redownload
$ results: chr "hide"
$ echo : logi FALSE
$ message: logi FALSE
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8059.bam'
Content type 'binary/octet-stream' length 617154673 bytes (588.6 MB)
==================================================
downloaded 588.6 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8059.bam.bai'
Content type 'binary/octet-stream' length 5321936 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8086.bam'
Content type 'binary/octet-stream' length 243983790 bytes (232.7 MB)
==================================================
downloaded 232.7 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8086.bam.bai'
Content type 'binary/octet-stream' length 5276984 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8108.bam'
Content type 'binary/octet-stream' length 343361633 bytes (327.5 MB)
==================================================
downloaded 327.5 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8108.bam.bai'
Content type 'binary/octet-stream' length 5324456 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8113.bam'
Content type 'binary/octet-stream' length 325151168 bytes (310.1 MB)
==================================================
downloaded 310.1 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8113.bam.bai'
Content type 'binary/octet-stream' length 5347848 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
|
|.............. | 19%
ordinary text without R code
|
|.............. | 20%
label: mapstat
|
|............... | 21%
ordinary text without R code
|
|............... | 22%
label: unnamed-chunk-10 (with options)
List of 2
$ eval : symbol remap
$ results: chr "hide"
|
|................ | 23%
inline R code fragments
|
|................ | 24%
label: unnamed-chunk-11 (with options)
List of 4
$ eval : symbol redownload
$ message: logi FALSE
$ echo : logi FALSE
$ results: chr "hide"
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/mm10.blacklist.bed.gz'
Content type 'application/vnd.realvnc.bed' length 1263 bytes
==================================================
downloaded 1263 bytes
|
|................. | 24%
ordinary text without R code
|
|.................. | 25%
label: unnamed-chunk-12 (with options)
List of 1
$ message: logi FALSE
|
|.................. | 26%
inline R code fragments
|
|................... | 27%
label: unnamed-chunk-13
|
|................... | 28%
inline R code fragments
|
|.................... | 29%
label: unnamed-chunk-14 (with options)
List of 1
$ message: logi FALSE
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply
|
|..................... | 29%
ordinary text without R code
|
|..................... | 30%
label: unnamed-chunk-15
|
|...................... | 31%
ordinary text without R code
|
|...................... | 32%
label: ccfplot (with options)
List of 1
$ fig.cap: chr "Cross-correlation function (CCF) against delay distance for the H3K9ac data set. The delay with the maximum cor"| __truncated__
|
|....................... | 33%
inline R code fragments
|
|........................ | 34%
label: unnamed-chunk-16
ordinary text without R code
|
|......................... | 35%
label: unnamed-chunk-17
|
|......................... | 36%
ordinary text without R code
|
|.......................... | 37%
label: bghistplot (with options)
List of 1
$ fig.cap: chr "Histogram of average abundances across all 2 kbp genomic bins. The filter threshold is shown as the red line."
|
|.......................... | 38%
ordinary text without R code
|
|........................... | 39%
label: unnamed-chunk-18
|
|............................ | 39%
ordinary text without R code
|
|............................ | 40%
label: trendplot (with options)
List of 1
$ fig.cap: chr "Abundance-dependent trend in the log-fold change between two H3K9ac libraries (mature B over pro-B), across all"| __truncated__
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
|
|............................. | 41%
inline R code fragments
|
|............................. | 42%
label: unnamed-chunk-19
|
|.............................. | 43%
ordinary text without R code
|
|............................... | 44%
label: normplot (with options)
List of 1
$ fig.cap: chr "Effect of non-linear normalization on the trended bias between two H3K9ac libraries. Normalized log-fold change"| __truncated__
|
|............................... | 45%
inline R code fragments
|
|................................ | 45%
label: unnamed-chunk-20
|
|................................ | 46%
inline R code fragments
|
|................................. | 47%
label: unnamed-chunk-21
|
|.................................. | 48%
ordinary text without R code
|
|.................................. | 49%
label: bcvplot (with options)
List of 1
$ fig.cap: chr "Abundance-dependent trend in the BCV for each window, represented by the blue line. Common (red) and tagwise es"| __truncated__
|
|................................... | 50%
inline R code fragments
label: qlplot (with options)
List of 1
$ fig.cap: chr "Effect of EB shrinkage on the raw QL dispersion estimate for each window (black) towards the abundance-dependen"| __truncated__
|
|.................................... | 51%
ordinary text without R code
|
|.................................... | 52%
label: unnamed-chunk-22
|
|..................................... | 53%
ordinary text without R code
|
|...................................... | 54%
label: mdsplot (with options)
List of 1
$ fig.cap: chr "MDS plot with two dimensions for all libraries in the H3K9ac data set. Libraries are labelled and coloured acco"| __truncated__
|
|...................................... | 55%
ordinary text without R code
|
|....................................... | 55%
label: unnamed-chunk-23
|
|....................................... | 56%
ordinary text without R code
|
|........................................ | 57%
label: unnamed-chunk-24
|
|......................................... | 58%
ordinary text without R code
|
|......................................... | 59%
label: unnamed-chunk-25
|
|.......................................... | 60%
ordinary text without R code
|
|.......................................... | 61%
label: unnamed-chunk-26
|
|........................................... | 61%
ordinary text without R code
|
|............................................ | 62%
label: unnamed-chunk-27
|
|............................................ | 63%
ordinary text without R code
|
|............................................. | 64%
label: unnamed-chunk-28
|
|............................................. | 65%
ordinary text without R code
|
|.............................................. | 66%
label: unnamed-chunk-29
ordinary text without R code
|
|............................................... | 67%
label: unnamed-chunk-30
|
|................................................ | 68%
inline R code fragments
|
|................................................ | 69%
label: unnamed-chunk-31
|
|................................................. | 70%
inline R code fragments
|
|................................................. | 71%
label: unnamed-chunk-32
|
|.................................................. | 71%
inline R code fragments
|
|................................................... | 72%
label: unnamed-chunk-33 (with options)
List of 1
$ message: logi FALSE
Loading required package: AnnotationDbi
Loading required package: GenomicFeatures
|
|................................................... | 73%
ordinary text without R code
|
|.................................................... | 74%
label: unnamed-chunk-34
|
|.................................................... | 75%
ordinary text without R code
|
|..................................................... | 76%
label: unnamed-chunk-35
|
|...................................................... | 76%
inline R code fragments
|
|...................................................... | 77%
label: unnamed-chunk-36 (with options)
List of 1
$ message: logi FALSE
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger
|
|....................................................... | 78%
ordinary text without R code
|
|....................................................... | 79%
label: unnamed-chunk-37
'select()' returned many:1 mapping between keys and columns
|
|........................................................ | 80%
ordinary text without R code
|
|........................................................ | 81%
label: unnamed-chunk-38
|
|......................................................... | 82%
inline R code fragments
|
|.......................................................... | 82%
label: unnamed-chunk-39 (with options)
List of 1
$ message: logi FALSE
'select()' returned 1:1 mapping between keys and columns
|
|.......................................................... | 83%
ordinary text without R code
|
|........................................................... | 84%
label: unnamed-chunk-40
|
|........................................................... | 85%
ordinary text without R code
|
|............................................................ | 86%
label: unnamed-chunk-41 (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
|
|............................................................. | 87%
ordinary text without R code
label: simplebroadplot (with options)
List of 3
$ fig.width: num 8
$ fig.asp : num 0.75
$ fig.cap : chr "Coverage tracks for a simple DB event between pro-B and mature B cells, across a broad region in the H3K9ac dat"| __truncated__
|
|.............................................................. | 88%
ordinary text without R code
|
|.............................................................. | 89%
label: unnamed-chunk-42
|
|............................................................... | 90%
ordinary text without R code
|
|................................................................ | 91%
label: unnamed-chunk-43 (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
|
|................................................................ | 92%
ordinary text without R code
|
|................................................................. | 92%
label: complexplot (with options)
List of 3
$ fig.width: num 8
$ fig.asp : num 0.75
$ fig.cap : chr "Coverage tracks for a complex DB event in the H3K9ac data set, shown as per-million values."
|
|................................................................. | 93%
inline R code fragments
|
|.................................................................. | 94%
label: unnamed-chunk-44
|
|.................................................................. | 95%
ordinary text without R code
|
|................................................................... | 96%
label: unnamed-chunk-45 (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
|
|.................................................................... | 97%
ordinary text without R code
label: simplesharpplot (with options)
List of 3
$ fig.width: num 8
$ fig.asp : num 0.75
$ fig.cap : chr "Coverage tracks for a sharp and simple DB event in the H3K9ac data set, shown as per-million values."
|
|..................................................................... | 98%
ordinary text without R code
|
|..................................................................... | 99%
label: unnamed-chunk-46
|
|......................................................................| 100%
ordinary text without R code
output file: work-3-h3k9ac.knit.md
/usr/bin/pandoc +RTS -K512m -RTS work-3-h3k9ac.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-3-h3k9ac.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.8-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc
Output created: work-3-h3k9ac.html
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 9 out-of-bound ranges located on sequences
chr1_GL456212_random, chr1_GL456221_random, chr4_GL456350_random,
chr4_JH584293_random, and chr4_JH584294_random. Note that ranges
located on a sequence whose length is unknown (NA) or on a circular
sequence are not considered out-of-bound (use seqlengths() and
isCircular() to get the lengths and circularity flags of the underlying
sequences). You can use trim() to trim these ranges. See
?`trim,GenomicRanges-method` for more information.
>
>
> knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")
processing file: .buildwebvig/chipseqDB/work-3-h3k9ac.Rmd
|
| | 0%
|
|. | 1%
|
|. | 2%
|
|.. | 3%
|
|... | 4%
|
|... | 5%
|
|.... | 6%
|
|.... | 7%Error in eval(x, envir = envir) : object 'remap' not found
|
|..... | 8%Error in eval(x, envir = envir) : object 'remap' not found
|
|...... | 9%
|
|....... | 10%Error in eval(x, envir = envir) : object 'remap' not found
|
|....... | 11%
|
|........ | 12%Error in eval(x, envir = envir) : object 'remap' not found
|
|........ | 13%
|
|......... | 13%Error in eval(x, envir = envir) : object 'remap' not found
|
|......... | 14%
|
|.......... | 15%Error in eval(x, envir = envir) : object 'remap' not found
|
|.......... | 16%
|
|........... | 17%Error in eval(x, envir = envir) : object 'remap' not found
|
|........... | 18%
|
|............ | 18%Error in eval(x, envir = envir) : object 'redownload' not found
|
|............. | 19%
|
|............. | 20%
|
|.............. | 21%
|
|.............. | 22%Error in eval(x, envir = envir) : object 'remap' not found
|
|............... | 23%
|
|............... | 24%Error in eval(x, envir = envir) : object 'redownload' not found
|
|................ | 24%
|
|................ | 25%
|
|................. | 26%
|
|................. | 27%
|
|.................. | 28%
|
|................... | 29%
|
|.................... | 30%
|
|.................... | 31%
|
|..................... | 32%
|
|..................... | 33%
|
|...................... | 34%
|
|....................... | 35%
|
|....................... | 36%
|
|........................ | 37%
|
|......................... | 38%
|
|......................... | 39%
|
|.......................... | 39%
|
|.......................... | 40%
|
|........................... | 41%
|
|........................... | 42%
|
|............................ | 43%
|
|............................ | 44%
|
|............................. | 45%
|
|.............................. | 46%
|
|............................... | 47%
|
|............................... | 48%
|
|................................ | 49%
|
|................................ | 50%
|
|................................. | 50%
|
|................................. | 51%
|
|.................................. | 52%
|
|.................................. | 53%
|
|................................... | 54%
|
|.................................... | 55%
|
|..................................... | 56%
|
|..................................... | 57%
|
|...................................... | 58%
|
|...................................... | 59%
|
|....................................... | 60%
|
|....................................... | 61%
|
|........................................ | 61%
|
|........................................ | 62%
|
|......................................... | 63%
|
|.......................................... | 64%
|
|.......................................... | 65%
|
|........................................... | 66%
|
|............................................ | 67%
|
|............................................ | 68%
|
|............................................. | 69%
|
|............................................. | 70%
|
|.............................................. | 71%
|
|............................................... | 72%
|
|................................................ | 73%
|
|................................................ | 74%
|
|................................................. | 75%
|
|................................................. | 76%
|
|.................................................. | 76%
|
|.................................................. | 77%
|
|................................................... | 78%
|
|................................................... | 79%
|
|.................................................... | 80%
|
|.................................................... | 81%
|
|..................................................... | 82%
|
|...................................................... | 82%
|
|...................................................... | 83%
|
|....................................................... | 84%
|
|....................................................... | 85%
|
|........................................................ | 86%
|
|........................................................ | 87%
|
|......................................................... | 87%
|
|......................................................... | 88%
|
|.......................................................... | 89%
|
|.......................................................... | 90%
|
|........................................................... | 91%
|
|............................................................ | 92%
|
|............................................................. | 93%
|
|............................................................. | 94%
|
|.............................................................. | 95%
|
|.............................................................. | 96%
|
|............................................................... | 97%
|
|................................................................ | 98%
|
|................................................................ | 99%
|
|.................................................................| 100%
output file: .buildwebvig/chipseqDB/work-3-h3k9ac.R
[1] ".buildwebvig/chipseqDB/work-3-h3k9ac.R"
>
>
> rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")
processing file: work-4-cbp.Rmd
|
| | 0%
|
|. | 2%
inline R code fragments
|
|... | 4%
label: style (with options)
List of 3
$ echo : logi FALSE
$ results: chr "hide"
$ message: logi FALSE
|
|.... | 6%
ordinary text without R code
|
|..... | 8%
label: unnamed-chunk-1
|
|....... | 9%
ordinary text without R code
|
|........ | 11%
label: unnamed-chunk-2 (with options)
List of 2
$ echo : logi FALSE
$ results: chr "hide"
|
|......... | 13%
ordinary text without R code
|
|........... | 15%
label: unnamed-chunk-3 (with options)
List of 1
$ eval: symbol remap
|
|............ | 17%
inline R code fragments
|
|............. | 19%
label: unnamed-chunk-4 (with options)
List of 3
$ eval : symbol remap
$ message: logi FALSE
$ results: chr "hide"
|
|............... | 21%
ordinary text without R code
|
|................ | 23%
label: unnamed-chunk-5 (with options)
List of 2
$ eval : symbol remap
$ results: chr "hide"
|
|................. | 25%
ordinary text without R code
|
|.................. | 26%
label: unnamed-chunk-6 (with options)
List of 3
$ eval : symbol remap
$ echo : logi FALSE
$ results: chr "hide"
|
|.................... | 28%
ordinary text without R code
|
|..................... | 30%
label: unnamed-chunk-7 (with options)
List of 4
$ echo : logi FALSE
$ results: chr "hide"
$ eval : language !remap
$ message: logi FALSE
|
|...................... | 32%
ordinary text without R code
|
|........................ | 34%
label: unnamed-chunk-8 (with options)
List of 4
$ echo : logi FALSE
$ results: chr "hide"
$ eval : symbol redownload
$ message: logi FALSE
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145787.bam'
Content type 'binary/octet-stream' length 1651985856 bytes (1575.5 MB)
==================================================
downloaded 1575.5 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145787.bam.bai'
Content type 'binary/octet-stream' length 6204920 bytes (5.9 MB)
==================================================
downloaded 5.9 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145788.bam'
Content type 'binary/octet-stream' length 1469690293 bytes (1401.6 MB)
==================================================
downloaded 1401.6 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145788.bam.bai'
Content type 'binary/octet-stream' length 6053400 bytes (5.8 MB)
==================================================
downloaded 5.8 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145789.bam'
Content type 'binary/octet-stream' length 2082656812 bytes (1986.2 MB)
==================================================
downloaded 1986.2 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145789.bam.bai'
Content type 'binary/octet-stream' length 6358392 bytes (6.1 MB)
==================================================
downloaded 6.1 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145790.bam'
Content type 'binary/octet-stream' length 1921979447 bytes (1832.9 MB)
==================================================
downloaded 1832.9 MB
trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145790.bam.bai'
Content type 'binary/octet-stream' length 6297216 bytes (6.0 MB)
==================================================
downloaded 6.0 MB
|
|......................... | 36%
ordinary text without R code
|
|.......................... | 38%
label: unnamed-chunk-9
Loading required package: GenomeInfoDb
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, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, 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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
|
|............................ | 40%
inline R code fragments
|
|............................. | 42%
label: unnamed-chunk-10
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply
|
|.............................. | 43%
ordinary text without R code
|
|................................ | 45%
label: unnamed-chunk-11
|
|................................. | 47%
inline R code fragments
|
|.................................. | 49%
label: unnamed-chunk-12
|
|.................................... | 51%
ordinary text without R code
|
|..................................... | 53%
label: unnamed-chunk-13
|
|...................................... | 55%
ordinary text without R code
|
|........................................ | 57%
label: compoplot (with options)
List of 3
$ fig.width: num 12
$ fig.asp : num 0.5
$ fig.cap : chr "Mean-difference plots for the bin counts, comparing library 4 to all other libraries. The red line represents t"| __truncated__
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
|
|......................................... | 58%
ordinary text without R code
|
|.......................................... | 60%
label: unnamed-chunk-14
|
|............................................ | 62%
inline R code fragments
|
|............................................. | 64%
label: unnamed-chunk-15
|
|.............................................. | 66%
ordinary text without R code
|
|................................................ | 68%
label: unnamed-chunk-16
|
|................................................. | 70%
ordinary text without R code
|
|.................................................. | 72%
label: mdsplot (with options)
List of 1
$ fig.cap: chr "MDS plot with two dimensions for all libraries in the CBP data set. Libraries are labelled and coloured accordi"| __truncated__
|
|.................................................... | 74%
ordinary text without R code
|
|..................................................... | 75%
label: unnamed-chunk-17
|
|...................................................... | 77%
ordinary text without R code
|
|....................................................... | 79%
label: unnamed-chunk-18
|
|......................................................... | 81%
ordinary text without R code
|
|.......................................................... | 83%
label: unnamed-chunk-19
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
|
|........................................................... | 85%
ordinary text without R code
|
|............................................................. | 87%
label: unnamed-chunk-20
|
|.............................................................. | 89%
ordinary text without R code
|
|............................................................... | 91%
label: unnamed-chunk-21 (with options)
List of 2
$ results: chr "hide"
$ echo : logi FALSE
|
|................................................................. | 92%
inline R code fragments
|
|.................................................................. | 94%
label: tfplot (with options)
List of 3
$ fig.width: num 8
$ fig.asp : num 0.75
$ fig.cap : chr "Coverage tracks for TF binding sites that are differentially bound in the WT (top two tracks) against the KO (l"| __truncated__
Loading required package: grid
|
|................................................................... | 96%
ordinary text without R code
|
|..................................................................... | 98%
label: unnamed-chunk-22
|
|......................................................................| 100%
ordinary text without R code
output file: work-4-cbp.knit.md
/usr/bin/pandoc +RTS -K512m -RTS work-4-cbp.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-4-cbp.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.8-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc
Output created: work-4-cbp.html
>
>
> knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")
processing file: .buildwebvig/chipseqDB/work-4-cbp.Rmd
|
| | 0%
|
|. | 2%
|
|.. | 4%
|
|.... | 6%
|
|..... | 8%
|
|...... | 9%
|
|....... | 11%
|
|......... | 13%
|
|.......... | 15%Error in eval(x, envir = envir) : object 'remap' not found
|
|........... | 17%
|
|............ | 19%Error in eval(x, envir = envir) : object 'remap' not found
|
|............. | 21%
|
|............... | 23%Error in eval(x, envir = envir) : object 'remap' not found
|
|................ | 25%
|
|................. | 26%Error in eval(x, envir = envir) : object 'remap' not found
|
|.................. | 28%
|
|.................... | 30%Error in eval(x, envir = envir) : object 'remap' not found
|
|..................... | 32%
|
|...................... | 34%Error in eval(x, envir = envir) : object 'redownload' not found
|
|....................... | 36%
|
|......................... | 38%
|
|.......................... | 40%
|
|........................... | 42%
|
|............................ | 43%
|
|............................. | 45%
|
|............................... | 47%
|
|................................ | 49%
|
|................................. | 51%
|
|.................................. | 53%
|
|.................................... | 55%
|
|..................................... | 57%
|
|...................................... | 58%
|
|....................................... | 60%
|
|........................................ | 62%
|
|.......................................... | 64%
|
|........................................... | 66%
|
|............................................ | 68%
|
|............................................. | 70%
|
|............................................... | 72%
|
|................................................ | 74%
|
|................................................. | 75%
|
|.................................................. | 77%
|
|.................................................... | 79%
|
|..................................................... | 81%
|
|...................................................... | 83%
|
|....................................................... | 85%
|
|........................................................ | 87%
|
|.......................................................... | 89%
|
|........................................................... | 91%
|
|............................................................ | 92%
|
|............................................................. | 94%
|
|............................................................... | 96%
|
|................................................................ | 98%
|
|.................................................................| 100%
output file: .buildwebvig/chipseqDB/work-4-cbp.R
[1] ".buildwebvig/chipseqDB/work-4-cbp.R"
>
>