Matthew Ritchie
| Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018) |
| URL: https://git.bioconductor.org/packages/RNAseq123 |
| Branch: RELEASE_3_7 |
| Last Commit: 662df8f |
| Last Changed Date: 2018-04-30 10:07:09 -0400 (Mon, 30 Apr 2018) |
| Back to Workflows build report for BioC 3.7 |
This page was generated on 2018-05-18 12:48:06 -0400 (Fri, 18 May 2018).
| Package 15/21 | Hostname | OS / Arch | INSTALL | BUILD | BUILD WEB VIG | ||||||
| RNAseq123 1.2.0 Matthew Ritchie
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: RNAseq123 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", ".buildwebvig/RNAseq123/limmaWorkflow.R")' |
| StartedAt: 2018-05-18 08:48:45 -0400 (Fri, 18 May 2018) |
| EndedAt: 2018-05-18 08:49:34 -0400 (Fri, 18 May 2018) |
| EllapsedTime: 48.6 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", ".buildwebvig/RNAseq123/limmaWorkflow.R")'
###
##############################################################################
##############################################################################
> rmarkdown::render(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", output_format="BiocStyle:::html_fragment")
processing file: limmaWorkflow.Rmd
|
| | 0%
|
|. | 2%
inline R code fragments
|
|.. | 3%
label: setup (with options)
List of 2
$ message: logi FALSE
$ echo : logi FALSE
|
|... | 5%
ordinary text without R code
|
|.... | 6%
label: setup2 (with options)
List of 1
$ eval: logi TRUE
|
|...... | 8%
ordinary text without R code
|
|....... | 10%
label: downloadData
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63310&format=file'
Content type 'application/x-tar' length 1996800 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
|
|........ | 11%
ordinary text without R code
|
|......... | 13%
label: import1
|
|.......... | 14%
ordinary text without R code
|
|........... | 16%
label: import2
|
|............ | 17%
ordinary text without R code
|
|............. | 19%
label: annotatesamples
|
|.............. | 21%
ordinary text without R code
|
|................ | 22%
label: annotategenes (with options)
List of 1
$ message: logi FALSE
'select()' returned 1:many mapping between keys and columns
|
|................. | 24%
ordinary text without R code
|
|.................. | 25%
label: removedups
|
|................... | 27%
ordinary text without R code
|
|.................... | 29%
label: assigngeneanno
|
|..................... | 30%
ordinary text without R code
|
|...................... | 32%
label: cpm
|
|....................... | 33%
ordinary text without R code
|
|........................ | 35%
label: zeroes
|
|.......................... | 37%
ordinary text without R code
|
|........................... | 38%
label: filter
|
|............................ | 40%
ordinary text without R code
|
|............................. | 41%
label: filterplot1 (with options)
List of 3
$ fig.height: num 4
$ fig.width : num 8
$ fig.cap : chr "The density of log-CPM values for raw pre-filtered data (A) and post-filtered data (B) are shown for each sampl"| __truncated__
|
|.............................. | 43%
ordinary text without R code
|
|............................... | 44%
label: normalize
|
|................................ | 46%
ordinary text without R code
|
|................................. | 48%
label: normalizemodifieddata
|
|.................................. | 49%
ordinary text without R code
|
|.................................... | 51%
label: plotmodifieddata (with options)
List of 3
$ fig.height: num 4
$ fig.width : num 8
$ fig.cap : chr "Example data: Boxplots of log-CPM values showing expression distributions for unnormalised data (A) and normali"| __truncated__
|
|..................................... | 52%
ordinary text without R code
|
|...................................... | 54%
label: MDS1 (with options)
List of 3
$ fig.height: num 4
$ fig.width : num 8
$ fig.cap : chr "MDS plots of log-CPM values over dimensions 1 and 2 with samples coloured and labeled by sample groups (A) and "| __truncated__
|
|....................................... | 56%
ordinary text without R code
|
|........................................ | 57%
label: GlimmaMDSplot
|
|......................................... | 59%
ordinary text without R code
|
|.......................................... | 60%
label: design
|
|........................................... | 62%
ordinary text without R code
|
|............................................ | 63%
label: contrasts
|
|.............................................. | 65%
ordinary text without R code
|
|............................................... | 67%
label: voom (with options)
List of 3
$ fig.height: num 4
$ fig.width : num 8
$ plot.cap : chr "Means (x-axis) and variances (y-axis) of each gene are plotted to show the dependence between the two before `v"| __truncated__
|
|................................................ | 68%
ordinary text without R code
|
|................................................. | 70%
label: decidetests
|
|.................................................. | 71%
ordinary text without R code
|
|................................................... | 73%
label: treat
|
|.................................................... | 75%
ordinary text without R code
|
|..................................................... | 76%
label: venn (with options)
List of 3
$ fig.height: num 6
$ fig.width : num 6
$ fig.cap : chr "Venn diagram showing the number of genes DE in the comparison between basal versus LP only (left), basal versus"| __truncated__
|
|...................................................... | 78%
ordinary text without R code
|
|........................................................ | 79%
label: toptables
|
|......................................................... | 81%
ordinary text without R code
|
|.......................................................... | 83%
label: MDplot (with options)
List of 1
$ fig.keep: chr "none"
|
|........................................................... | 84%
ordinary text without R code
|
|............................................................ | 86%
label: GlimmaMDplot
|
|............................................................. | 87%
ordinary text without R code
|
|.............................................................. | 89%
label: heatmap (with options)
List of 4
$ fig.height: num 10
$ fig.width : num 7
$ fig.cap : chr "Heatmap of log-CPM values for top 100 genes DE in basal versus LP. Expression across each gene (or row) have be"| __truncated__
$ message : logi FALSE
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
|
|............................................................... | 90%
ordinary text without R code
|
|................................................................ | 92%
label: camera
|
|.................................................................. | 94%
ordinary text without R code
|
|................................................................... | 95%
label: barcodeplot (with options)
List of 3
$ fig.height: num 6
$ fig.width : num 6
$ fig.cap : chr "Barcode plot of `LIM_MAMMARY_LUMINAL_MATURE_UP` (red bars, top of plot) and `LIM_MAMMARY_LUMINAL_MATURE_DN` (bl"| __truncated__
|
|.................................................................... | 97%
ordinary text without R code
|
|..................................................................... | 98%
label: softwareinfo
|
|......................................................................| 100%
ordinary text without R code
output file: limmaWorkflow.knit.md
/usr/bin/pandoc +RTS -K512m -RTS limmaWorkflow.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output limmaWorkflow.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.7-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: limmaWorkflow.html
>
>
> knitr::purl(".buildwebvig/RNAseq123/limmaWorkflow.Rmd", ".buildwebvig/RNAseq123/limmaWorkflow.R")
processing file: .buildwebvig/RNAseq123/limmaWorkflow.Rmd
|
| | 0%
|
|. | 2%
|
|.. | 3%
|
|... | 5%
|
|.... | 6%
|
|..... | 8%
|
|...... | 10%
|
|....... | 11%
|
|........ | 13%
|
|......... | 14%
|
|.......... | 16%
|
|........... | 17%
|
|............ | 19%
|
|............. | 21%
|
|.............. | 22%
|
|............... | 24%
|
|................. | 25%
|
|.................. | 27%
|
|................... | 29%
|
|.................... | 30%
|
|..................... | 32%
|
|...................... | 33%
|
|....................... | 35%
|
|........................ | 37%
|
|......................... | 38%
|
|.......................... | 40%
|
|........................... | 41%
|
|............................ | 43%
|
|............................. | 44%
|
|.............................. | 46%
|
|............................... | 48%
|
|................................ | 49%
|
|................................. | 51%
|
|.................................. | 52%
|
|................................... | 54%
|
|.................................... | 56%
|
|..................................... | 57%
|
|...................................... | 59%
|
|....................................... | 60%
|
|........................................ | 62%
|
|......................................... | 63%
|
|.......................................... | 65%
|
|........................................... | 67%
|
|............................................ | 68%
|
|............................................. | 70%
|
|.............................................. | 71%
|
|............................................... | 73%
|
|................................................ | 75%
|
|.................................................. | 76%
|
|................................................... | 78%
|
|.................................................... | 79%
|
|..................................................... | 81%
|
|...................................................... | 83%
|
|....................................................... | 84%
|
|........................................................ | 86%
|
|......................................................... | 87%
|
|.......................................................... | 89%
|
|........................................................... | 90%
|
|............................................................ | 92%
|
|............................................................. | 94%
|
|.............................................................. | 95%
|
|............................................................... | 97%
|
|................................................................ | 98%
|
|.................................................................| 100%
output file: .buildwebvig/RNAseq123/limmaWorkflow.R
[1] ".buildwebvig/RNAseq123/limmaWorkflow.R"
>
>