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This page was generated on 2018-05-18 09:51:47 -0400 (Fri, 18 May 2018).
Package 17/21 | Hostname | OS / Arch | INSTALL | BUILD | ||||||
RnaSeqGeneEdgeRQL 1.3.3 Yunshun Chen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK |
Package: RnaSeqGeneEdgeRQL |
Version: 1.3.3 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R")' |
StartedAt: 2018-05-18 08:51:25 -0400 (Fri, 18 May 2018) |
EndedAt: 2018-05-18 08:52:23 -0400 (Fri, 18 May 2018) |
EllapsedTime: 58.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R")' ### ############################################################################## ############################################################################## > rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment") processing file: edgeRQL.Rmd | | | 0% | |. | 1% inline R code fragments | |. | 2% label: setup (with options) List of 3 $ echo : logi FALSE $ results: chr "hide" $ warning: logi FALSE | |.. | 3% ordinary text without R code | |... | 4% label: sra | |.... | 5% ordinary text without R code | |.... | 6% label: group | |..... | 7% ordinary text without R code | |...... | 8% label: checkdownload (with options) List of 3 $ echo : logi FALSE $ results: chr "hide" $ message: logi FALSE trying URL 'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE60450&format=file&file=GSE60450_Lactation-GenewiseCounts.txt.gz' Content type 'application/octet-stream' length 513592 bytes (501 KB) ================================================== downloaded 501 KB | |...... | 9% ordinary text without R code | |....... | 10% label: download (with options) List of 1 $ eval: logi FALSE | |........ | 11% ordinary text without R code | |........ | 12% label: readcounts | |......... | 13% ordinary text without R code | |.......... | 14% label: DGEList (with options) List of 1 $ message: logi FALSE | |........... | 15% ordinary text without R code | |........... | 16% label: symbols (with options) List of 1 $ message: logi FALSE 'select()' returned 1:1 mapping between keys and columns | |............ | 17% ordinary text without R code | |............. | 18% label: dropNAsymbols | |............. | 19% ordinary text without R code | |.............. | 20% label: design | |............... | 21% ordinary text without R code | |................ | 22% label: keep | |................ | 23% ordinary text without R code | |................. | 24% label: filter | |.................. | 25% ordinary text without R code | |.................. | 26% label: aveLogCPM (with options) List of 1 $ fig.cap: chr "Histogram of average log2 CPM." | |................... | 27% ordinary text without R code | |.................... | 28% label: norm | |..................... | 29% ordinary text without R code | |..................... | 30% label: mdsplot (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "MDS plot showing distances between expression profiles. This provides a type of unsupervised clustering of the "| __truncated__ | |...................... | 31% ordinary text without R code | |....................... | 32% label: mdplot1 (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "Mean-difference plot of log2-expression in sample 1 versus the average log2-expression across all other samples"| __truncated__ | |....................... | 33% ordinary text without R code | |........................ | 34% label: mdplot11 (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "Mean-difference plot of log2-expression in sample 11 versus the average log2-expression across all other sample"| __truncated__ | |......................... | 35% ordinary text without R code | |......................... | 36% label: estimateDisp | |.......................... | 37% ordinary text without R code | |........................... | 38% label: plotBCV (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "Scatterplot of the biological coefficient of variation (BCV) against the average abundance of each gene. The pl"| __truncated__ | |............................ | 39% ordinary text without R code | |............................ | 40% label: glmQLFit | |............................. | 41% ordinary text without R code | |.............................. | 42% label: QLDisp (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "A plot of the quarter-root QL dispersion against the average abundance of each gene. Estimates are shown for th"| __truncated__ | |.............................. | 43% ordinary text without R code | |............................... | 44% label: df.prior | |................................ | 45% ordinary text without R code | |................................. | 46% label: B.PvsL | |................................. | 47% ordinary text without R code | |.................................. | 48% label: glmQLFTest | |................................... | 49% ordinary text without R code | |................................... | 51% label: topTags | |.................................... | 52% ordinary text without R code | |..................................... | 53% label: decideTests | |..................................... | 54% ordinary text without R code | |...................................... | 55% label: plotMDfit (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "MD plot showing the log-fold change and average abundance of each gene. Significantly up and down DE genes are "| __truncated__ | |....................................... | 56% ordinary text without R code | |........................................ | 57% label: treat | |........................................ | 58% ordinary text without R code | |......................................... | 59% label: treatdecideTests | |.......................................... | 60% ordinary text without R code | |.......................................... | 61% label: plotMDtreat (with options) List of 3 $ fig.width : num 7 $ fig.height: num 7 $ fig.cap : chr "MD plot showing the log-fold change and average abundance of each gene. Genes with fold-changes significantly g"| __truncated__ | |........................................... | 62% ordinary text without R code | |............................................ | 63% label: cpm | |............................................. | 64% ordinary text without R code | |............................................. | 65% label: order | |.............................................. | 66% ordinary text without R code | |............................................... | 67% label: scale | |............................................... | 68% ordinary text without R code | |................................................ | 69% label: heatmap (with options) List of 4 $ message : logi FALSE $ fig.width : num 8 $ fig.height: num 12 $ fig.cap : chr "Heat map across all the samples using the top 30 most DE genes between the basal lactating group and the basal "| __truncated__ | |................................................. | 70% ordinary text without R code | |................................................. | 71% label: makeContrasts | |.................................................. | 72% ordinary text without R code | |................................................... | 73% label: anovaQLFtest | |.................................................... | 74% ordinary text without R code | |.................................................... | 75% label: complicatedContrasts | |..................................................... | 76% ordinary text without R code | |...................................................... | 77% label: complicatedQLTest | |...................................................... | 78% ordinary text without R code | |....................................................... | 79% label: goana | |........................................................ | 80% ordinary text without R code | |......................................................... | 81% label: kegga | |......................................................... | 82% ordinary text without R code | |.......................................................... | 83% label: select (with options) List of 1 $ message: logi FALSE 'select()' returned 1:1 mapping between keys and columns | |........................................................... | 84% ordinary text without R code | |........................................................... | 85% label: GO2ALLEGS | |............................................................ | 86% ordinary text without R code | |............................................................. | 87% label: fry | |.............................................................. | 88% ordinary text without R code | |.............................................................. | 89% label: barcode (with options) List of 3 $ fig.width : num 8 $ fig.height: num 5 $ fig.cap : chr "Barcode plot showing enrichment of the GO term GO:0032465 in the basal virgin group compared to the basal lacta"| __truncated__ | |............................................................... | 90% ordinary text without R code | |................................................................ | 91% label: camera | |................................................................ | 92% ordinary text without R code | |................................................................. | 93% label: id2indices.Mm.c2 | |.................................................................. | 94% ordinary text without R code | |.................................................................. | 95% label: cam.BVvsLV | |................................................................... | 96% ordinary text without R code | |.................................................................... | 97% label: barcode2 (with options) List of 3 $ fig.width : num 8 $ fig.height: num 6.4 $ fig.cap : chr "Barcode plot showing strong enrichment of mammary stem cell signature in the stem cell vs luminal cell comparis"| __truncated__ | |..................................................................... | 98% ordinary text without R code | |..................................................................... | 99% label: info | |......................................................................| 100% ordinary text without R code output file: edgeRQL.knit.md /usr/bin/pandoc +RTS -K512m -RTS edgeRQL.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output edgeRQL.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: edgeRQL.html > > > knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R") processing file: .buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd | | | 0% | |. | 1% | |. | 2% | |.. | 3% | |... | 4% | |... | 5% | |.... | 6% | |..... | 7% | |..... | 8% | |...... | 9% | |....... | 10% | |....... | 11% | |........ | 12% | |......... | 13% | |......... | 14% | |.......... | 15% | |........... | 16% | |........... | 17% | |............ | 18% | |............ | 19% | |............. | 20% | |.............. | 21% | |.............. | 22% | |............... | 23% | |................ | 24% | |................ | 25% | |................. | 26% | |.................. | 27% | |.................. | 28% | |................... | 29% | |.................... | 30% | |.................... | 31% | |..................... | 32% | |...................... | 33% | |...................... | 34% | |....................... | 35% | |........................ | 36% | |........................ | 37% | 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|.............................................................. | 95% | |.............................................................. | 96% | |............................................................... | 97% | |................................................................ | 98% | |................................................................ | 99% | |.................................................................| 100% output file: .buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R [1] ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R" > >