Mercurial > repos > lecorguille > xcms_summary
changeset 40:00be6777edc5 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
| author | lecorguille |
|---|---|
| date | Mon, 29 Apr 2019 06:15:21 -0400 |
| parents | 1d2cc6c87acf |
| children | a7db001bfdaf |
| files | README.rst abims_xcms_summary.xml lib.r macros_xcms.xml test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html |
| diffstat | 5 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/README.rst Fri Feb 08 10:04:57 2019 -0500 +++ b/README.rst Mon Apr 29 06:15:21 2019 -0400 @@ -2,9 +2,11 @@ Changelog/News -------------- -**Version 3.4.3.0 - 08/02/2019** +.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 +**Version 3.4.4.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) **Version 3.0.0.0 - 14/02/2018**
--- a/abims_xcms_summary.xml Fri Feb 08 10:04:57 2019 -0500 +++ b/abims_xcms_summary.xml Mon Apr 29 06:15:21 2019 -0400 @@ -8,8 +8,7 @@ </macros> <requirements> - <requirement type="package" version="3.0.0">bioconductor-xcms</requirement> - <requirement type="package" version="1.32.0">bioconductor-camera</requirement> + <requirement type="package" version="1.38.1">bioconductor-camera</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> @@ -87,9 +86,11 @@ Changelog/News -------------- -**Version 3.4.3.0 - 08/02/2019** +.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 +**Version 3.4.4.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) **Version 3.0.0.0 - 14/02/2018**
--- a/lib.r Fri Feb 08 10:04:57 2019 -0500 +++ b/lib.r Mon Apr 29 06:15:21 2019 -0400 @@ -69,7 +69,7 @@ chromBPI_adjusted_merged <- chromBPI_adjusted } else { if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) - else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) + else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") singlefile_merged <- c(singlefile_merged,singlefile) @@ -333,7 +333,7 @@ files[exists] <- sub("//","/",files[exists]) # WHAT IS ON THE FILESYSTEM - filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) + filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] # COMPARISON
--- a/macros_xcms.xml Fri Feb 08 10:04:57 2019 -0500 +++ b/macros_xcms.xml Mon Apr 29 06:15:21 2019 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.4.3</token> + <token name="@WRAPPER_VERSION@">3.4.4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
--- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Fri Feb 08 10:04:57 2019 -0500 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Mon Apr 29 06:15:21 2019 -0400 @@ -84,7 +84,7 @@ <h2>Informations about the XCMSnExp object:</h2> <div><pre> MSn experiment data ("XCMSnExp") -Object size in memory: 1.36 Mb +Object size in memory: 1.41 Mb - - - Spectra data - - - MS level(s): 1 Number of spectra: 5112 @@ -136,7 +136,7 @@ Profile settings: method = bin step = 0.1 -Memory usage: 2.98 MB +Memory usage: 3.11 MB </pre></div> <h2>Citations:</h2> <div><ul>