From 2d626e73c1e3b9750bf9f0385d86d432cc8fe9c1 Mon Sep 17 00:00:00 2001 From: Leonardo Collado Torres Date: Fri, 24 Apr 2020 01:30:46 -0400 Subject: [PATCH] v1.21.11 -- Expand on the magick::image_trim() problem and the workaround taken This is also an opportunity to link to the relevant GitHub issues and Bioc-devel threads. Cropping images through `magick::image_trim()` as done by default by `BiocStyle::html_document()` can fail on Linux. This could be an ImageMagick issue or an issue about lack of resources. The full investigative report is at https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016650.html. This is related to: https://github.com/yihui/knitr/issues/1785#issuecomment-574723631 https://github.com/yihui/knitr/issues/1796 https://github.com/Bioconductor/BiocStyle/issues/65#issuecomment-552832630 https://github.com/ropensci/magick/issues/171 https://github.com/ropensci/magick/issues/194 In regionReport version 1.21.10 I have opted by using `crop = NULL` to disable cropping of images by `BiocStyle::html_document()` and thus avoid the issues with `ImageMagick` either coming from `magick`, from the version of `ImageMagick` installed on the Linux Bioconductor build machine and devel docker, or from resources in these two Linux environments as described in the investigative report. About a month ago I also saw failures on Windows on Bioc 3.10. Whether they were caused by ggbio 1.35.1 or this issue will remain a mystery. But it's likely that this `magick::image_trim()` issue also affected the Bioconductor windows builder. The related bioc-devel threads are: https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016365.html --- DESCRIPTION | 2 +- NEWS.md | 28 ++++++++++++++++++++++++++++ 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6c4f08b..c3183c1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: regionReport Type: Package Title: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results -Version: 1.21.10 +Version: 1.21.11 Date: 2020-04-23 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")), diff --git a/NEWS.md b/NEWS.md index 1db5945..dba280a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,31 @@ +# regionReport 1.21.11 + +BUG FIXES + +* Cropping images through `magick::image_trim()` as done by default by +`BiocStyle::html_document()` can fail on Linux. This could be an ImageMagick +issue or an issue about lack of resources. The full investigative report is at +https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016650.html. +This is related to: +https://github.com/yihui/knitr/issues/1785#issuecomment-574723631 +https://github.com/yihui/knitr/issues/1796 +https://github.com/Bioconductor/BiocStyle/issues/65#issuecomment-552832630 +https://github.com/ropensci/magick/issues/171 +https://github.com/ropensci/magick/issues/194 +In regionReport version 1.21.10 I have opted by using `crop = NULL` to disable +cropping of images by `BiocStyle::html_document()` and thus avoid the +issues with `ImageMagick` either coming from `magick`, from the version of +`ImageMagick` installed on the Linux Bioconductor build machine and devel +docker, or from resources in these two Linux environments as described in the +investigative report. +About a month ago I also saw failures on Windows on Bioc 3.10. Whether they were +caused by ggbio 1.35.1 or this issue will remain a mystery. But it's likely +that this `magick::image_trim()` issue also affected the Bioconductor windows +builder. +The related bioc-devel threads are: +https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html +https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016365.html + # regionReport 1.21.10 BUG FIXES