[Bioc-devel] Issues with images in vignette
Mike Smith
gr|mbough @end|ng |rom gm@||@com
Fri Nov 20 00:32:41 CET 2020
Thanks for the information Sudeep.
I'm not sure there should be any changes in BiocStyle between 2.18.0 and
2.19.0 (other than the version number!) but there's clearly something weird
going on. I'll take a look tomorrow and report back in
https://github.com/Bioconductor/BiocStyle/issues/83
Cheers,
Mike
On Thu, 19 Nov 2020 at 15:14, Sudeep Sahadevan <sudeep.sahadevan using embl.de>
wrote:
> Thank you...
> Perhaps I can add some additional info here. I was comparing the
> sessionInfo from my local build based on RELEASE 3_12 docker image (where
> the images are rendered fine) against the sessionInfo from the release
> vignette. This is what I found:
> Packages/Package versions unique to sessionInfo from bioconductor
> release: R6_2.4.1, dbplyr_1.4.4, generics_0.0.2, png_0.1-7,
> xfun_0.18
> Packages/Package versions unique to sessionInfo from local build based on
> RELEASE_3_12 docker image: R6_2.5.0, dbplyr_2.0.0, generics_0.1.0,
> xfun_0.19
> I've pasted both sessionInfos below.
> Kind regards,Sudeep.
> ### sessionInfo from bioconductor release vignette
> ## R Under development (unstable) (2020-10-17 r79346)## Platform:
> x86_64-pc-linux-gnu (64-bit)
> ## Running under: Ubuntu 20.04.1 LTS
> ##
> ## Matrix products: default
> ## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
> ## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
> ##
> ## locale:
> ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
> ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> ## [9] LC_ADDRESS=C LC_TELEPHONE=C
> ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> ##
> ## attached base packages:
> ## [1] parallel stats4 stats graphics grDevices utils
> datasets
> ## [8] methods base
> ##
> ## other attached packages:
> ## [1] data.table_1.13.2 forcats_0.5.0
> ## [3] stringr_1.4.0 dplyr_1.0.2
> ## [5] purrr_0.3.4 readr_1.4.0
> ## [7] tidyr_1.1.2 tibble_3.0.4
> ## [9] ggplot2_3.3.2 tidyverse_1.3.0
> ## [11] IHW_1.19.0 DEWSeq_1.5.0
> ## [13] BiocParallel_1.25.0 DESeq2_1.31.0
> ## [15] SummarizedExperiment_1.21.0 Biobase_2.51.0
> ## [17] MatrixGenerics_1.3.0 matrixStats_0.57.0
> ## [19] GenomicRanges_1.43.0 GenomeInfoDb_1.27.0
> ## [21] IRanges_2.25.0 S4Vectors_0.29.0
> ## [23] BiocGenerics_0.37.0 R.utils_2.10.1
> ## [25] R.oo_1.24.0 R.methodsS3_1.8.1
> ## [27] BiocStyle_2.19.0
> ##
> ## loaded via a namespace (and not attached):
> ## [1] fs_1.5.0 bitops_1.0-6 lubridate_1.7.9
>
> ## [4] bit64_4.0.5 RColorBrewer_1.1-2 httr_1.4.2
>
> ## [7] tools_4.1.0 backports_1.1.10 utf8_1.1.4
>
> ## [10] R6_2.4.1 DBI_1.1.0 colorspace_1.4-1
>
> ## [13] withr_2.3.0 tidyselect_1.1.0 bit_4.0.4
>
> ## [16] compiler_4.1.0 fdrtool_1.2.15 cli_2.1.0
>
> ## [19] rvest_0.3.6 xml2_1.3.2 DelayedArray_0.17.0
>
> ## [22] bookdown_0.21 slam_0.1-47 scales_1.1.1
>
> ## [25] genefilter_1.73.0 digest_0.6.27 rmarkdown_2.5
>
> ## [28] XVector_0.31.0 pkgconfig_2.0.3 htmltools_0.5.0
>
> ## [31] lpsymphony_1.19.0 dbplyr_1.4.4 highr_0.8
>
> ## [34] readxl_1.3.1 rlang_0.4.8 rstudioapi_0.11
>
> ## [37] RSQLite_2.2.1 generics_0.0.2 jsonlite_1.7.1
>
> ## [40] RCurl_1.98-1.2 magrittr_1.5
> GenomeInfoDbData_1.2.4
> ## [43] Matrix_1.2-18 fansi_0.4.1 Rcpp_1.0.5
>
> ## [46] munsell_0.5.0 lifecycle_0.2.0 stringi_1.5.3
>
> ## [49] yaml_2.2.1 zlibbioc_1.37.0 grid_4.1.0
>
> ## [52] blob_1.2.1 crayon_1.3.4 lattice_0.20-41
>
> ## [55] haven_2.3.1 splines_4.1.0 annotate_1.69.0
>
> ## [58] hms_0.5.3 magick_2.5.0 locfit_1.5-9.4
>
> ## [61] ps_1.4.0 knitr_1.30 pillar_1.4.6
>
> ## [64] geneplotter_1.69.0 reprex_0.3.0 XML_3.99-0.5
>
> ## [67] glue_1.4.2 evaluate_0.14 modelr_0.1.8
>
> ## [70] BiocManager_1.30.10 png_0.1-7 vctrs_0.3.4
>
> ## [73] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
>
> ## [76] xfun_0.18 xtable_1.8-4 broom_0.7.2
>
> ## [79] survival_3.2-7 AnnotationDbi_1.53.0 memoise_1.1.0
>
> ## [82] ellipsis_0.3.1
>
> ### sessionInfo from local build based on RELEAE_3_12 docker image
> ## R version 4.0.3 (2020-10-10)
> ## Platform: x86_64-pc-linux-gnu (64-bit)
> ## Running under: Ubuntu 20.04 LTS
> ##
> ## Matrix products: default
> ## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/
> libopenblasp-r0.3.8.so
> ##
> ## locale:
> ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
> ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> ## [9] LC_ADDRESS=C LC_TELEPHONE=C
> ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> ##
> ## attached base packages:
> ## [1] parallel stats4 stats graphics grDevices utils
> datasets
> ## [8] methods base
> ##
> ## other attached packages:
> ## [1] data.table_1.13.2 forcats_0.5.0
> ## [3] stringr_1.4.0 dplyr_1.0.2
> ## [5] purrr_0.3.4 readr_1.4.0
> ## [7] tidyr_1.1.2 tibble_3.0.4
> ## [9] ggplot2_3.3.2 tidyverse_1.3.0
> ## [11] IHW_1.18.0 DEWSeq_1.4.0
> ## [13] BiocParallel_1.24.0 DESeq2_1.30.0
> ## [15] SummarizedExperiment_1.20.0 Biobase_2.50.0
> ## [17] MatrixGenerics_1.2.0 matrixStats_0.57.0
> ## [19] GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
> ## [21] IRanges_2.24.0 S4Vectors_0.28.0
> ## [23] BiocGenerics_0.36.0 R.utils_2.10.1
> ## [25] R.oo_1.24.0 R.methodsS3_1.8.1
> ## [27] BiocStyle_2.18.0
> ##
> ## loaded via a namespace (and not attached):
> ## [1] fs_1.5.0 bitops_1.0-6 lubridate_1.7.9
>
> ## [4] bit64_4.0.5 RColorBrewer_1.1-2 httr_1.4.2
>
> ## [7] tools_4.0.3 backports_1.1.10 utf8_1.1.4
>
> ## [10] R6_2.5.0 DBI_1.1.0 colorspace_1.4-1
>
> ## [13] withr_2.3.0 tidyselect_1.1.0 bit_4.0.4
>
> ## [16] compiler_4.0.3 fdrtool_1.2.15 cli_2.1.0
>
> ## [19] rvest_0.3.6 xml2_1.3.2 DelayedArray_0.16.0
>
> ## [22] bookdown_0.21 slam_0.1-47 scales_1.1.1
>
> ## [25] genefilter_1.72.0 digest_0.6.27 rmarkdown_2.5
>
> ## [28] XVector_0.30.0 pkgconfig_2.0.3 htmltools_0.5.0
>
> ## [31] lpsymphony_1.18.0 dbplyr_2.0.0 highr_0.8
>
> ## [34] readxl_1.3.1 rlang_0.4.8 rstudioapi_0.11
>
> ## [37] RSQLite_2.2.1 generics_0.1.0 jsonlite_1.7.1
>
> ## [40] RCurl_1.98-1.2 magrittr_1.5
> GenomeInfoDbData_1.2.4
> ## [43] Matrix_1.2-18 fansi_0.4.1 Rcpp_1.0.5
>
> ## [46] munsell_0.5.0 lifecycle_0.2.0 stringi_1.5.3
>
> ## [49] yaml_2.2.1 zlibbioc_1.36.0 grid_4.0.3
>
> ## [52] blob_1.2.1 crayon_1.3.4 lattice_0.20-41
>
> ## [55] haven_2.3.1 splines_4.0.3 annotate_1.68.0
>
> ## [58] hms_0.5.3 magick_2.5.0 locfit_1.5-9.4
>
> ## [61] ps_1.4.0 knitr_1.30 pillar_1.4.6
>
> ## [64] geneplotter_1.68.0 reprex_0.3.0 XML_3.99-0.5
>
> ## [67] glue_1.4.2 evaluate_0.14 BiocManager_1.30.10
>
> ## [70] modelr_0.1.8 vctrs_0.3.4 cellranger_1.1.0
>
> ## [73] gtable_0.3.0 assertthat_0.2.1 xfun_0.19
>
> ## [76] xtable_1.8-4 broom_0.7.2 survival_3.2-7
>
> ## [79] AnnotationDbi_1.52.0 memoise_1.1.0 ellipsis_0.3.1
>
> On Thu, 2020-11-19 at 13:45 +0000, Martin Morgan wrote:
> > Nice images!
> > If I narrow the browser window, the figures appear!
> > When I 'inspect' the source, for instance for 'Figure 4: chance of cross
> talk' I see that the image has tag <img ... class="smallfigure"> whereas
> figures that show up have class="widefigure".
> > I guess smallfigure is because in the Rmd there is
> > ```{r, fig.cap = "Chance of crosslinking", fig.small = TRUE, echo =
> FALSE}# fig.width=200,
> out.width="200px"knitr::include_graphics("crosslinking_chance.png")```
> > So this looks like a bug in BiocStyle...
> > I opened an issue at
> > https://github.com/Bioconductor/BiocStyle/issues/83
> >
> > Martin
> > On 11/19/20, 8:28 AM, "Bioc-devel on behalf of Sudeep Sahadevan" <
> bioc-devel-bounces using r-project.org on behalf of sudeep.sahadevan using embl.de>
> wrote:
> > Dear all,
> > We are facing some issues with the html vignette of our package
> DEWSeq (
> https://bioconductor.org/packages/release/bioc/vignettes/DEWSeq/inst/doc/DEWSeq.html).
> The issue is that some of the images are rendered too small and for a
> couple of images, the size of the final rendered images is 0 x 0 pixels
> (that is, only the figure captions are visible). What I've also noticed
> is that this issue does not occur when I build package locally based on the
> bioconductor docker image for RELEASE_3_12 (
> https://hub.docker.com/layers/bioconductor/bioconductor_docker/RELEASE_3_12/images/sha256-9f9d1d481e51e335db273621e82841117851b0de4e28984a7b3ada03b32046ad?context=explore
> > ). I'm not entirely sure what is going on here. Have you faced this
> issue/ do you have any suggestions ?
> > Thank you in advance,
> > Kind regards, Sudeep Sahadevan.
> > [[alternative HTML version deleted]]
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