[Bioc-devel] Issues with images in vignette
Sudeep Sahadevan
@udeep@@@h@dev@n @end|ng |rom emb|@de
Thu Nov 19 15:13:24 CET 2020
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.
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> _______________________________________________ Bioc-devel using r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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