[Bioc-devel] Issues with images in vignette

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 at r-project.org on behalf of sudeep.sahadevan at 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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