Rmarkdown html plots absent

rmarkdown

#1

Hi,

I have recently updated R and my packages. After the update, one script based upon the package DESeq2 fails to output the plots to the html file. Warnings are generated for each plot:

17: running command 'C:\Windows\system32\cmd.exe /c convert "DESeq2_Figures/Heatmaps-2.png" -trim "DESeq2_Figures/Heatmaps-2.png"' had status 4
18: In shell(paste(c(cmd, args), collapse = " ")) :
  'convert "DESeq2_Figures/Heatmaps-2.png" -trim "DESeq2_Figures/Heatmaps-2.png"' execution failed with error code 4

The .png figures output correctly to a file even though they are not present in the html report.
In the report I see this,

\end{kframe}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/MAplot-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/MAplot-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/dispest-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/dispest-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/Histograms-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/Histograms-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/Barplot_pvalue_vs_counts-1} \end{adjustwidth}
\begin{adjustwidth}{}{0mm} [width=100%]{DESeq2_Figures/Barplot_pvalue_vs_counts-1} \end{adjustwidth}
\begin{kframe}

I do not have the same error in another r markdown script based upon the package phyloseq. I have tried eliminating spaces and characters from my .rmd file name. I have loaded packages caTools and httpuv. I have tried running the script in the same volume as my R and RStudio installation.

Here is an example of the plot code:

```{r MAplot}
pdf(paste("DESeq2 MA Plot.pdf"))
plotMA(resCooks, ylim = c(-6,6))
dev.off()

plotMA(resCooks, ylim = c(-6,6))

I am not a developer so please provide technical details step by step or refer me to an answer if the answer to this issue is not simple.

Regards,

Susan

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] RColorBrewer_1.1-2         dplyr_0.7.4                plyr_1.8.4                
 [4] gplots_3.0.1               genefilter_1.60.0          lattice_0.20-35           
 [7] gtools_3.5.0               DESeq2_1.18.1              SummarizedExperiment_1.8.1
[10] DelayedArray_0.4.1         matrixStats_0.52.2         Biobase_2.38.0            
[13] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0        IRanges_2.12.0            
[16] S4Vectors_0.16.0           BiocGenerics_0.24.0        ape_5.0                   
[19] phyloseq_1.23.1           

loaded via a namespace (and not attached):
 [1] nlme_3.1-131           bitops_1.0-6           bit64_0.9-7           
 [4] rprojroot_1.3-2        tools_3.4.3            backports_1.1.2       
 [7] R6_2.2.2               vegan_2.4-5            rpart_4.1-11          
[10] KernSmooth_2.23-15     Hmisc_4.1-1            DBI_0.7               
[13] lazyeval_0.2.1         mgcv_1.8-22            colorspace_1.3-2      
[16] permute_0.9-4          ade4_1.7-10            nnet_7.3-12           
[19] gridExtra_2.3          bit_1.1-12             compiler_3.4.3        
[22] formatR_1.5            htmlTable_1.11.1       caTools_1.17.1        
[25] scales_0.5.0           checkmate_1.8.5        stringr_1.2.0         
[28] digest_0.6.13          foreign_0.8-69         rmarkdown_1.8         
[31] XVector_0.18.0         base64enc_0.1-3        pkgconfig_2.0.1       
[34] htmltools_0.3.6        htmlwidgets_0.9        rlang_0.1.6           
[37] rstudioapi_0.7         RSQLite_2.0            bindr_0.1             
[40] jsonlite_1.5           BiocParallel_1.12.0    acepack_1.4.1         
[43] RCurl_1.95-4.10        magrittr_1.5           GenomeInfoDbData_1.0.0
[46] Formula_1.2-2          biomformat_1.6.0       Matrix_1.2-12         
[49] Rcpp_0.12.14           munsell_0.4.3          stringi_1.1.6         
[52] yaml_2.1.16            MASS_7.3-48            zlibbioc_1.24.0       
[55] rhdf5_2.22.0           grid_3.4.3             blob_1.1.0            
[58] gdata_2.18.0           Biostrings_2.46.0      splines_3.4.3         
[61] multtest_2.34.0        annotate_1.56.1        locfit_1.5-9.1        
[64] knitr_1.18             pillar_1.0.1           igraph_1.1.2          
[67] geneplotter_1.56.0     reshape2_1.4.3         codetools_0.2-15      
[70] glue_1.2.0             XML_3.98-1.9           evaluate_0.10.1       
[73] latticeExtra_0.6-28    data.table_1.10.4-3    foreach_1.4.4         
[76] gtable_0.2.0           assertthat_0.2.0       ggplot2_2.2.1         
[79] xtable_1.8-2           survival_2.41-3        tibble_1.4.1          
[82] iterators_1.0.9        AnnotationDbi_1.40.0   memoise_1.1.0         
[85] bindrcpp_0.2           cluster_2.0.6          BiocStyle_2.6.1