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