graph2ppt connection error when exporting Seurat FeaturePlot in R 4.2 Rmarkdown

[JesseRop]

Dear developer,

Many thanks for the great tool! Very handy. I'll be grateful for your assistance with the issue below.

I updated my rstudio to the latest version and R to 4.2 and now not able to export getting the error _'Warning in .Internal(environment(fun)) : closing unused connection 3 (/var/folders/9h/zbzv_b3j3wz2r6mdgw9s2p04000lw8/T//RtmpkTyPis/filee19561b44ad/raster-rId000002.png) Warning: cannot open file '/var/folders/9h/zbzvb3j3wz2r6mdgw9s2p04000lw8/T//RtmpkTyPis/filee197fc756a/raster-rId000002.png': No such file or directoryError in open.connection(con, "rb") : cannot open the connection'

I have tried making a reproducible example with the dataset loaded into pbmc found here ( https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz )

The code can be run in rmarkdown as below

---

title: "export trial" output: html_document date: "2023-01-25"

knitr::opts_chunk$set(echo = TRUE)

library(dplyr)
library(Seurat)
library(export)

# Load the PBMC dataset
pbmc.data <- Read10X(data.dir = "/Users/jr35/Google Drive/My Drive/PHD_documents/trial_datasets/filtered_gene_bc_matrices/hg19/")
# Initialize the Seurat object with the raw (non-normalized data).
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)

pbmc <- FindVariableFeatures(pbmc, selection.method = "vst", nfeatures = 2000)

pbmc <- ScaleData(pbmc)
pbmc <- RunPCA(pbmc, features = VariableFeatures(object = pbmc))

pbmc <- FindNeighbors(pbmc, dims = 1:10)
pbmc <- FindClusters(pbmc, resolution = 0.5)

pbmc <- RunUMAP(pbmc, dims = 1:10)

Plotting and exporting

FeaturePlot(pbmc, features = "CCR7", dims = c(1,2), pt.size = 1.5, label = T, label.size = 5, repel = T) 
graph2ppt(file = '/Users/jr35/Google Drive/My Drive/PHD_documents/test_exp.ppt')

The output of session info is below

sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] gdtools_0.3.0      export_0.3.0       patchwork_1.1.2    SeuratObject_4.1.3 Seurat_4.3.0       dplyr_1.0.10      

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  spatstat.explore_3.0-5      reticulate_1.27             tidyselect_1.2.0           
  [5] RSQLite_2.2.20              AnnotationDbi_1.60.0        htmlwidgets_1.6.1           grid_4.2.2                 
  [9] BiocParallel_1.32.5         Rtsne_0.16                  scatterpie_0.1.8            munsell_0.5.0              
 [13] codetools_0.2-18            ica_1.0-3                   future_1.30.0               miniUI_0.1.1.1             
 [17] withr_2.5.0                 spatstat.random_3.1-3       colorspace_2.1-0            GOSemSim_2.24.0            
 [21] progressr_0.13.0            Biobase_2.58.0              uuid_1.1-0                  knitr_1.42                 
 [25] rstudioapi_0.14             stats4_4.2.2                SingleCellExperiment_1.20.0 ROCR_1.0-11                
 [29] officer_0.5.1               tensor_1.5                  DOSE_3.25.0.002             listenv_0.9.0              
 [33] labeling_0.4.2              MatrixGenerics_1.10.0       GenomeInfoDbData_1.2.9      polyclip_1.10-4            
 [37] bit64_4.0.5                 farver_2.1.1                pheatmap_1.0.12             downloader_0.4             
 [41] treeio_1.22.0               parallelly_1.34.0           vctrs_0.5.2                 generics_0.1.3             
 [45] gson_0.0.9                  xfun_0.36                   qpdf_1.3.0                  R6_2.5.1                   
 [49] GenomeInfoDb_1.34.6         graphlayouts_0.8.4          bitops_1.0-7                spatstat.utils_3.0-1       
 [53] cachem_1.0.6                reshape_0.8.9               fgsea_1.24.0                gridGraphics_0.5-1         
 [57] DelayedArray_0.24.0         assertthat_0.2.1            promises_1.2.0.1            scales_1.2.1               
 [61] ggraph_2.1.0                enrichplot_1.19.1.991       gtable_0.3.1                globals_0.16.2             
 [65] goftest_1.2-3               tidygraph_1.2.2             rlang_1.0.6                 systemfonts_1.0.4          
 [69] splines_4.2.2               lazyeval_0.2.2              broom_1.0.3                 spatstat.geom_3.0-5        
 [73] rgl_1.0.1                   yaml_2.3.7                  reshape2_1.4.4              abind_1.4-5                
 [77] backports_1.4.1             httpuv_1.6.8                qvalue_2.30.0               clusterProfiler_4.7.0      
 [81] tools_4.2.2                 ggplotify_0.1.0             ggplot2_3.4.0               ellipsis_0.3.2             
 [85] RColorBrewer_1.1-3          BiocGenerics_0.44.0         stargazer_5.2.3             ggridges_0.5.4             
 [89] devEMF_4.2                  Rcpp_1.0.10                 plyr_1.8.8                  base64enc_0.1-3            
 [93] zlibbioc_1.44.0             purrr_1.0.1                 RCurl_1.98-1.9              openssl_2.0.5              
 [97] deldir_1.0-6                pbapply_1.7-0               viridis_0.6.2               cowplot_1.1.1              
[101] S4Vectors_0.36.1            zoo_1.8-11                  SummarizedExperiment_1.28.0 ggrepel_0.9.2              
[105] cluster_2.1.4               crul_1.3                    magrittr_2.0.3              data.table_1.14.6          
[109] scattermore_0.8             openxlsx_4.2.5.1            flextable_0.8.4             lmtest_0.9-40              
[113] RANN_2.6.1                  fitdistrplus_1.1-8          matrixStats_0.63.0          mime_0.12                  
[117] evaluate_0.20               xtable_1.8-4                HDO.db_0.99.1               readxl_1.4.1               
[121] IRanges_2.32.0              gridExtra_2.3               compiler_4.2.2              tibble_3.1.8               
[125] shadowtext_0.1.2            KernSmooth_2.23-20          crayon_1.5.2                htmltools_0.5.4            
[129] ggfun_0.0.9                 later_1.3.0                 tidyr_1.3.0                 aplot_0.1.9                
[133] DBI_1.1.3                   tweenr_2.0.2                MASS_7.3-58.2               Matrix_1.5-3               
[137] cli_3.6.0                   parallel_4.2.2              igraph_1.3.5                GenomicRanges_1.50.2       
[141] pkgconfig_2.0.3             sp_1.6-0                    plotly_4.10.1               spatstat.sparse_3.0-0      
[145] xml2_1.3.3                  ggtree_3.6.2                XVector_0.38.0              rvg_0.3.2                  
[149] yulab.utils_0.0.6           stringr_1.5.0               digest_0.6.31               sctransform_0.3.5          
[153] RcppAnnoy_0.0.20            httpcode_0.3.0              spatstat.data_3.0-0         Biostrings_2.66.0          
[157] rmarkdown_2.20              cellranger_1.1.0            leiden_0.4.3                fastmatch_1.1-3            
[161] tidytree_0.4.2              uwot_0.1.14                 curl_5.0.0                  shiny_1.7.4                
[165] lifecycle_1.0.3             nlme_3.1-161                jsonlite_1.8.4              askpass_1.1                
[169] viridisLite_0.4.1           fansi_1.0.4                 pillar_1.8.1                lattice_0.20-45            
[173] GGally_2.1.2                KEGGREST_1.38.0             fastmap_1.1.0               httr_1.4.4                 
[177] survival_3.5-0              GO.db_3.16.0                glue_1.6.2                  zip_2.2.2                  
[181] png_0.1-8                   bit_4.0.5                   ggforce_0.4.1               stringi_1.7.12             
[185] blob_1.2.3                  gfonts_0.2.0                pdftools_3.3.2              memoise_2.0.1              
[189] irlba_2.3.5.1               future.apply_1.10.0         ape_5.6-2                  

[tomwenseleers]

Hmm thanks for the bug report. I can confirm that

library(Seurat)
data("pbmc_small")
pl = FeaturePlot(object = pbmc_small, features = 'PC_1')
graph2ppt(x=pl, file="./test.pptx", width=7, height=5)

also produces the error

Error in open.connection(con, "rb") : cannot open the connection
In addition: Warning message:
In open.connection(con, "rb") :
  cannot open file 'C:\Users\bherr\AppData\Local\Temp\RtmpCQqwZP\file1f6849f02517/raster-rId000002.png': No such file or directory

for me - haven't figured out yet where that is coming from...

graph2doc(x=pl, file="./test.docx", width=7, height=5) does seem to work though, if that's of any help...

Will try to look a bit further where this is coming from...

[xjin15]

I have the similar problem, and I have just updated all my R CRAN packages 3 hours ago. But I found that the ggplot object (like plots made through ggsurvplot() and ggplot2() function ) works fine, but the plotsI build through dotplot() function using the enrichr package for enrichment analysis got the error. I hope my experience will help to find the bug.

> ggsurvplot(fit, data = lung)
> export::graph2ppt(file = './output/test.pptx',append=T)
Exported graph as ./output/test.pptx
> ggplot(df, aes(gp, y)) +
+   geom_point()
> export::graph2ppt(file = './output/test.pptx',append=T)
Exported graph as ./output/test.pptx
> dotplot(Case_go)
> export::graph2ppt(file = './output/test.pptx',append=T)
Error in open.connection(con, "rb") : cannot open the connection
In addition: Warning message:
In open.connection(con, "rb") :
  cannot open file 'C:\Users\JinXing\AppData\Local\Temp\RtmpMTp2kQ\file2bb8508d12e7/raster-rId000002.png': No such file or directory

[Liqyao]

Help!!! I also suffered the same problem.

Error in open.connection(con, "rb") : cannot open the connection In addition: Warning message: In open.connection(con, "rb") : cannot open file 'C:\Users\yaolq\AppData\Local\Temp\Rtmpu4jUEU\filecf8430fca3/raster-rId000002.png': No such file or directory

Hope some can find the solutions, really thanks.