DeSciDe
Tool for Unbiased Literature Searching and Gene List Curation
v1.0.2
·
Aug 31, 2025
·
MIT + file LICENSE
Description
Designed for genomic and proteomic data analysis, enabling unbiased PubMed searching, protein interaction network visualization, and comprehensive data summarization. This package aims to help users identify novel targets within their data sets based on protein network interactions and publication precedence of target's association with research context based on literature precedence. Methods in this package are described in detail in: Douglas (Year) <to-be-added DOI or link to the preprint>. Key functionalities of this package also leverage methodologies from previous works, such as: - Szklarczyk et al. (2023) <doi:10.1093/nar/gkac1000> - Winter (2017) <doi:10.32614/RJ-2017-066>.
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ERROR
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OK
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | ERROR |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | ERROR |
Check details (3 non-OK)
ERROR
r-devel-macos-arm64
examples
Running examples in ‘DeSciDe-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot_string_network
> ### Title: Plot STRING Network
> ### Aliases: plot_string_network
>
> ### ** Examples
>
> library(STRINGdb)
> string_db <- STRINGdb$new(species = 9606)
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
WARNING: You didn't specify a version of the STRING database to use. Hence we will use STRING 12.0
> string_ids <- c("9606.ENSP00000269305", "9606.ENSP00000357940")
> plot_string_network(string_db, string_ids, file_directory = tempdir(), export = FALSE)
Error in readPNG(postFormSmart(urlStr, .params = params, .ctype = "raw")) :
libpng error: Not a PNG file
Calls: plot_string_network -> <Anonymous> -> get_png -> readPNG
Execution halted
ERROR
r-oldrel-windows-x86_64
examples
Running examples in 'DeSciDe-Ex.R' failed
The error most likely occurred in:
> ### Name: plot_string_network
> ### Title: Plot STRING Network
> ### Aliases: plot_string_network
>
> ### ** Examples
>
> library(STRINGdb)
> string_db <- STRINGdb$new(species = 9606)
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
WARNING: You didn't specify a version of the STRING database to use. Hence we will use STRING 12.0
> string_ids <- c("9606.ENSP00000269305", "9606.ENSP00000357940")
> plot_string_network(string_db, string_ids, file_directory = tempdir(), export = FALSE)
Error in readPNG(postFormSmart(urlStr, .params = params, .ctype = "raw")) :
libpng error: Not a PNG file
Calls: plot_string_network -> <Anonymous> -> get_png -> readPNG
Execution halted
ERROR
r-release-windows-x86_64
examples
Running examples in 'DeSciDe-Ex.R' failed
The error most likely occurred in:
> ### Name: plot_string_network
> ### Title: Plot STRING Network
> ### Aliases: plot_string_network
>
> ### ** Examples
>
> library(STRINGdb)
> string_db <- STRINGdb$new(species = 9606)
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
WARNING: You didn't specify a version of the STRING database to use. Hence we will use STRING 12.0
> string_ids <- c("9606.ENSP00000269305", "9606.ENSP00000357940")
> plot_string_network(string_db, string_ids, file_directory = tempdir(), export = FALSE)
Error in readPNG(postFormSmart(urlStr, .params = params, .ctype = "raw")) :
libpng error: Not a PNG file
Calls: plot_string_network -> <Anonymous> -> get_png -> readPNG
Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 20, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
examples
Running examples in ‘DeSciDe-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_string_network
> ### Title: Plot STRING Network
> ### Aliases: plot_string_network
>
> ### ** Ex
...[truncated]...
g_db, string_ids, file_directory = tempdir(), export = FALSE)
Error in readPNG(postFormSmart(urlStr, .params = params, .ctype = "raw")) :
libpng error: Not a PNG file
Calls: plot_string_network -> <Anonymous> -> get_png -> readPNG
Execution halted