import_Omnipath_PTMS() not working

[humzalikhan]

Seems like something on the server side or formatting of data? So odd, I was using it 2 days ago just fine...

Error below:
Downloaded 0 PTMs
Error in strsplit(interactions$sources, ";") : non-character argument
In addition: Warning message:
In FUN(URL, ...) :
incomplete final line found by readTableHeader on 'http://omnipathdb.org/ptms/?fields=sources&fields=references&fields=curation_effort&genesymbols=1'

[deeenes]

Hi,

For me it works with the recent version (1.3.5):

e <- import_omnipath_enzsub()
# Downloaded 39201 enzyme-substrate relationships.

# or the old name, which works the same apart from a deprecation warning:
e <- import_Omnipath_PTMS()
# Downloaded 39201 enzyme-substrate relationships.
# Warning message:
# 'import_Omnipath_PTMS' is deprecated.
# Use 'import_omnipath_enzsub' instead.

Based on the incomplete final line found by readTableHeader it looks like a failed network transfer? Please let us know if this error persists.

Best,

Denes

[deeenes]

Closing because no confirmation if the issue persists. Please feel free to re-open.

[humzalikhan]

Thought I had this fixed, but now it seems to throw me a similar error! Any thoughts? No idea why this would be happening; I had things working for a while.

ptms = import_omnipath_enzsub(resources=c("PhosphoSite", "SIGNOR"))
Error in strsplit(x, sep) : non-character argument

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] RColorBrewer_1.1-2 HGNChelper_0.8.1 biomaRt_2.45.2 OmnipathR_1.3.3 jsonlite_1.7.0 igraph_1.2.5 rmutil_1.1.5
[8] readxl_1.3.1 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.3.1 tidyr_1.1.1
[15] tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lubridate_1.7.9 prettyunits_1.1.1 assertthat_0.2.1 digest_0.6.25 BiocFileCache_1.13.1
[7] R6_2.4.1 cellranger_1.1.0 backports_1.1.8 reprex_0.3.0 stats4_4.0.2 RSQLite_2.2.0
[13] httr_1.4.2 pillar_1.4.6 rlang_0.4.7 progress_1.2.2 curl_4.3 rstudioapi_0.11
[19] blob_1.2.1 S4Vectors_0.27.12 bit_4.0.4 munsell_0.5.0 broom_0.7.0 compiler_4.0.2
[25] modelr_0.1.8 pkgconfig_2.0.3 askpass_1.1 BiocGenerics_0.35.4 openssl_1.4.2 tidyselect_1.1.0
[31] IRanges_2.23.10 XML_3.99-0.5 fansi_0.4.1 crayon_1.3.4 dbplyr_1.4.4 withr_2.2.0
[37] rappdirs_0.3.1 grid_4.0.2 gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5
[43] scales_1.1.1 cli_2.0.2 stringi_1.4.6 fs_1.5.0 xml2_1.3.2 ellipsis_0.3.1
[49] generics_0.0.2 vctrs_0.3.2 tools_4.0.2 bit64_4.0.2 Biobase_2.49.0 glue_1.4.1
[55] hms_0.5.3 parallel_4.0.2 AnnotationDbi_1.51.3 colorspace_1.4-1 rvest_0.3.6 memoise_1.1.0
[61] haven_2.3.1

[deeenes]

Hi @humzalikhan

Thanks for opening the issue again, now I could reproduce it.
It revealed a server side bug which was likely introduced by an update just 2 days ago, so I think your first issue is unrelated, despite the same error message.
The non-character argument error usually comes from a missing column (which is NULL, hence not character), this time the sources column (listing the resources for each interaction) was missing.

Now I fixed it, works for me, I hope for you too.

Best,

Denes