[ Started: 2022-12-26 01:22:10 CET ] [ OmnipathR v3.6.0 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ] * using log directory ‘/home/omnipath/testing/bioc/omnipathr/bioc-3.16/2022-12-26_0115/OmnipathR/OmnipathR.Rcheck’ * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.6.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2022-12-26 01:22:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:22:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-12-26 01:22:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:22:33] [TRACE] [OmnipathR] Contains 1 files. [2022-12-26 01:22:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-12-26 01:22:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:22:33] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2022-12-26 01:22:34] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: pivot_annotations > ### Title: Converts annotation tables to a wide format > ### Aliases: pivot_annotations > > ### ** Examples > > # single resource: the result is a data frame > disgenet <- import_omnipath_annotations(resources = 'DisGeNet') > disgenet <- pivot_annotations(disgenet) > disgenet # A tibble: 126,906 × 11 uniprot genesymbol entity_t…¹ disease type score dsi dpi nof_p…² nof_s…³ 1 P04217 A1BG protein Schizo… dise… 0.3 0.7 0.538 1 0 2 P04217 A1BG protein Hepato… phen… 0.3 0.7 0.538 1 0 3 P01023 A2M protein Acute … dise… 0.3 0.529 0.769 1 0 4 P01023 A2M protein Alzhei… dise… 0.3 0.529 0.769 3 0 5 P01023 A2M protein Presen… dise… 0.3 0.529 0.769 3 0 6 P01023 A2M protein Hepato… dise… 0.5 0.529 0.769 1 0 7 P01023 A2M protein Alzhei… dise… 0.37 0.529 0.769 3 0 8 P01023 A2M protein Famili… dise… 0.31 0.529 0.769 3 0 9 P01023 A2M protein Acute … dise… 0.3 0.529 0.769 3 0 10 P01023 A2M protein Coloni… group 0.3 0.529 0.769 1 0 # … with 126,896 more rows, 1 more variable: source , and abbreviated # variable names ¹​entity_type, ²​nof_pmids, ³​nof_snps > # # A tibble: 126,588 × 11 > # uniprot genesymbol entity_type disease type score dsi dpi > # > # 1 P04217 A1BG protein Schizophren. dise. 0.3 0.7 0.538 > # 2 P04217 A1BG protein Hepatomegaly phen. 0.3 0.7 0.538 > # 3 P01023 A2M protein Fibrosis, L. dise. 0.3 0.529 0.769 > # 4 P01023 A2M protein Acute kidne. dise. 0.3 0.529 0.769 > # 5 P01023 A2M protein Mental Depr. dise. 0.3 0.529 0.769 > # # . with 126,583 more rows, and 3 more variables: nof_pmids , > # # nof_snps , source > > # multiple resources: the result is a list > annotations <- import_omnipath_annotations( + resources = c('DisGeNet', 'SignaLink_function', 'DGIdb', 'kinase.com') + ) Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE, : OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Calls: import_omnipath_annotations ... import_omnipath -> do.call -> -> download_base Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2022-12-26 01:37:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Contains 12 files. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-12-26 01:37:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2022-12-26 01:37:41] [TRACE] [OmnipathR] Cache locked: FALSE [2022-12-26 01:37:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2022-12-26 01:37:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2022-12-26 01:37:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2022-12-26 01:37:44] [INFO] [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`. [2022-12-26 01:37:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`. [2022-12-26 01:37:45] [INFO] [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1] [2022-12-26 01:37:45] [INFO] [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:47] [SUCCESS] [OmnipathR] Downloaded 74513 interactions. [2022-12-26 01:37:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:50] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2022-12-26 01:37:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2022-12-26 01:37:51] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2022-12-26 01:37:51] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:52] [SUCCESS] [OmnipathR] Downloaded 42248 enzyme-substrate relationships. [2022-12-26 01:37:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:37:53] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2022-12-26 01:37:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2022-12-26 01:37:53] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2022-12-26 01:37:53] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:55] [SUCCESS] [OmnipathR] Downloaded 40014 interactions. [2022-12-26 01:37:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2022-12-26 01:37:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2022-12-26 01:37:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2022-12-26 01:37:55] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2022-12-26 01:37:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2022-12-26 01:37:56] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2022-12-26 01:37:56] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:56] [SUCCESS] [OmnipathR] Downloaded 32761 protein complexes. [2022-12-26 01:37:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2022-12-26 01:37:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2022-12-26 01:37:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2022-12-26 01:37:58] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2022-12-26 01:37:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2022-12-26 01:37:58] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2022-12-26 01:37:58] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:58] [SUCCESS] [OmnipathR] Downloaded 73481 annotation records. [2022-12-26 01:37:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2022-12-26 01:37:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2022-12-26 01:37:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2022-12-26 01:37:59] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2022-12-26 01:37:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2022-12-26 01:37:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2022-12-26 01:37:59] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2022-12-26 01:37:59] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2022-12-26 01:37:59] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2022-12-26 01:37:59] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2022-12-26 01:37:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2022-12-26 01:37:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2022-12-26 01:37:59] [SUCCESS] [OmnipathR] Loaded 73481 annotation records from cache. [2022-12-26 01:37:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2022-12-26 01:37:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2022-12-26 01:37:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2022-12-26 01:38:01] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2022-12-26 01:38:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2022-12-26 01:38:01] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2022-12-26 01:38:01] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:01] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2022-12-26 01:38:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2022-12-26 01:38:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2022-12-26 01:38:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2022-12-26 01:38:01] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2022-12-26 01:38:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2022-12-26 01:38:01] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2022-12-26 01:38:01] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:01] [SUCCESS] [OmnipathR] Downloaded 2451 annotation records. [2022-12-26 01:38:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2022-12-26 01:38:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:38:03] [SUCCESS] [OmnipathR] Loaded 40014 interactions from cache. [2022-12-26 01:38:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2022-12-26 01:38:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2022-12-26 01:38:03] [SUCCESS] [OmnipathR] Loaded 2451 annotation records from cache. [2022-12-26 01:38:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2022-12-26 01:38:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2022-12-26 01:38:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2022-12-26 01:38:04] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-12-26 01:38:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-12-26 01:38:06] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2022-12-26 01:38:06] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:06] [SUCCESS] [OmnipathR] Downloaded 323572 intercellular communication role records. [2022-12-26 01:38:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:10] [INFO] [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`. [2022-12-26 01:38:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/498f91238951df23d4d71705063f40254eddbfbf-1.rds`. [2022-12-26 01:38:10] [INFO] [OmnipathR] Download ready [key=498f91238951df23d4d71705063f40254eddbfbf, version=1] [2022-12-26 01:38:10] [INFO] [OmnipathR] Cache item `498f91238951df23d4d71705063f40254eddbfbf` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:11] [SUCCESS] [OmnipathR] Downloaded 40681 interactions. [2022-12-26 01:38:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-12-26 01:38:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-12-26 01:38:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-12-26 01:38:12] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-12-26 01:38:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-12-26 01:38:12] [INFO] [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1] [2022-12-26 01:38:12] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:12] [SUCCESS] [OmnipathR] Downloaded 27928 intercellular communication role records. [2022-12-26 01:38:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-12-26 01:38:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-12-26 01:38:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-12-26 01:38:12] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-12-26 01:38:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-12-26 01:38:12] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2022-12-26 01:38:12] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:12] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records. [2022-12-26 01:38:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-12-26 01:38:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-12-26 01:38:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-12-26 01:38:13] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-12-26 01:38:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-12-26 01:38:13] [INFO] [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1] [2022-12-26 01:38:13] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:13] [SUCCESS] [OmnipathR] Downloaded 43967 intercellular communication role records. [2022-12-26 01:38:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-12-26 01:38:18] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-12-26 01:38:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-12-26 01:38:19] [INFO] [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1] [2022-12-26 01:38:19] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:22] [SUCCESS] [OmnipathR] Downloaded 80237 interactions. [2022-12-26 01:38:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-12-26 01:38:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-12-26 01:38:22] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache. [2022-12-26 01:38:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-12-26 01:38:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-12-26 01:38:22] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache. [2022-12-26 01:38:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-12-26 01:38:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic` [2022-12-26 01:38:51] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache. [2022-12-26 01:38:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-12-26 01:38:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-12-26 01:38:51] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache. [2022-12-26 01:38:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2022-12-26 01:38:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2022-12-26 01:38:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2022-12-26 01:38:52] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2022-12-26 01:38:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2022-12-26 01:38:52] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2022-12-26 01:38:52] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:52] [SUCCESS] [OmnipathR] Downloaded 1097 records. [2022-12-26 01:38:52] [INFO] [OmnipathR] Loading database `Ensembl organism names`. [2022-12-26 01:38:52] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2022-12-26 01:38:52] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2022-12-26 01:38:52] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2022-12-26 01:38:52] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2022-12-26 01:38:52] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2022-12-26 01:38:53] [TRACE] [OmnipathR] HTTP 200 [2022-12-26 01:38:53] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2022-12-26 01:38:53] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2022-12-26 01:38:53] [INFO] [OmnipathR] Loaded database `Ensembl organism names`. [2022-12-26 01:38:53] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2022-12-26 01:38:53] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE) [2022-12-26 01:38:53] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED) [2022-12-26 01:38:53] [TRACE] [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`. [2022-12-26 01:38:53] [INFO] [OmnipathR] Cache record does not exist: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2022-12-26 01:38:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`. [2022-12-26 01:38:53] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`. [2022-12-26 01:38:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2022-12-26 01:38:53] [INFO] [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2022-12-26 01:38:53] [TRACE] [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2022-12-26 01:38:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2022-12-26 01:38:58] [INFO] [OmnipathR] Download ready [key=1ada9cda5e2120624b9e561db9e74f4ddcc5185b, version=1] [2022-12-26 01:38:58] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `started` to `ready`. [2022-12-26 01:38:58] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): downloaded 20404 records [2022-12-26 01:38:59] [INFO] [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, no version available. [2022-12-26 01:38:59] [INFO] [OmnipathR] Created new version for cache record 663f8a0321e09c16870d151bd7559c9385d22288: version 1. [2022-12-26 01:38:59] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo [2022-12-26 01:38:59] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/go/go-basic.obo` [2022-12-26 01:38:59] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/go/go-basic.obo` [2022-12-26 01:38:59] [TRACE] [OmnipathR] HTTP 200 [2022-12-26 01:38:59] [INFO] [OmnipathR] Download ready [key=663f8a0321e09c16870d151bd7559c9385d22288, version=1] [2022-12-26 01:38:59] [INFO] [OmnipathR] Cache item `663f8a0321e09c16870d151bd7559c9385d22288` version 1: status changed from `unknown` to `ready`. [2022-12-26 01:38:59] [TRACE] [OmnipathR] Processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`. [2022-12-26 01:39:02] [TRACE] [OmnipathR] Finished processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`. [2022-12-26 01:39:02] [TRACE] [OmnipathR] Converting ontology relations from table to graph. [2022-12-26 01:39:02] [INFO] [OmnipathR] Loading database `Gene Ontology (basic)`. [2022-12-26 01:39:02] [INFO] [OmnipathR] Looking up in cache `http://purl.obolibrary.org/obo/go/go-basic.obo`: key=663f8a0321e09c16870d151bd7559c9385d22288, latest version=1. [2022-12-26 01:39:02] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo [2022-12-26 01:39:02] [TRACE] [OmnipathR] Processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`. [2022-12-26 01:39:04] [TRACE] [OmnipathR] Finished processing OBO file `/home/omnipath/.cache/OmnipathR/663f8a0321e09c16870d151bd7559c9385d22288-1.obo`. [2022-12-26 01:39:04] [INFO] [OmnipathR] Loaded database `Gene Ontology (basic)`. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2022-12-26 01:39:05] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2022-12-26 01:39:05] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE) [2022-12-26 01:39:05] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED) [2022-12-26 01:39:05] [TRACE] [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`. [2022-12-26 01:39:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2022-12-26 01:39:05] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): loaded 20404 records from cache [2022-12-26 01:39:05] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2022-12-26 01:39:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2022-12-26 01:39:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:39:18] [SUCCESS] [OmnipathR] Loaded 40014 interactions from cache. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2022-12-26 01:39:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-12-26 01:39:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-12-26 01:39:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-12-26 01:39:25] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2022-12-26 01:39:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2022-12-26 01:39:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2022-12-26 01:39:26] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2022-12-26 01:39:26] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2022-12-26 01:39:31] [SUCCESS] [OmnipathR] Downloaded 80237 interactions. [2022-12-26 01:41:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2022-12-26 01:41:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2022-12-26 01:41:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2022-12-26 01:41:35] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:41:40] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2022-12-26 01:41:43] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:41:48] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2022-12-26 01:41:51] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 258-272 (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown Warning in for (i in seq_len(n)) { : closing unused connection 5 (https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic) Warning in for (i in seq_len(n)) { : closing unused connection 4 (https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic) [2022-12-26 01:41:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:55] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2022-12-26 01:41:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2022-12-26 01:41:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2022-12-26 01:41:55] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2022-12-26 01:41:55] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2022-12-26 01:41:55] [SUCCESS] [OmnipathR] Downloaded 14767 interactions. [2022-12-26 01:41:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:41:57] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:42:02] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:42:02] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:42:07] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2022-12-26 01:42:08] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 263-274 (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2022-12-26 01:42:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2022-12-26 01:42:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2022-12-26 01:42:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2022-12-26 01:42:08] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:42:13] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2022-12-26 01:42:13] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2022-12-26 01:42:18] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2022-12-26 01:42:19] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 Quitting from lines 56-67 (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/omnipath/testing/bioc/omnipathr/bioc-3.16/2022-12-26_0115/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2022-12-26 01:42:25 CET ]