[ Started: 2022-05-04 13:31:13 ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘liana’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘liana_custom_op.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' Loading required package: tidyverse ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ✔ tibble 3.1.7 ✔ dplyr 1.0.9 ✔ tidyr 1.2.0 ✔ stringr 1.4.0 ✔ readr 2.1.2 ✔ forcats 0.5.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: OmnipathR [2022-05-04 13:32:03] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-05-04 13:32:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-05-04 13:32:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-05-04 13:32:03] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-05-04 13:32:03] [TRACE] [OmnipathR] Cache locked: FALSE Loading required package: liana Loading required package: magrittr Attaching package: 'magrittr' The following object is masked from 'package:purrr': set_names The following object is masked from 'package:tidyr': extract [2022-05-04 13:32:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:21] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2022-05-04 13:32:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2022-05-04 13:32:21] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1] [2022-05-04 13:32:21] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:22] [SUCCESS] [OmnipathR] Downloaded 4580 interactions. [2022-05-04 13:32:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:23] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2022-05-04 13:32:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2022-05-04 13:32:23] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1] [2022-05-04 13:32:23] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:24] [SUCCESS] [OmnipathR] Downloaded 1475 interactions. [2022-05-04 13:32:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:27] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2022-05-04 13:32:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2022-05-04 13:32:28] [INFO] [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1] [2022-05-04 13:32:28] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:28] [SUCCESS] [OmnipathR] Downloaded 3765 interactions. [2022-05-04 13:32:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:31] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2022-05-04 13:32:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2022-05-04 13:32:31] [INFO] [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1] [2022-05-04 13:32:31] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:32] [SUCCESS] [OmnipathR] Downloaded 2485 interactions. [2022-05-04 13:32:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2022-05-04 13:32:34] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2022-05-04 13:32:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2022-05-04 13:32:34] [INFO] [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1] [2022-05-04 13:32:34] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:35] [SUCCESS] [OmnipathR] Downloaded 1894 interactions. [2022-05-04 13:32:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2022-05-04 13:32:36] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2022-05-04 13:32:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2022-05-04 13:32:36] [INFO] [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1] [2022-05-04 13:32:36] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:36] [SUCCESS] [OmnipathR] Downloaded 1797 interactions. [2022-05-04 13:32:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2022-05-04 13:32:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2022-05-04 13:32:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2022-05-04 13:32:37] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`. [2022-05-04 13:32:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2022-05-04 13:32:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2022-05-04 13:32:37] [INFO] [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1] [2022-05-04 13:32:37] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`. [2022-05-04 13:32:37] [SUCCESS] [OmnipathR] Downloaded 1981 annotation records. [2022-05-04 13:32:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2022-05-04 13:32:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2022-05-04 13:32:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2022-05-04 13:34:03] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2022-05-04 13:34:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-05-04 13:34:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-05-04 13:34:04] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2022-05-04 13:34:04] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2022-05-04 13:34:05] [SUCCESS] [OmnipathR] Downloaded 323572 intercellular communication role records. [2022-05-04 13:34:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-05-04 13:34:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-05-04 13:34:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-05-04 13:34:13] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2022-05-04 13:34:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-05-04 13:34:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-05-04 13:34:13] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2022-05-04 13:34:13] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2022-05-04 13:34:13] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records. [2022-05-04 13:34:13] [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` [2022-05-04 13:34:13] [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` [2022-05-04 13:34:13] [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` [2022-05-04 13:34:33] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`. [2022-05-04 13:34:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-05-04 13:34:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-05-04 13:34:33] [INFO] [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1] [2022-05-04 13:34:33] [INFO] [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`. [2022-05-04 13:34:34] [SUCCESS] [OmnipathR] Downloaded 80237 interactions. [2022-05-04 13:34:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-05-04 13:34:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-05-04 13:34:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-05-04 13:34:43] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`. [2022-05-04 13:34:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-05-04 13:34:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-05-04 13:34:43] [INFO] [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1] [2022-05-04 13:34:43] [INFO] [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`. [2022-05-04 13:34:43] [SUCCESS] [OmnipathR] Downloaded 27928 intercellular communication role records. [2022-05-04 13:34:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-05-04 13:34:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-05-04 13:34:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-05-04 13:34:56] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`. [2022-05-04 13:34:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-05-04 13:34:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-05-04 13:34:56] [INFO] [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1] [2022-05-04 13:34:56] [INFO] [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`. [2022-05-04 13:34:56] [SUCCESS] [OmnipathR] Downloaded 43967 intercellular communication role records. [2022-05-04 13:36:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-05-04 13:36:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic` [2022-05-04 13:36:03] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache. [2022-05-04 13:36:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-05-04 13:36:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-05-04 13:36:05] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache. [2022-05-04 13:36:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-05-04 13:36:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-05-04 13:36:07] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache. [2022-05-04 13:36:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-05-04 13:36:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-05-04 13:36:07] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache. [2022-05-04 13:36:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-05-04 13:36:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-05-04 13:36:07] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache. Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! LIANA: LR summary stats calculated! Now Running: Natmi Now Running: Connectome Now Running: Logfc Now Running: Sca Now Running: Cellphonedb Now aggregating natmi Now aggregating connectome Now aggregating logfc Now aggregating sca Now aggregating cellphonedb Aggregating Ranks [2022-05-04 13:39:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-05-04 13:39:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-05-04 13:39:49] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache. [2022-05-04 13:39:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-05-04 13:39:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-05-04 13:39:49] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache. [2022-05-04 13:39:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-05-04 13:39:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-05-04 13:39:50] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache. [2022-05-04 13:40:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-05-04 13:40:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic` [2022-05-04 13:40:54] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache. [2022-05-04 13:40:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-05-04 13:40:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-05-04 13:40:56] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache. --- finished re-building ‘liana_custom_op.Rmd’ --- re-building ‘liana_devel.Rmd’ using rmarkdown Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! Warning in exec(output, ...) : 3465 genes and/or 0 cells were removed as they had no counts! LIANA: LR summary stats calculated! Quitting from lines 141-149 (liana_devel.Rmd) Error: processing vignette 'liana_devel.Rmd' failed with diagnostics: there is no package called 'SCAomni' --- failed re-building ‘liana_devel.Rmd’ --- re-building ‘liana_intracell.rmd’ using rmarkdown [2022-05-04 13:41:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2022-05-04 13:41:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2022-05-04 13:41:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2022-05-04 13:41:05] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2022-05-04 13:41:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2022-05-04 13:41:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2022-05-04 13:41:05] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2022-05-04 13:41:05] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2022-05-04 13:41:05] [SUCCESS] [OmnipathR] Downloaded 1145 annotation records. Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! LIANA: LR summary stats calculated! Now Running: Natmi Now Running: Connectome Now Running: Logfc Now Running: Sca Now Running: Cellphonedb Now aggregating natmi Now aggregating connectome Now aggregating logfc Now aggregating sca Now aggregating cellphonedb Aggregating Ranks [2022-05-04 13:45:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=MSigDB&license=academic` [2022-05-04 13:45:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=MSigDB&license=academic` [2022-05-04 13:45:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=MSigDB&license=academic` [2022-05-04 14:00:27] [INFO] [OmnipathR] Cache item `5cbd6eef07085d333f425bc50fb18bf52c2a140d` version 1: status changed from `unknown` to `started`. [2022-05-04 14:00:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cbd6eef07085d333f425bc50fb18bf52c2a140d-1.rds`. [2022-05-04 14:00:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cbd6eef07085d333f425bc50fb18bf52c2a140d-1.rds`. [2022-05-04 14:00:48] [INFO] [OmnipathR] Download ready [key=5cbd6eef07085d333f425bc50fb18bf52c2a140d, version=1] [2022-05-04 14:00:48] [INFO] [OmnipathR] Cache item `5cbd6eef07085d333f425bc50fb18bf52c2a140d` version 1: status changed from `started` to `ready`. [2022-05-04 14:00:48] [SUCCESS] [OmnipathR] Downloaded 6413072 annotation records. --- finished re-building ‘liana_intracell.rmd’ --- re-building ‘liana_nichenet.Rmd’ using rmarkdown Quitting from lines 35-42 (liana_nichenet.Rmd) Error: processing vignette 'liana_nichenet.Rmd' failed with diagnostics: there is no package called 'nichenetr' --- failed re-building ‘liana_nichenet.Rmd’ --- re-building ‘liana_ortho.Rmd’ using rmarkdown Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! Warning in exec(output, ...) : 3465 genes and/or 0 cells were removed as they had no counts! LIANA: LR summary stats calculated! Now Running: Sca Now Running: Natmi Now aggregating sca Now aggregating natmi Aggregating Ranks Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. --- finished re-building ‘liana_ortho.Rmd’ --- re-building ‘liana_tutorial.Rmd’ using rmarkdown Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! LIANA: LR summary stats calculated! Now Running: Natmi Now Running: Connectome Now Running: Logfc Now Running: Sca Now Running: Cellphonedb Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Running LIANA with `label` as labels! LIANA: LR summary stats calculated! Now Running: Cellphonedb Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! LIANA: LR summary stats calculated! Now Running: Natmi Now Running: Sca Now Running: Logfc Now aggregating natmi Now aggregating sca Now aggregating logfc Aggregating Ranks Expression from the `RNA` assay will be used Running LIANA with `seurat_annotations` as labels! LIANA: LR summary stats calculated! Now Running: Cellphonedb Now Running: Sca --- finished re-building ‘liana_tutorial.Rmd’ SUMMARY: processing the following files failed: ‘liana_devel.Rmd’ ‘liana_nichenet.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2022-05-04 14:04:38 ]