v1.2.0

DESCRIPTION

@@ -14,6 +14,18 @@ Authors@R: c(
       family = "Zhang", 
       email = "[email protected]", 
       role = c("ctb")
+    ),
+    person(
+      given = "Ruining",
+      family = "Zhu", 
+      email = "[email protected]", 
+      role = c("ctb")
+    ),
+    person(
+      given = "Feng",
+      family = "Zhao", 
+      email = "[email protected]", 
+      role = c("ctb")
     ))
 Maintainer: Xin Guo <[email protected]>
 Description: Interface for 'g3-lollipop' 'JavaScript' library.
@@ -22,7 +34,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.2.0)
 biocViews:
 Imports:
     jsonlite,

NEWS.md

@@ -1,3 +1,7 @@
+## Version 1.2.0 
+  - Updated Pfam (v37.0) (date: 2024-07-29)
+  - Updated UniProtKB (date: 2024-07-29)
+
 ## Version 1.15 (2022/06/30)
   - Updated `hgnc2pfam.df.rda` data
   - Remove cgdsr dependencies; add cBioPortalData as the substitution

R/getMutationsFromCbioportal.R

@@ -53,11 +53,32 @@ getMutationsFromCbioportal <- function(study.id,
 
   # ========================
   # server
-  cbio <- cBioPortal()
+  # cbio <- cBioPortal()
+  # cbio <- suppressWarnings({
+  #   cBioPortal(
+  #    hostname = "www.cbioportal.org",
+  #     protocol = "https",
+  #     api. = "/api/v2/api-docs"
+  #   )
+  # })
+
+  cbio <- tryCatch({
+    cBioPortal(
+      hostname = "www.cbioportal.org",
+      protocol = "https",
+      api. = "/api/v2/api-docs"
+    )
+  }, warning = function(w){
+    # message(w)
+  }, error = function(e){
+    stop("Connection error: can not connect to cBioPortal API")
+  }, finally = {
+    #
+  })
 
   # ========================
   # get study information
-  genetic.profiles <- molecularProfiles(cbio,studyId = study.id)
+  genetic.profiles <- molecularProfiles(cbio, studyId = study.id)
   message("Found study ", study.id)
 
   # ========================
@@ -71,7 +92,6 @@ getMutationsFromCbioportal <- function(study.id,
   message("Found mutation data set ", mutation.profile)
 
   # ========================
-
   case.list.details <- sampleLists(cbio, study.id)
 
   mutation.case.list.id <- case.list.details$sampleListId