Sure, it’s pretty long but here it is:
git show 8210e1e04e8dc6819b84820077293d8d61914cf5
commit 8210e1e04e8dc6819b84820077293d8d61914cf5
Author: Kevin Horan <kho...@cs.ucr.edu>
Date: Fri Jun 30 21:37:15 2017 +0000
fix for RSQLite 2
git-svn-id:
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
bc3139a8-67e5-0310-9ffc-ced21a209358
diff --git a/DESCRIPTION b/DESCRIPTION
index 4b4d514..c96da6e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: ChemmineR
Type: Package
Title: Cheminformatics Toolkit for R
-Version: 2.28.0
-Date: 2016-11-30
+Version: 2.28.1
+Date: 2017-6-30
Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Maintainer: Thomas Girke <thomas.gi...@ucr.edu>
Description: ChemmineR is a cheminformatics package for analyzing
drug-like small molecule data in R. Its latest version contains
functions for efficient processing of large numbers of molecules,
physicochemical
diff --git a/R/compound_db.R b/R/compound_db.R
index 76d1f6c..970c4a2 100644
--- a/R/compound_db.R
+++ b/R/compound_db.R
@@ -38,7 +38,7 @@ initDb <- function(handle){
collapse=""),";",fixed=TRUE))
#print(statements)
- Map(function(sql) dbOp(dbGetQuery(conn,sql)),statements)
+ Map(function(sql) dbOp(dbExecute(conn,sql)),statements)
}
conn
}
@@ -54,7 +54,7 @@ dbTransaction <- function(conn,expr){
# be paranoid about setting this as bad things will
happen if its not set
enableForeignKeys(conn)
- dbGetQuery(conn,"BEGIN TRANSACTION")
+ dbExecute(conn,"BEGIN TRANSACTION")
ret=expr
dbCommit(conn)
ret
@@ -64,8 +64,11 @@ dbTransaction <- function(conn,expr){
stop(paste("db error inside transaction: ",e$message))
})
}
-dbGetQueryChecked <- function(conn,statement,...){
- ret=dbGetQuery(conn,statement)
+dbGetQueryChecked <- function(conn,statement,execute=FALSE,...){
+ if(execute == TRUE)
+ ret=dbExecute(conn,statement)
+ else
+ ret=dbGetQuery(conn,statement)
err=dbGetException(conn)
if(err$errorMsg[1] != "OK")
stop("error in dbGetQuery: ",err$errorMsg," ",traceback())
@@ -895,10 +898,10 @@ createFeature <- function(conn,name, isNumeric){
dbGetQueryChecked(conn,
paste("CREATE TABLE feature_",name," (
compound_id INTEGER PRIMARY KEY REFERENCES
compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, ",
- "",name," ",sqlType," )",sep=""))
+ "",name," ",sqlType," )",sep=""),execute=TRUE)
#print("made table")
- dbGetQuery(conn,paste("CREATE INDEX feature_",name,"_index ON
+ dbExecute(conn,paste("CREATE INDEX feature_",name,"_index ON
feature_",name,"(\"",name,"\")",sep=""))
#print("made index")
@@ -913,7 +916,7 @@ insertDef <- function(conn,data) {
"VALUES(:definition,:definition_checksum,:format)",sep=""),
bind.data=data[fields])
}else if(inherits(conn,"PostgreSQLConnection")){
if(debug) print(data[,"definition_checksum"])
- apply(data[,fields],1,function(row) dbOp(dbGetQuery(conn,
+ apply(data[,fields],1,function(row) dbOp(dbExecute(conn,
"INSERT INTO
compounds(definition,definition_checksum,format) VALUES($1,$2,$3)",
row)))
}else{
@@ -990,7 +993,7 @@ insertDescriptor <- function(conn,data){
})
apply(data[,fields2],1,function(row) {
row[2] = descTypes[row[2]] #translate
descriptor_type to descriptor_type_id
- dbTransaction(conn,dbGetQuery(conn,
paste("INSERT INTO compound_descriptors(compound_id,
+ dbTransaction(conn,dbExecute(conn,
paste("INSERT INTO compound_descriptors(compound_id,
descriptor_id) ",
"VALUES( (SELECT compound_id
FROM compounds WHERE definition_checksum = $1),
(SELECT descriptor_id FROM descriptors
@@ -1006,7 +1009,7 @@ insertDescriptorType <- function(conn,data){
bind.data=data)
}else if(inherits(conn,"PostgreSQLConnection")){
apply(data,1,function(row)
- dbGetQuery(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
+ dbExecute(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
}else{
stop("database ",class(conn)," unsupported")
}
@@ -1019,7 +1022,7 @@ updatePriorities <- function(conn,data){
descriptor_id=:descriptor_id", bind.data=data)
}else if(inherits(conn,"PostgreSQLConnection")){
apply(data[,c("compound_id","descriptor_id","priority")],1,function(row)
- dbGetQuery(conn,paste("UPDATE
compound_descriptors SET priority = $3 WHERE compound_id=$1 AND
+ dbExecute(conn,paste("UPDATE
compound_descriptors SET priority = $3 WHERE compound_id=$1 AND
descriptor_id=$2"),row))
}else{
stop("database ",class(conn)," unsupported")
@@ -1036,13 +1039,12 @@ getPreparedQuery <- function(conn,statement,bind.data){
#dbSendPreparedQuery(conn,statement,bind.data)
#print("sending query")
- res <- dbSendQuery(conn,statement)
+ res <- dbSendStatement(conn,statement)
#print("after sendQuery")
on.exit(dbClearResult(res)) #clear result set when this function exits
#print("after exit callback registered")
- dbBind(res,bind.data)
+ suppressWarnings(dbBind(res,bind.data))
#print("after dbBind")
- dbFetch(res)
}
git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
commit f514d35b793e1d9462b899bf3c76cc06ab4dcc91
Author: Kevin Horan <kho...@cs.ucr.edu>
Date: Fri Jun 30 21:37:15 2017 +0000
fix for RSQLite 2
git-svn-id:
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
bc3139a8-67e5-0310-9ffc-ced21a209358
diff --git a/DESCRIPTION b/DESCRIPTION
index 4b4d514..c96da6e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: ChemmineR
Type: Package
Title: Cheminformatics Toolkit for R
-Version: 2.28.0
-Date: 2016-11-30
+Version: 2.28.1
+Date: 2017-6-30
Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Maintainer: Thomas Girke <thomas.gi...@ucr.edu>
Description: ChemmineR is a cheminformatics package for analyzing
drug-like small molecule data in R. Its latest version contains
functions for efficient processing of large numbers of molecules,
physicochemical
diff --git a/R/compound_db.R b/R/compound_db.R
index 76d1f6c..970c4a2 100644
--- a/R/compound_db.R
+++ b/R/compound_db.R
@@ -38,7 +38,7 @@ initDb <- function(handle){
collapse=""),";",fixed=TRUE))
#print(statements)
- Map(function(sql) dbOp(dbGetQuery(conn,sql)),statements)
+ Map(function(sql) dbOp(dbExecute(conn,sql)),statements)
}
conn
}
@@ -54,7 +54,7 @@ dbTransaction <- function(conn,expr){
# be paranoid about setting this as bad things will
happen if its not set
enableForeignKeys(conn)
- dbGetQuery(conn,"BEGIN TRANSACTION")
+ dbExecute(conn,"BEGIN TRANSACTION")
ret=expr
dbCommit(conn)
ret
@@ -64,8 +64,11 @@ dbTransaction <- function(conn,expr){
stop(paste("db error inside transaction: ",e$message))
})
}
-dbGetQueryChecked <- function(conn,statement,...){
- ret=dbGetQuery(conn,statement)
+dbGetQueryChecked <- function(conn,statement,execute=FALSE,...){
+ if(execute == TRUE)
+ ret=dbExecute(conn,statement)
+ else
+ ret=dbGetQuery(conn,statement)
err=dbGetException(conn)
if(err$errorMsg[1] != "OK")
stop("error in dbGetQuery: ",err$errorMsg," ",traceback())
@@ -895,10 +898,10 @@ createFeature <- function(conn,name, isNumeric){
dbGetQueryChecked(conn,
paste("CREATE TABLE feature_",name," (
compound_id INTEGER PRIMARY KEY REFERENCES
compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, ",
- "",name," ",sqlType," )",sep=""))
+ "",name," ",sqlType," )",sep=""),execute=TRUE)
#print("made table")
- dbGetQuery(conn,paste("CREATE INDEX feature_",name,"_index ON
+ dbExecute(conn,paste("CREATE INDEX feature_",name,"_index ON
feature_",name,"(\"",name,"\")",sep=""))
#print("made index")
@@ -913,7 +916,7 @@ insertDef <- function(conn,data) {
"VALUES(:definition,:definition_checksum,:format)",sep=""),
bind.data=data[fields])
}else if(inherits(conn,"PostgreSQLConnection")){
if(debug) print(data[,"definition_checksum"])
- apply(data[,fields],1,function(row) dbOp(dbGetQuery(conn,
+ apply(data[,fields],1,function(row) dbOp(dbExecute(conn,
"INSERT INTO
compounds(definition,definition_checksum,format) VALUES($1,$2,$3)",
row)))
}else{
@@ -990,7 +993,7 @@ insertDescriptor <- function(conn,data){
})
apply(data[,fields2],1,function(row) {
row[2] = descTypes[row[2]] #translate
descriptor_type to descriptor_type_id
- dbTransaction(conn,dbGetQuery(conn,
paste("INSERT INTO compound_descriptors(compound_id,
+ dbTransaction(conn,dbExecute(conn,
paste("INSERT INTO compound_descriptors(compound_id,
descriptor_id) ",
"VALUES( (SELECT compound_id
FROM compounds WHERE definition_checksum = $1),
(SELECT descriptor_id FROM descriptors
@@ -1006,7 +1009,7 @@ insertDescriptorType <- function(conn,data){
bind.data=data)
}else if(inherits(conn,"PostgreSQLConnection")){
apply(data,1,function(row)
- dbGetQuery(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
+ dbExecute(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
}else{
stop("database ",class(conn)," unsupported")
}
@@ -1019,7 +1022,7 @@ updatePriorities <- function(conn,data){
descriptor_id=:descriptor_id", bind.data=data)
}else if(inherits(conn,"PostgreSQLConnection")){
apply(data[,c("compound_id","descriptor_id","priority")],1,function(row)
- dbGetQuery(conn,paste("UPDATE
compound_descriptors SET priority = $3 WHERE compound_id=$1 AND
+ dbExecute(conn,paste("UPDATE
compound_descriptors SET priority = $3 WHERE compound_id=$1 AND
descriptor_id=$2"),row))
}else{
stop("database ",class(conn)," unsupported")
@@ -1036,13 +1039,12 @@ getPreparedQuery <- function(conn,statement,bind.data){
#dbSendPreparedQuery(conn,statement,bind.data)
#print("sending query")
- res <- dbSendQuery(conn,statement)
+ res <- dbSendStatement(conn,statement)
#print("after sendQuery")
on.exit(dbClearResult(res)) #clear result set when this function exits
#print("after exit callback registered")
- dbBind(res,bind.data)
+ suppressWarnings(dbBind(res,bind.data))
#print("after dbBind")
- dbFetch(res)
}
Thomas
On Thu, Sep 7, 2017 at 7:39 PM Turaga, Nitesh <nitesh.tur...@roswellpark.org>
wrote:
> Dear Thomas,
>
> Can you please send me the output of the two `git show` commands?
>
> > git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> > git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
>
>
> I’ll need to take a look at those to advice accordingly.
>
>
> Best,
>
> Nitesh
>
>
> > On Sep 7, 2017, at 7:04 PM, Thomas Girke <thomas.gi...@ucr.edu> wrote:
> >
> > Dear Nitesh,
> >
> > In the release branch of our ChemmineR package I am getting a duplicate
> commit error. Last week we had a similar error across several of our
> packages but then you made some changes in response to a similar problem
> reported on the bioc-developer site which eliminated the problem by itself.
> Now the problem is back again and it is not clear to me how to resolve it.
> The suggestions given here https://goo.gl/5mk8vV sound a bit harsh.
> >
> > tgirke@tgirke-XPS-13-9343
> > :~/Dropbox/Software/ChemmineR/ChemmineR$ git push upstream RELEASE_3_5
> > Counting objects:
> > 26
> > , done.
> > Delta compression using up to
> > 4
> > threads.
> > Compressing objects:
> > 100% (4/4
> > ), done.
> > Writing objects:
> > 100% (4/4), 387 bytes | 0
> > bytes/s, done.
> > Total
> > 4 (delta 3), reused 0 (delta 0
> > )
> > remote: Error: duplicate commits.
> > remote:
> > remote: There are duplicate commits
> > in
> > your commit history, These cannot be
> > remote: pushed to the Bioconductor git server. Please make sure that
> this is
> > remote: resolved.
> > remote:
> > remote: Take a look at the documentation to fix this,
> > remote:
> >
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> > ,
> > remote: particularly, point
> > #8 (force Bioconductor master to Github master).
> >
> > remote:
> > remote: For more information, or help resolving this issue, contact
> > remote: <
> > bioc-devel@r-project.org
> > >. Provide the error, the package name and
> > remote: any other details we might need.
> > remote:
> > remote: Use
> > remote:
> > remote: git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> > remote: git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
> > remote:
> > remote: to see body of commits.
> > remote:
> > To g...@git.bioconductor.org:packages/ChemmineR.git
> > ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook
> declined)
> > error: failed to push some refs to
> > 'g...@git.bioconductor.org:packages/ChemmineR.git'
> > Thanks,
> >
> > Thomas
> >
> > --
> >
> > Thomas Girke, Ph.D.
> >
> > Professor of Bioinformatics
> >
> > Director of HPC Center
> >
> > 1207F Genomics Building
> >
> > University of California
> >
> > Riverside, CA 92521
> >
> >
> >
> >
> > E-mail: thomas.gi...@ucr.edu
> >
> > Phone/Cell/Text: 951-732-7072 <(951)%20732-7072>
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
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