On Sep 7, 2017, at 11:02 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
Sure, it?s pretty long but here it is:
git show 8210e1e04e8dc6819b84820077293d8d61914cf5
commit 8210e1e04e8dc6819b84820077293d8d61914cf5
Author: Kevin Horan <
khoran at 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 at 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.girke at 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 <
khoran at 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 at 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.girke at 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=$2"
),row))
}
else
{
stop("database ",class(conn)," unsupported"
)
@@ -
1036,13 +1039,12 @@ getPreparedQuery <- function
(conn,statement,bind.data){
#dbSendPreparedQuery(conn,statement,bind.data)
#print("sending query")
- res <- dbSendQuery(conn,statement)
+ res <- dbSendStatement(conn,statement)
#print("after sendQuery")
on.exit(dbClearResult(res))
#clear result set when this function exits
#print("after exit callback registered")
- dbBind(res,bind.data)
+ suppressWarnings(dbBind(res,bind.data))
#print("after dbBind")
- dbFetch(res)
}
Thomas
On Thu, Sep 7, 2017 at 7:39 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
Dear Thomas,
Can you please send me the output of the two `git show` commands?
git show 8210e1e04e8dc6819b84820077293d8d61914cf5
git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
I?ll need to take a look at those to advice accordingly.
Best,
Nitesh
On Sep 7, 2017, at 7:04 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:
Dear Nitesh,
In the release branch of our ChemmineR package I am getting a duplicate commit error. Last week we had a similar error across several of our packages but then you made some changes in response to a similar problem reported on the bioc-developer site which eliminated the problem by itself. Now the problem is back again and it is not clear to me how to resolve it. The suggestions given here https://goo.gl/5mk8vV sound a bit harsh.
tgirke at tgirke-XPS-13-9343
:~/Dropbox/Software/ChemmineR/ChemmineR$ 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 at 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 git at 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
'git at 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.girke at ucr.edu
Phone/Cell/Text: 951-732-7072
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 recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.