[Bioc-devel] Duplicate commit error on and off
Turaga, Nitesh
Nitesh.Turaga at RoswellPark.org
Fri Sep 8 15:34:04 CEST 2017
Hi Thomas,
So, you do actually have a “duplicate” commit and you should NOT be pushing this to the bioc-git server. Notice that the body of both those commits is the same.
If you want to check the rest of your commit history, please try `git log - -oneline` . And you will see that you will have multiple duplicate commits. This compromises your commit history on both your Github repo, and on the bioc-git server.
As suggested in the error message,
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
particularly, point #8 (force Bioconductor master to Github master).
I would advice you to take a look at that. If you have other thoughts on how to solve this problem, I’d be happy to listen.
Best,
Nitesh
> 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
>
>
>
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