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.gi...@ucr.edu> wrote: > > 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 > > > > 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. 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