Re: [Bioc-devel] Duplicate commit error on and off

Fri, 08 Sep 2017 06:53:22 -0700 

On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:

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.
Seemed like Thomas wasn't eager to replace his current master with git.bicoonductor.org's master (swap branches). Maybe one thing that makes it more palatable is that the current master can be retained, e.g., as a branch master_archive.
What are the alternatives to forcing master branch to be git.bioconductor.org's version? 

Selectively removing duplicate commits (how does one  do that?)

Cherry-picking (into the official Bioconductor branch) rather than merging?
I know it'll get hairy here, and maybe no easy or complete or simple solution... maybe seeing the steps required for alternative solutions would make the branch swap solution more palatable :) 

Martin



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




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