[Bioc-devel] banocc: Bioconductor BUILD error

Mon Aug 5 14:01:48 CEST 2019

Can you please display the results from

git remote -v

It looks like you may have not setup the remote to point to the Biocondutor repository.

# 2 from here:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

The code below looks like it is pulling and comparing to origin  which is normally your own github repository not the Bioconductor git repository.

If you did not have a github repository and were only linking to Bioconductor (not normally the case but possible) See #4  http://bioconductor.org/developers/how-to/git/maintain-bioc-only/.

Again most likely you will want this not the above:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

Please also consider glancing at more of the following help steps

http://bioconductor.org/developers/how-to/git/

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: George Weingart <george.weingart using gmail.com>
Sent: Sunday, August 4, 2019 4:43:15 PM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Bioc-devel <bioc-devel using r-project.org>
Subject: Re: banocc: Bioconductor BUILD error

Hi Lori and Bioc-Devel,

I followed Lori's instructions but the push is failing - I must be doing something wrong.
Here is the log:

Can you tell me how to do it right ?

Thanks!
George Weingart PhD
Huttenhower Lab
Harvard School of Public Health

Tanias-MacBook-Air:banocc georgeweingart$ git checkout RELEASE_3_9

Branch 'RELEASE_3_9' set up to track remote branch 'RELEASE_3_9' from 'origin'.

Switched to a new branch 'RELEASE_3_9'

Tanias-MacBook-Air:banocc georgeweingart$ git pull

Already up to date.

Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION

Tanias-MacBook-Air:vignettes georgeweingart$ vim banocc-vignette.Rmd

Tanias-MacBook-Air:vignettes georgeweingart$ git status

On branch RELEASE_3_9

Your branch is up to date with 'origin/RELEASE_3_9'.

Changes not staged for commit:

  (use "git add <file>..." to update what will be committed)

  (use "git checkout -- <file>..." to discard changes in working directory)

modified:   ../DESCRIPTION

modified:   banocc-vignette.Rmd

no changes added to commit (use "git add" and/or "git commit -a")

Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION

Tanias-MacBook-Air:banocc georgeweingart$ git add vignettes/banocc-vignette.Rmd

Tanias-MacBook-Air:banocc georgeweingart$ git status

On branch RELEASE_3_9

Your branch is up to date with 'origin/RELEASE_3_9'.

Changes to be committed:

  (use "git reset HEAD <file>..." to unstage)

modified:   DESCRIPTION

modified:   vignettes/banocc-vignette.Rmd

Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Updated: Release to 1.8.1 and removed C+11 references that were causing BUILD to fail"

[RELEASE_3_9 26bd0f7] Updated: Release to 1.8.1 and removed C+11 references that were causing BUILD to fail

 2 files changed, 2 insertions(+), 4 deletions(-)

Tanias-MacBook-Air:banocc georgeweingart$ git push upstream RELEASE_3_9

fatal: 'upstream' does not appear to be a git repository

fatal: Could not read from remote repository.

Please make sure you have the correct access rights

and the repository exists.

Tanias-MacBook-Air:banocc georgeweingart$ git push origin/RELEASE_3_9

fatal: 'origin/RELEASE_3_9' does not appear to be a git repository

fatal: Could not read from remote repository.

On Fri, Aug 2, 2019 at 4:52 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:

Hello,

The package was failing in release and devel.  There are two separate branches in Bioconductor.

The master branch of a package is always the devel branch of Bioconductor where you pushed "1.9.1".  We do see this clean report.

http://bioconductor.org/checkResults/devel/bioc-LATEST/banocc/

You will also have to make and push changes to the RELEASE_3_9  branch on bioconductor and bump the version to "1.8.1".

http://bioconductor.org/checkResults/release/bioc-LATEST/banocc/

This help page references fixes on a RELEASE branch:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

Summary:

git fetch --all

git checkout -b RELEASE_3_9  upstream/RELEASE_3_9
# or if you have already done this once
# git checkout RELEASE_3_9

git pull

# make necessary changes to code
# add and commit with a valid version bump (1.8.1)
# git add / git commit

git push upstream RELEASE_3_9

Hope this helps!  If you have further git issues for pushing to release I suggest checking out the help pages and then asking on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> mailing list so that others may assist as well.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: George Weingart <george.weingart using gmail.com<mailto:george.weingart using gmail.com>>
Sent: Thursday, August 1, 2019 2:57:21 PM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: banocc: Bioconductor BUILD error

Hi Lori,

I pushed about two weeks ago the changes that result in a good Build and Check at version 1.9.1 (of Banocc)  but I am still getting errors pertaining to Build at release 1.8.0.

Did I do something wrong ?  Perhaps I did not push correctly ?

Can I trouble you to look at it and let me know?

Thanks and best regards,
George Weingart PhD
Huttenhower Lab
Harvard School of Public Health

On Mon, Jul 15, 2019 at 5:57 PM George Weingart <george.weingart using gmail.com<mailto:george.weingart using gmail.com>> wrote:
Hello Lori,

Done !

I removed the two references to c++11 from the package,  ran a BUILD and a CHECK and they were clean.
Pushed the changes.

Below,  the log of the push.

Let me know what you find in the BiocCheck space pertaining the Sweave error.

Thank you !
Best regards,
George Weingart PhD
Huttenhower Lab
Harvard School of Public Health

LOG OF PUSH

Tanias-MacBook-Air:Harvard georgeweingart$ cd banocc

Tanias-MacBook-Air:banocc georgeweingart$ git status

On branch master

Your branch is up to date with 'origin/master'.

Changes not staged for commit:

  (use "git add <file>..." to update what will be committed)

  (use "git checkout -- <file>..." to discard changes in working directory)

modified:   DESCRIPTION

modified:   vignettes/banocc-vignette.Rmd

no changes added to commit (use "git add" and/or "git commit -a")

Tanias-MacBook-Air:banocc georgeweingart$ git add DESCRIPTION

Tanias-MacBook-Air:banocc georgeweingart$ git add vignettes/banocc-vignette.Rmd

Tanias-MacBook-Air:banocc georgeweingart$ git status

On branch master

Your branch is up to date with 'origin/master'.

Changes to be committed:

  (use "git reset HEAD <file>..." to unstage)

modified:   DESCRIPTION

modified:   vignettes/banocc-vignette.Rmd

Tanias-MacBook-Air:banocc georgeweingart$ git commit -m "Removed c++11 references that are making BUILD fail in R3.6.0"

[master d145287] Removed c++11 references that are making BUILD fail in R3.6.0

 2 files changed, 2 insertions(+), 4 deletions(-)

Tanias-MacBook-Air:banocc georgeweingart$ git push

Enumerating objects: 9, done.

Counting objects: 100% (9/9), done.

Delta compression using up to 4 threads

Compressing objects: 100% (5/5), done.

Writing objects: 100% (5/5), 481 bytes | 481.00 KiB/s, done.

Total 5 (delta 4), reused 0 (delta 0)

To git.bioconductor.org:packages/banocc

   5aefed9..d145287  master -> master

On Mon, Jul 15, 2019 at 11:35 AM George Weingart <george.weingart using gmail.com<mailto:george.weingart using gmail.com>> wrote:
Thanks Lori!

Will do.

Let me know about BiocCheck.

Thanks!
George Weingart

On Mon, Jul 15, 2019 at 10:26 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:

I can look into the BiocCheck ERROR for future development. It would be good to figure out why this is happening.  But in the meantime,  if your solution passes R CMD build and R CMD check please continue with pushing to the git.bioconductor.org<http://git.bioconductor.org> server  as BiocCheck is not run on the nightly builds.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: George Weingart <george.weingart using gmail.com<mailto:george.weingart using gmail.com>>
Sent: Monday, July 15, 2019 1:03:28 PM
To: stvjc using channing.harvard.edu<mailto:stvjc using channing.harvard.edu>; Shepherd, Lori
Cc: Bioc-devel; Lauren McIver; Huttenhower, Curtis; Eric Franzosa
Subject: banocc: Bioconductor BUILD error

Hello Lori and Vincent,

I am looking at the Bioconductor problem building banocc.

Can I trouble you to look into that?

If you cannot figure it out,   can you advise me what would be the correct forum / helpdesk to request assistance to resolve the issue?

I am posting the following logs:

  1.  Failed Build

  2.  Successful BUILD after removing c++11 references

  3.  Successful R CMD CHECK

  4.  Failed BiocCheck

Thank you!

George Weingart PhD

Huttenhower Lab

Harvard School of Public Health

Summary of the problem:

  1.  Banocc has been in Bioconductor for a while

  2.  Around April this year we started getting messages that the Build was failing

  3.  We have not changed anything in banocc

  4.  Build succeeds in R3.5.1

  5.  Recreated the problem on my Mac - Build fails in R3.6.0 with the following message:

Error: processing vignette 'banocc-vignette.Rmd' failed with diagnostics:

invalid connection

--- failed re-building �banocc-vignette.Rmd�

  1.  Solved the Build problem by removing 2 references to c++11

Removed from DESCRIPTION:

SystemRequirements: C++11

Removed from vignettes/banocc-vignette.Rmd:

Sys.setenv("PKG_CXXFLAGS"="-std=c++11")

  1.  R CMD CHECK works fine

  2.  BiocCheck fails with a message about SweaveParseOptions

* Checking coding practice...

    * NOTE: Avoid 1:...; use seq_len() or seq_along()

      Found in files:

        stan-output-make_samples_list.R (line 59, column 51)

Error in SweaveParseOptions(chunkopts, drobj$options, driver$checkopts) :

  parse error or empty option in

fit-model, cache=TRUE, dependson=c('compile-stan-model', 'generate-data'), echo=FALSE

  1.  I don�t understand why are we getting a Sweave error under BiocCheck  as we are using knitr and could not find a good reference for the rror.

Log #1: Recreation of error: Failed BUILD in R3.6.0

$ R CMD BUILD banocc

* checking for file �banocc/DESCRIPTION� ... OK

* preparing �banocc�:

* checking DESCRIPTION meta-information ... OK

* installing the package to build vignettes

* creating vignettes ... ERROR

--- re-building �banocc-vignette.Rmd� using rmarkdown

Quitting from lines 138-143 (banocc-vignette.Rmd)

Quitting from lines 138-143 (banocc-vignette.Rmd)

Error: processing vignette 'banocc-vignette.Rmd' failed with diagnostics:

invalid connection

--- failed re-building �banocc-vignette.Rmd�

SUMMARY: processing the following file failed:

  �banocc-vignette.Rmd�

Error: Vignette re-building failed.

Execution halted

Log #2: Successful build after removing references to c++11

Removed from DESCRIPTION:

SystemRequirements: C++11

Removed from vignettes/banocc-vignette.Rmd:

Sys.setenv("PKG_CXXFLAGS"="-std=c++11")

Tanias-MacBook-Air:Harvard georgeweingart$ R CMD BUILD banocc

* checking for file �banocc/DESCRIPTION� ... OK

* preparing �banocc�:

* checking DESCRIPTION meta-information ... OK

* installing the package to build vignettes

* creating vignettes ... OK

Warning: �inst/doc� files

    �banocc-vignette.Rmd�, �banocc-vignette.html�, �banocc-vignette.R�

  ignored as vignettes have been rebuilt.

  Run R CMD build with --no-build-vignettes to prevent rebuilding.

* checking for LF line-endings in source and make files and shell scripts

* checking for empty or unneeded directories

* looking to see if a �data/datalist� file should be added

* building �banocc_1.8.0.tar.gz�

Log #3 Successful R CMD CHECK

Tanias-MacBook-Air:Harvard georgeweingart$ R CMD BUILD banocc

* checking for file �banocc/DESCRIPTION� ... OK

* preparing �banocc�:

* checking DESCRIPTION meta-information ... OK

* installing the package to build vignettes

* creating vignettes ... OK

Warning: �inst/doc� files

    �banocc-vignette.Rmd�, �banocc-vignette.html�, �banocc-vignette.R�

  ignored as vignettes have been rebuilt.

  Run R CMD build with --no-build-vignettes to prevent rebuilding.

* checking for LF line-endings in source and make files and shell scripts

* checking for empty or unneeded directories

* looking to see if a �data/datalist� file should be added

* building �banocc_1.8.0.tar.gz�

Tanias-MacBook-Air:Harvard georgeweingart$  R CMD CHECK "banocc_1.8.0.tar.gz"

* using log directory �/Users/georgeweingart/Documents/Harvard/banocc.Rcheck�

* using R version 3.6.1 (2019-07-05)

* using platform: x86_64-apple-darwin15.6.0 (64-bit)

* using session charset: UTF-8

* checking for file �banocc/DESCRIPTION� ... OK

* checking extension type ... Package

* this is package �banocc� version �1.8.0�

* checking package namespace information ... OK

* checking package dependencies ... OK

* checking if this is a source package ... OK

* checking if there is a namespace ... OK

* checking for executable files ... OK

* checking for hidden files and directories ... OK

* checking for portable file names ... OK

* checking for sufficient/correct file permissions ... OK

* checking whether package �banocc� can be installed ... OK

* checking installed package size ... OK

* checking package directory ... OK

* checking �build� directory ... OK

* checking DESCRIPTION meta-information ... OK

* checking top-level files ... OK

* checking for left-over files ... OK

* checking index information ... OK

* checking package subdirectories ... OK

* checking R files for non-ASCII characters ... OK

* checking R files for syntax errors ... OK

* checking whether the package can be loaded ... OK

* checking whether the package can be loaded with stated dependencies ... OK

* checking whether the package can be unloaded cleanly ... OK

* checking whether the namespace can be loaded with stated dependencies ... OK

* checking whether the namespace can be unloaded cleanly ... OK

* checking loading without being on the library search path ... OK

* checking dependencies in R code ... OK

* checking S3 generic/method consistency ... OK

* checking replacement functions ... OK

* checking foreign function calls ... OK

* checking R code for possible problems ... NOTE

calc_snc: no visible global function definition for �sd�

get_IVs : <anonymous>: no visible global function definition for

  �rgamma�

get_banocc_output : <anonymous>: no visible global function definition

  for �cov2cor�

get_posterior_quantiles: no visible binding for global variable

  �quantile�

rgbeta: no visible global function definition for �rbeta�

rgbeta: no visible global function definition for �rbinom�

Undefined global functions or variables:

  cov2cor quantile rbeta rbinom rgamma sd

Consider adding

  importFrom("stats", "cov2cor", "quantile", "rbeta", "rbinom", "rgamma",

             "sd")

to your NAMESPACE file.

* checking Rd files ... OK

* checking Rd metadata ... OK

* checking Rd cross-references ... OK

* checking for missing documentation entries ... OK

* checking for code/documentation mismatches ... OK

* checking Rd \usage sections ... OK

* checking Rd contents ... OK

* checking for unstated dependencies in examples ... OK

* checking contents of �data� directory ... OK

* checking data for non-ASCII characters ... OK

* checking data for ASCII and uncompressed saves ... OK

* checking installed files from �inst/doc� ... OK

* checking files in �vignettes� ... OK

* checking examples ... OK

* checking for unstated dependencies in �tests� ... OK

* checking tests ...

  Running �testthat.R�

 OK

* checking for unstated dependencies in vignettes ... OK

* checking package vignettes in �inst/doc� ... OK

* checking running R code from vignettes ...

  �banocc-vignette.Rmd�using �UTF-8�... OK

 NONE

* checking re-building of vignette outputs ... OK

* checking PDF version of manual ... OK

* DONE

Status: 1 NOTE

See

  �/Users/georgeweingart/Documents/Harvard/banocc.Rcheck/00check.log�

for details.

Log #4 Failed BiocCheck

Tanias-MacBook-Air:Harvard georgeweingart$ R

R version 3.6.1 (2019-07-05) -- "Action of the Toes"

Copyright (C) 2019 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

> library(BiocCheck)

>

> BiocCheck("banocc_1.8.0.tar.gz")

This is BiocCheck version 1.20.0. BiocCheck is a work in progress.

Output and severity of issues may change. Installing package...

* Checking Package Dependencies...

* Checking if other packages can import this one...

* Checking to see if we understand object initialization...

    * NOTE: Consider clarifying how 6 object(s) are initialized. Maybe

      they are part of a data set loaded with data(), or perhaps part

      of an object referenced in with() or within().

    function (object)

      calc_snc (sd)

      get_banocc_output  (cov2cor)

      get_IVs  (rgamma)

      get_posterior_quantiles (quantile)

      rgbeta (rbeta)

      rgbeta (rbinom)

* Checking for deprecated package usage...

* Checking for remote package usage...

* Checking version number...

* Checking for version number mismatch...

* Checking version number validity...

* Checking R Version dependency...

    * WARNING: Update R version dependency from 3.5.1 to 3.6.

* Checking package size...

    * ERROR: Package Source tarball exceeds Bioconductor size

      requirement.

        Package Size: 26.7562 MB

        Size Requirement: 5.0000 MB

* Checking individual file sizes...

    * WARNING: The following files are over 5MB in size:

      'tests/testthat/testthat_objects/banocc_model_test.RData

      tests/testthat/testthat_objects/sample_stan_fit.RData'

* Checking biocViews...

* Checking that biocViews are present...

* Checking package type based on biocViews...

    Software

* Checking for non-trivial biocViews...

* Checking that biocViews come from the same category...

* Checking biocViews validity...

* Checking for recommended biocViews...

* Checking build system compatibility...

* Checking for blank lines in DESCRIPTION...

* Checking if DESCRIPTION is well formatted...

* Checking for whitespace in DESCRIPTION field names...

* Checking that Package field matches directory/tarball name...

* Checking for Version field...

* Checking for valid maintainer...

* Checking DESCRIPTION/NAMESPACE consistency...

* Checking vignette directory...

    This is a software package

* Checking library calls...

* Checking for library/require of banocc...

* Checking coding practice...

    * NOTE: Avoid 1:...; use seq_len() or seq_along()

      Found in files:

        stan-output-make_samples_list.R (line 59, column 51)

Error in SweaveParseOptions(chunkopts, drobj$options, driver$checkopts) :

  parse error or empty option in

fit-model, cache=TRUE, dependson=c('compile-stan-model', 'generate-data'), echo=FALSE

>

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