[Bioc-devel] banocc: Bioconductor BUILD error

[George Weingart]

Hi Lori,

I followed your instructions and went as far as “git push upstream master”

Do I need to do the “(Optional) Merge changes to the current release
branch” ?

As I mentioned, I am being extra careful so I do not damage the repository.

Thanks so much for your  help !!

George

Here is the log:


Tanias-MacBook-Air:Harvard georgeweingart$ git clone
git using git.bioconductor.org:packages/banocc

Cloning into 'banocc'...

remote: Enumerating objects: 142, done.

remote: Counting objects: 100% (142/142), done.

remote: Compressing objects: 100% (138/138), done.

remote: Total 142 (delta 47), reused 0 (delta 0)

Receiving objects: 100% (142/142), 25.33 MiB | 880.00 KiB/s, done.

Resolving deltas: 100% (47/47), done.

Tanias-MacBook-Air:Harvard georgeweingart$ cd banocc

Tanias-MacBook-Air:banocc georgeweingart$ git remote -v

origin git using git.bioconductor.org:packages/banocc (fetch)

origin git using git.bioconductor.org:packages/banocc (push)

Tanias-MacBook-Air:banocc georgeweingart$ git remote rename origin upstream

Tanias-MacBook-Air:banocc georgeweingart$ git remote -v

*upstream* git using git.bioconductor.org:packages/banocc (fetch)

*upstream* git using git.bioconductor.org:packages/banocc (push)

Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION

Tanias-MacBook-Air:banocc georgeweingart$ cd vignettes/

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

Tanias-MacBook-Air:banocc georgeweingart$ git status

On branch master

Your branch is up to date with 'upstream/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 commit -m "Modified date in
the DESCRIPTION and removed reference to c+11 in vignette"

[master e59c70c] Modified date in the DESCRIPTION and removed reference to
c+11 in vignette

 2 files changed, 1 insertion(+), 2 deletions(-)

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

Already on 'master'

Your branch is ahead of 'upstream/master' by 1 commit.

  (use "git push" to publish your local commits)

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

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), 472 bytes | 472.00 KiB/s, done.

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

To git.bioconductor.org:packages/banocc

   d145287..e59c70c  master -> master


On Mon, Aug 5, 2019 at 7:56 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> So you only have a Bioconductor git repository,
>
> not your own github repository to also keep track of changes?
>
>
> Then these instructions are correct:
>
>  http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
>
> We normal recommend changing the name of the remote from origin to
> upstream so that it is consistent with all the help documentation (Step #4
> above) we have written.
>
>
> If you do not want to rename  then the following will push to the git
> bioconductor repository,
>
> git push origin RELEASE_3_9
>
>
> The syntax of a git command like git push or git pull  can be broken down
> to
>
> git push  <name of remote>  <name of branch>
>
>
> so git push origin RELEASE_3_9
>
>
> based on git remote -v
>
> your origin remote points to the git.bioconductor.org location
>
>
> Tanias-MacBook-Air:banocc georgeweingart$ git remote -v
> origin git using git.bioconductor.org:packages/banocc (fetch)
> origin git using git.bioconductor.org:packages/banocc (push)
>
> So git push origin RELEASE_3_9
>
> will push to the bioconductor git repository (your origin remote)  and to
> the RELEASE_3_9 branch.
>
>
>
> Hope this helps
>
>
>
> 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:* Monday, August 5, 2019 10:48:30 AM
> *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,
> Here is the display you wanted to see.
>
> Tanias-MacBook-Air:banocc georgeweingart$ *git remote -v*
>
> origin git using git.bioconductor.org:packages/banocc (fetch)
>
> origin git using git.bioconductor.org:packages/banocc (push)
>
> Tanias-MacBook-Air:banocc georgeweingart$
>
>
> So what should the next step be?
>
>
> I don't want to 'try'  things so I do not cause damage to the repository .
>
>
> Thanks!
>
> George Weingart
>
>
> Thanks!
>
>
>
> On Mon, Aug 5, 2019 at 5:01 AM Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
> 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> 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 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>
> *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>
> *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>
> 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> 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> 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 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>
> *Sent:* Monday, July 15, 2019 1:03:28 PM
> *To:* 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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