Hi Lori, I followed all the instructions in http://bioconductor.org/developers/how-to/git/maintain-bioc-only/. See log below. Is there anything that I need to do at this point ?
Thanks so much for all your help ! George Weingart PhD Huttenhower Lab Harvard School of Public Health *Log:* Tanias-MacBook-Air:banocc georgeweingart$ vim DESCRIPTION Tanias-MacBook-Air:banocc georgeweingart$ git status On branch RELEASE_3_9 Your branch is ahead of 'upstream/RELEASE_3_9' by 4 commits. (use "git push" to publish your local commits) 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 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 commit -m "Updated version number" [RELEASE_3_9 3bf4a1d] Updated version number 1 file changed, 1 insertion(+), 1 deletion(-) Tanias-MacBook-Air:banocc georgeweingart$ git push upstream RELEASE_3_9 Enumerating objects: 8, done. Counting objects: 100% (8/8), done. Delta compression using up to 4 threads Compressing objects: 100% (6/6), done. Writing objects: 100% (6/6), 573 bytes | 573.00 KiB/s, done. Total 6 (delta 4), reused 0 (delta 0) To git.bioconductor.org:packages/banocc e689ef5..3bf4a1d RELEASE_3_9 -> RELEASE_3_9 On Mon, Aug 5, 2019 at 9:34 AM Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > Hi George, > > > No problem at all. We are glad to help and glad you are being so > cautious. > > > I am able to see the successful commit/changes on devel (master branch). > So that has been successful. > > > You would need to make similar changes to the RELEASE_3_9 branch as your > package was failing in both release and devel > > > release build report: > > http://bioconductor.org/checkResults/release/bioc-LATEST/banocc/ > > > So yes the > (Optional) Merge changes to the current release branch > does apply. > > A note about these commands: > > git merge master > > will merge all the files from the current devel branch into the release > branch. Sometime this is okay and recommended but sometimes this is not > what you want (if you has been testing features that are in the devel > branch but need to correct a bug on release). Sometimes it's better to > checkout the release branch: > > git checkout -b <RELEASE_X_Y> upstream/<RELEASE_X_Y> > > git pull > > > but then individually modify and commit changes like you did for the other > branch. > > > > However, In this case you should be okay with a merge - > > > The current release branch is RELEASE_3_9 (instead of RELEASE_X_Y in the > instructions) > > > Also note the version in the DESCRIPTION file for the RELEASE_3_9 branch > will need to be changed. The current version is 1.8.0 so this should be > changed to 1.8.1 and committed before doing > > > git push upstream RELEASE_3_9 > > > > Hopefully this all makes sense. If something seems unclear don't > hesistate to ask. > > > 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.weing...@gmail.com> > *Sent:* Monday, August 5, 2019 12:17:29 PM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* Bioc-devel <bioc-devel@r-project.org> > *Subject:* Re: banocc: Bioconductor BUILD error > > > 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 > g...@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 g...@git.bioconductor.org:packages/banocc (fetch) > > origin g...@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* g...@git.bioconductor.org:packages/banocc (fetch) > > *upstream* g...@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.sheph...@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 g...@git.bioconductor.org:packages/banocc (fetch) > origin g...@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.weing...@gmail.com> > *Sent:* Monday, August 5, 2019 10:48:30 AM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* Bioc-devel <bioc-devel@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 g...@git.bioconductor.org:packages/banocc (fetch) > > origin g...@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.sheph...@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.weing...@gmail.com> > *Sent:* Sunday, August 4, 2019 4:43:15 PM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* Bioc-devel <bioc-devel@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.sheph...@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@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.weing...@gmail.com> > *Sent:* Thursday, August 1, 2019 2:57:21 PM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* Bioc-devel <bioc-devel@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.weing...@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.weing...@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.sheph...@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.weing...@gmail.com> > *Sent:* Monday, July 15, 2019 1:03:28 PM > *To:* st...@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 > > > > > > > > This email message may contain legally privileged and/or confidential > information. 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