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
>>
>> >
>>
>>
>>
>>
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