[Bioc-devel] banocc: Bioconductor BUILD error

George Weingart george@we|ng@rt @end|ng |rom gm@||@com
Thu Aug 1 20:57:21 CEST 2019


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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