[Bioc-devel] banocc: Bioconductor BUILD error

George Weingart george@we|ng@rt @end|ng |rom gm@||@com
Mon Jul 15 20:35:39 CEST 2019


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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