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 at 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 at gmail.com>
*Sent:* Monday, July 15, 2019 1:03:28 PM
*To:* stvjc at 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.
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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