From murdoch@dunc@n @ending from gm@il@com  Tue Sep 18 22:23:47 2018
From: murdoch@dunc@n @ending from gm@il@com (Duncan Murdoch)
Date: Tue, 18 Sep 2018 16:23:47 -0400
Subject: [Rd] 
 Suggested Patch: Adding commas to list of packages after R CMD check
In-Reply-To: <7e1e0dfa-714f-aab8-1011-4d32fcb1c5e6@roswellpark.org>
References: <7e1e0dfa-714f-aab8-1011-4d32fcb1c5e6@roswellpark.org>
Message-ID: <5d8e2a34-4f71-6002-8e50-09fed8a74c97@gmail.com>

On 18/09/2018 2:16 PM, Marcel Ramos wrote:
> Dear R-devs,
> 
> 
> Scenario:
> 
> When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces).
> 
> Example:
> 
> ```
> R CMD check glmSparseNet_0.99.13.tar.gz
> * using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck'
> * using R Under development (unstable) (2018-06-06 r74855)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file 'glmSparseNet/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'glmSparseNet' version '0.99.13'
> * package encoding: UTF-8
> * checking package namespace information ... OK
> * checking package dependencies ... ERROR
> Packages required but not available:
>    'MultiAssayExperiment' 'glmnet' 'SummarizedExperiment' 'STRINGdb'
>    'biomaRt' 'futile.logger' 'sparsebn' 'sparsebnUtils' 'forcats'
>    'dplyr' 'readr' 'ggplot2' 'ggfortify' 'reshape2' 'rlang' 'loose.rock'
> 
> Packages suggested but not available:
>    'testthat' 'knitr' 'rmarkdown' 'survcomp' 'pROC' 'devtools'
>    'VennDiagram' 'BiocStyle' 'curatedTCGAData'
> 
> VignetteBuilder package required for checking but not installed: 'knitr'
> 
> The suggested packages are required for a complete check.
> Checking can be attempted without them by setting the environment
> variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
> 
> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
> manual.
> * DONE
> 
> Status: 1 ERROR
> See
>    '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck/00check.log'
> for details.
> ```
> 
> 
> Suggested Patch:
> 
> To return a list of missing dependencies delimited by a comma and a space (", ") so to make it easier for the user to copy and paste this list.
> This would be especially helpful when the list of missing dependencies is extensive.

This seems like a reasonable suggestion, considering how easy it is to do.

Another suggestion would be to (optionally) automatically install 
missing dependencies.  I think the devtools::install_deps function will 
do that.  (I don't use it, I have a homebrewed function for that purpose.)

Duncan Murdoch


> 
> 
> Example output:
> 
> ```
> R CMD check glmSparseNet_0.99.13.tar.gz
> * using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck'
> * using R Under development (unstable) (2018-09-18 r75322)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file 'glmSparseNet/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'glmSparseNet' version '0.99.13'
> * package encoding: UTF-8
> * checking package namespace information ... OK
> * checking package dependencies ... ERROR
> Packages required but not available:
>    'MultiAssayExperiment', 'glmnet', 'SummarizedExperiment', 'STRINGdb',
>    'biomaRt', 'futile.logger', 'sparsebn', 'sparsebnUtils', 'forcats',
>    'dplyr', 'readr', 'ggplot2', 'ggfortify', 'reshape2', 'stringr',
>    'rlang', 'loose.rock'
> 
> Packages suggested but not available:
>    'testthat', 'knitr', 'rmarkdown', 'survcomp', 'pROC', 'devtools',
>    'roxygen2', 'VennDiagram', 'BiocStyle', 'curatedTCGAData'
> 
> VignetteBuilder package required for checking but not installed: 'knitr'
> 
> The suggested packages are required for a complete check.
> Checking can be attempted without them by setting the environment
> variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
> 
> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
> manual.
> * DONE
> 
> Status: 1 ERROR
> See
>    '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck/00check.log'
> for details.
> ```
> 
> 
> svn diff:
> 
> 
> Index: src/library/tools/R/QC.R
> ===================================================================
> --- src/library/tools/R/QC.R    (revision 75322)
> +++ src/library/tools/R/QC.R    (working copy)
> @@ -8536,13 +8536,13 @@
>   .pretty_format <-
>   function(x)
>   {
> -    strwrap(paste(sQuote(x), collapse = " "),
> +    strwrap(paste(sQuote(x), collapse = ", "),
>               indent = 2L, exdent = 2L)
>   }
>   .pretty_format2 <-
>   function(msg, x)
>   {
> -    xx <- strwrap(paste(sQuote(x), collapse = " "), exdent = 2L)
> +    xx <- strwrap(paste(sQuote(x), collapse = ", "), exdent = 2L)
>       if (length(xx) > 1L || nchar(msg) + nchar(xx) + 1L > 75L)
>           c(msg, .pretty_format(x))
>       else paste(msg, xx)
> 
> 
> 
> PS. I would also advocate for setting `useFancyQuotes` to `FALSE` by default but it would be better to get more
> input from the community.
> 
> Thanks!
> 
> 
> Best regards,
> 
> Marcel
> 
> --
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Care Center
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> 
> 
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[Rd] Suggested Patch: Adding commas to list of packages after R CMD check
Duncan Murdoch