From M@rcel@R@mo@ @ending from ro@wellp@rk@org  Tue Sep 18 20:16:27 2018
From: M@rcel@R@mo@ @ending from ro@wellp@rk@org (Marcel Ramos)
Date: Tue, 18 Sep 2018 18:16:27 +0000
Subject: [Rd] Suggested Patch: Adding commas to list of packages after R CMD
 check
Message-ID: <7e1e0dfa-714f-aab8-1011-4d32fcb1c5e6@roswellpark.org>

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.


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
Marcel Ramos