R devel - Sep 2018 - Suggested Patch: Adding commas to list of packages after R CMD check

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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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
> 
> 
> This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

>>>>> Duncan Murdoch 
>>>>>     on Tue, 18 Sep 2018 16:23:47 -0400 writes:
> 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.
Your patch to *both* internal functions is small and in that
respect very nice, but it would effect really many of the R CMD
check messages.

I had been testing a modularized version of your proposed change
which only changes the defaults of  pretty_format2(.)   which
indeed is most often used in the context of listing package names.
In addition, I also did use regular quotes instead of the fancy
quotes there.

This has been committed to R-devel  (accidentally already
together with the \Sexpr{} related bug fix) in svn rev 75378, last Friday.

> 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
The new facilities (in R-devel only, by Luke Tierney) with NEWS entries

    ? Many ?package not found? errors are now signaled as errors of
      class packageNotFoundError.

    ? As an experimental feature, when loadNamespace() fails because
      the requested package is not available the error is initially
      signaled with a retry_loadNamespace restart available. This
      allows a calling handler to try to install the package and continue.

indeed should "easily" allow to go in that direction.

Thank you, Marcel and Duncan!

Martin
> 
> > 
> > 
> > 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