R help - Jan 2019 - Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?

I'm trying to install a devel package called gGnome (
https://github.com/mskilab/gGnome). One of its dependencies is another
package from the same group, called gTrack, which causes several warning
messages to be generated because it overloads a couple of functions that
are part of other packages that gTrack is dependent upon.  The specific
warnings are provided below.  During the lazy-loading step of gGnome's
install, gTrack is loaded, and when these warnings come up, they are
converted to errors, causing the install to fail. This behavior is new to
version 3.5.2, as I've been able to successfully install these packages
with R versions 3.5.0 and 3.5.1. Is there a workaround for this for version
3.5.2?

Thanks!

Error message during gGnome install:
> install_github('mskilab/gGnome')
Downloading GitHub repo mskilab/gGnome at master
Skipping 3 packages not available: GenomicRanges, rtracklayer,
VariantAnnotation
?  checking for file
?/tmp/Rtmp4hnMMO/remotes7fb938cd0553/mskilab-gGnome-81f661e/DESCRIPTION? ...
?  preparing ?gGnome?:
?  checking DESCRIPTION meta-information ...
?  checking for LF line-endings in source and make files and shell scripts
?  checking for empty or unneeded directories
   Removed empty directory ?gGnome/inst/extdata/gTrack.js?
?  building ?gGnome_0.1.tar.gz?

* installing *source* package ?gGnome? ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ?gTrack?:
* (converted from warning)* multiple methods tables found for ?seqinfo<-?
Error : package ?gTrack? could not be loaded
ERROR: lazy loading failed for package ?gGnome?
* removing ?/home/waltman/bin/R/3.5.2/lib/R/library/gGnome?
Error in i.p(...) :
  (converted from warning) installation of package
?/tmp/Rtmp4hnMMO/file7fb929638ed8/gGnome_0.1.tar.gz? had non-zero exit
status


warning from gTrack when it is loaded:

Attaching package: ?gTrack?

The following object is masked from ?package:GenomicRanges?:

    seqinfo<-

The following object is masked from ?package:GenomeInfoDb?:

    seqinfo<-

Warning message:
multiple methods tables found for ?seqinfo<-?

	[[alternative HTML version deleted]]

On 19/01/2019 8:22 p.m., Peter Waltman wrote:
> I'm trying to install a devel package called gGnome (
> https://github.com/mskilab/gGnome). One of its dependencies is another
> package from the same group, called gTrack, which causes several warning
> messages to be generated because it overloads a couple of functions that
> are part of other packages that gTrack is dependent upon.  The specific
> warnings are provided below.  During the lazy-loading step of gGnome's
> install, gTrack is loaded, and when these warnings come up, they are
> converted to errors, causing the install to fail. This behavior is new to
> version 3.5.2, as I've been able to successfully install these packages
> with R versions 3.5.0 and 3.5.1. Is there a workaround for this for version
> 3.5.2?
> 
> Thanks!
> 
> Error message during gGnome install:
> 
>> install_github('mskilab/gGnome')
> Downloading GitHub repo mskilab/gGnome at master
> Skipping 3 packages not available: GenomicRanges, rtracklayer,
> VariantAnnotation
> ?  checking for file
> ?/tmp/Rtmp4hnMMO/remotes7fb938cd0553/mskilab-gGnome-81f661e/DESCRIPTION?
...
> ?  preparing ?gGnome?:
> ?  checking DESCRIPTION meta-information ...
> ?  checking for LF line-endings in source and make files and shell scripts
> ?  checking for empty or unneeded directories
>     Removed empty directory ?gGnome/inst/extdata/gTrack.js?
> ?  building ?gGnome_0.1.tar.gz?
> 
> * installing *source* package ?gGnome? ...
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Error: package or namespace load failed for ?gTrack?:
> * (converted from warning)* multiple methods tables found for
?seqinfo<-?
> Error : package ?gTrack? could not be loaded
> ERROR: lazy loading failed for package ?gGnome?
> * removing ?/home/waltman/bin/R/3.5.2/lib/R/library/gGnome?
> Error in i.p(...) :
>    (converted from warning) installation of package
> ?/tmp/Rtmp4hnMMO/file7fb929638ed8/gGnome_0.1.tar.gz? had non-zero exit
> status
That message indicates that options("warn") is 2 or higher when the 
warning occurs.  What is its setting before you start the install?

Duncan Murdoch

Looks like you're using remotes::install_github(), which in turn uses
remotes::install().

The README

 
https://github.com/r-lib/remotes/blob/254c67ed6502e092a316553f2a44f04b0e595b64/README.md

says "Setting R_REMOTES_NO_ERRORS_FROM_WARNINGS=true avoids stopping the
installation for warning messages. Warnings usually mean installation errors, so
by default remotes stops for a warning. However, sometimes other warnings might
happen, that could be ignored by setting this environment variable.

So I'd guess

  Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)

before installing the package would address this problem.

Martin Morgan

?On 1/20/19, 6:58 AM, "R-help on behalf of Duncan Murdoch"
<r-help-bounces at r-project.org on behalf of murdoch.duncan at gmail.com>
wrote:

    On 19/01/2019 8:22 p.m., Peter Waltman wrote:
    > I'm trying to install a devel package called gGnome (
    > https://github.com/mskilab/gGnome). One of its dependencies is another
    > package from the same group, called gTrack, which causes several
warning
    > messages to be generated because it overloads a couple of functions
that
    > are part of other packages that gTrack is dependent upon.  The specific
    > warnings are provided below.  During the lazy-loading step of
gGnome's
    > install, gTrack is loaded, and when these warnings come up, they are
    > converted to errors, causing the install to fail. This behavior is new
to
    > version 3.5.2, as I've been able to successfully install these
packages
    > with R versions 3.5.0 and 3.5.1. Is there a workaround for this for
version
    > 3.5.2?
    > 
    > Thanks!
    > 
    > Error message during gGnome install:
    > 
    >> install_github('mskilab/gGnome')
    > Downloading GitHub repo mskilab/gGnome at master
    > Skipping 3 packages not available: GenomicRanges, rtracklayer,
    > VariantAnnotation
    > ?  checking for file
    >
?/tmp/Rtmp4hnMMO/remotes7fb938cd0553/mskilab-gGnome-81f661e/DESCRIPTION? ...
    > ?  preparing ?gGnome?:
    > ?  checking DESCRIPTION meta-information ...
    > ?  checking for LF line-endings in source and make files and shell
scripts
    > ?  checking for empty or unneeded directories
    >     Removed empty directory ?gGnome/inst/extdata/gTrack.js?
    > ?  building ?gGnome_0.1.tar.gz?
    > 
    > * installing *source* package ?gGnome? ...
    > ** R
    > ** inst
    > ** byte-compile and prepare package for lazy loading
    > Error: package or namespace load failed for ?gTrack?:
    > * (converted from warning)* multiple methods tables found for
?seqinfo<-?
    > Error : package ?gTrack? could not be loaded
    > ERROR: lazy loading failed for package ?gGnome?
    > * removing ?/home/waltman/bin/R/3.5.2/lib/R/library/gGnome?
    > Error in i.p(...) :
    >    (converted from warning) installation of package
    > ?/tmp/Rtmp4hnMMO/file7fb929638ed8/gGnome_0.1.tar.gz? had non-zero exit
    > status
    
    That message indicates that options("warn") is 2 or higher when
the
    warning occurs.  What is its setting before you start the install?
    
    Duncan Murdoch
    
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