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

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

Peter Waltman-2
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@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]]

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Re: Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?

Duncan Murdoch-2
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@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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Re: Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?

Martin Morgan-4
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" <[hidden email] on behalf of [hidden email]> 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@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
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Was there a change to R ver. 3.5.2 so that it now treats warnings during installs as errors?

Peter Waltman-2
Fantastic - that was it! Thanks so much!

On Sun, Jan 20, 2019 at 7:29 AM Martin Morgan <[hidden email]>
wrote:

> 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" <
> [hidden email] on behalf of [hidden email]> 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@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
>
>     ______________________________________________
>     [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>     https://stat.ethz.ch/mailman/listinfo/r-help
>     PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>     and provide commented, minimal, self-contained, reproducible code.
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.