Re: [Bioc-devel] Suppressing messages from Rprofile
Thanks both for the suggestions.
I ended up piping the output to tail -n1 I've no idea how portable that is,
but presumably similar to trying a grep/sed approach.
Cheers,
Mike
On Thu, 8 Apr 2021 at 15:48, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> You could also preprend your cat so it outputs something like
> INCLUDE_DIR=..
> and then use grep and sed to trim it. Of course that can also end up being
> brittle.
>
> On Wed, Apr 7, 2021 at 10:48 PM Henrik Bengtsson <
> henrik.bengts...@gmail.com> wrote:
>
>> Correcting: the env var is R_LIBS_USER and nothing else.
>>
>> /Henrik
>>
>> On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson
>> wrote:
>> >
>> > Can you go via a temporary file instead, i.e. output what you want to
>> > grab to a temporary file and pull the info from that instead?
>> >
>> > Side tracking ...
>> >
>> > > I thought about using --vanilla but I use .Rprofile to set my library
>> path,
>> > > so ignoring that file completely defeats the point in my setup.
>> >
>> > I'm a proponent of customizing the library path via .Renviron instead
>> > of via .Rprofile. In your case, you can have a line in ~/.Renviron
>> > with:
>> >
>> > R_USER_LIBS=~/R/%p-library/%v-bioc_3.12
>> >
>> > Alternatively, you can set it elsewhere, e.g. ~/.bashrc, in a Linux
>> > environment module that is loaded, and so on.
>> >
>> > BTW, using Rscript --no-init-file ... would skip .Rprofile while still
>> > parsing .Renviron.
>> >
>> > /Henrik
>> >
>> > On Wed, Apr 7, 2021 at 8:16 AM Mike Smith wrote:
>> > >
>> > > I have the following line in the configure.ac for rhdf5filters, which
>> > > returns the location of the HDF5 headers distributed with Rhdf5lib:
>> > >
>> > > RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
>> > > 'cat(system.file("include", package="Rhdf5lib"))'`
>> > >
>> > > For me the output is a path like
>> > > /mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets
>> inserted into
>> > > the package Makevars file, and the package compilation works.
>> > >
>> > > However I've had multiple reports (
>> > > https://github.com/grimbough/rhdf5filters/issues/11) where this
>> doesn't
>> > > work, all of which seem to relate to messages printed when an
>> Rprofile is
>> > > loaded. They have well intentioned messages like below, which don't
>> work
>> > > so well when passed as compiler flags
>> > >
>> > > [1] "[BMRC] You have sourced the BMRC Rprofile provided at
>> > > /apps/misc/R/bmrc-r-user-tools/Rprofile"
>> > > [1] "[BMRC] Messages coming from this file (like this one) will be
>> > > prefixed with [BMRC]"
>> > > [1] "[BMRC] You are running R on host
>> > > with CPU "
>> > > [1] "[BMRC] While running on this host, local R packages will be
>> > > sourced from and installed to
>> > > /well/combat/users/ifl143/R/4.0/ivybridge"
>> > > /gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include
>> > >
>> > > I thought about using --vanilla but I use .Rprofile to set my library
>> path,
>> > > so ignoring that file completely defeats the point in my setup. Is
>> anyone
>> > > aware of either a more reliable way of getting the information I want
>> > > (maybe suppressing messages, different mechanism entirely, etc)?
>> > > Alternatively, is there anything definitive in WRE or the like that
>> > > suggests printing messages Rprofile is a bad idea that I can pass on
>> to the
>> > > users?
>> > >
>> > > Cheers,
>> > > Mike
>> > >
>> > > [[alternative HTML version deleted]]
>> > >
>> > > ___
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Best,
> Kasper
>
[[alternative HTML version deleted]]
___
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Re: [Bioc-devel] Suppressing messages from Rprofile
You could also preprend your cat so it outputs something like
INCLUDE_DIR=..
and then use grep and sed to trim it. Of course that can also end up being
brittle.
On Wed, Apr 7, 2021 at 10:48 PM Henrik Bengtsson
wrote:
> Correcting: the env var is R_LIBS_USER and nothing else.
>
> /Henrik
>
> On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson
> wrote:
> >
> > Can you go via a temporary file instead, i.e. output what you want to
> > grab to a temporary file and pull the info from that instead?
> >
> > Side tracking ...
> >
> > > I thought about using --vanilla but I use .Rprofile to set my library
> path,
> > > so ignoring that file completely defeats the point in my setup.
> >
> > I'm a proponent of customizing the library path via .Renviron instead
> > of via .Rprofile. In your case, you can have a line in ~/.Renviron
> > with:
> >
> > R_USER_LIBS=~/R/%p-library/%v-bioc_3.12
> >
> > Alternatively, you can set it elsewhere, e.g. ~/.bashrc, in a Linux
> > environment module that is loaded, and so on.
> >
> > BTW, using Rscript --no-init-file ... would skip .Rprofile while still
> > parsing .Renviron.
> >
> > /Henrik
> >
> > On Wed, Apr 7, 2021 at 8:16 AM Mike Smith wrote:
> > >
> > > I have the following line in the configure.ac for rhdf5filters, which
> > > returns the location of the HDF5 headers distributed with Rhdf5lib:
> > >
> > > RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
> > > 'cat(system.file("include", package="Rhdf5lib"))'`
> > >
> > > For me the output is a path like
> > > /mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets inserted
> into
> > > the package Makevars file, and the package compilation works.
> > >
> > > However I've had multiple reports (
> > > https://github.com/grimbough/rhdf5filters/issues/11) where this
> doesn't
> > > work, all of which seem to relate to messages printed when an Rprofile
> is
> > > loaded. They have well intentioned messages like below, which don't
> work
> > > so well when passed as compiler flags
> > >
> > > [1] "[BMRC] You have sourced the BMRC Rprofile provided at
> > > /apps/misc/R/bmrc-r-user-tools/Rprofile"
> > > [1] "[BMRC] Messages coming from this file (like this one) will be
> > > prefixed with [BMRC]"
> > > [1] "[BMRC] You are running R on host
> > > with CPU "
> > > [1] "[BMRC] While running on this host, local R packages will be
> > > sourced from and installed to
> > > /well/combat/users/ifl143/R/4.0/ivybridge"
> > > /gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include
> > >
> > > I thought about using --vanilla but I use .Rprofile to set my library
> path,
> > > so ignoring that file completely defeats the point in my setup. Is
> anyone
> > > aware of either a more reliable way of getting the information I want
> > > (maybe suppressing messages, different mechanism entirely, etc)?
> > > Alternatively, is there anything definitive in WRE or the like that
> > > suggests printing messages Rprofile is a bad idea that I can pass on
> to the
> > > users?
> > >
> > > Cheers,
> > > Mike
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Best,
Kasper
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Suppressing messages from Rprofile
Correcting: the env var is R_LIBS_USER and nothing else.
/Henrik
On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson
wrote:
>
> Can you go via a temporary file instead, i.e. output what you want to
> grab to a temporary file and pull the info from that instead?
>
> Side tracking ...
>
> > I thought about using --vanilla but I use .Rprofile to set my library path,
> > so ignoring that file completely defeats the point in my setup.
>
> I'm a proponent of customizing the library path via .Renviron instead
> of via .Rprofile. In your case, you can have a line in ~/.Renviron
> with:
>
> R_USER_LIBS=~/R/%p-library/%v-bioc_3.12
>
> Alternatively, you can set it elsewhere, e.g. ~/.bashrc, in a Linux
> environment module that is loaded, and so on.
>
> BTW, using Rscript --no-init-file ... would skip .Rprofile while still
> parsing .Renviron.
>
> /Henrik
>
> On Wed, Apr 7, 2021 at 8:16 AM Mike Smith wrote:
> >
> > I have the following line in the configure.ac for rhdf5filters, which
> > returns the location of the HDF5 headers distributed with Rhdf5lib:
> >
> > RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
> > 'cat(system.file("include", package="Rhdf5lib"))'`
> >
> > For me the output is a path like
> > /mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets inserted into
> > the package Makevars file, and the package compilation works.
> >
> > However I've had multiple reports (
> > https://github.com/grimbough/rhdf5filters/issues/11) where this doesn't
> > work, all of which seem to relate to messages printed when an Rprofile is
> > loaded. They have well intentioned messages like below, which don't work
> > so well when passed as compiler flags
> >
> > [1] "[BMRC] You have sourced the BMRC Rprofile provided at
> > /apps/misc/R/bmrc-r-user-tools/Rprofile"
> > [1] "[BMRC] Messages coming from this file (like this one) will be
> > prefixed with [BMRC]"
> > [1] "[BMRC] You are running R on host
> > with CPU "
> > [1] "[BMRC] While running on this host, local R packages will be
> > sourced from and installed to
> > /well/combat/users/ifl143/R/4.0/ivybridge"
> > /gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include
> >
> > I thought about using --vanilla but I use .Rprofile to set my library path,
> > so ignoring that file completely defeats the point in my setup. Is anyone
> > aware of either a more reliable way of getting the information I want
> > (maybe suppressing messages, different mechanism entirely, etc)?
> > Alternatively, is there anything definitive in WRE or the like that
> > suggests printing messages Rprofile is a bad idea that I can pass on to the
> > users?
> >
> > Cheers,
> > Mike
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
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Re: [Bioc-devel] Suppressing messages from Rprofile
Can you go via a temporary file instead, i.e. output what you want to
grab to a temporary file and pull the info from that instead?
Side tracking ...
> I thought about using --vanilla but I use .Rprofile to set my library path,
> so ignoring that file completely defeats the point in my setup.
I'm a proponent of customizing the library path via .Renviron instead
of via .Rprofile. In your case, you can have a line in ~/.Renviron
with:
R_USER_LIBS=~/R/%p-library/%v-bioc_3.12
Alternatively, you can set it elsewhere, e.g. ~/.bashrc, in a Linux
environment module that is loaded, and so on.
BTW, using Rscript --no-init-file ... would skip .Rprofile while still
parsing .Renviron.
/Henrik
On Wed, Apr 7, 2021 at 8:16 AM Mike Smith wrote:
>
> I have the following line in the configure.ac for rhdf5filters, which
> returns the location of the HDF5 headers distributed with Rhdf5lib:
>
> RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
> 'cat(system.file("include", package="Rhdf5lib"))'`
>
> For me the output is a path like
> /mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets inserted into
> the package Makevars file, and the package compilation works.
>
> However I've had multiple reports (
> https://github.com/grimbough/rhdf5filters/issues/11) where this doesn't
> work, all of which seem to relate to messages printed when an Rprofile is
> loaded. They have well intentioned messages like below, which don't work
> so well when passed as compiler flags
>
> [1] "[BMRC] You have sourced the BMRC Rprofile provided at
> /apps/misc/R/bmrc-r-user-tools/Rprofile"
> [1] "[BMRC] Messages coming from this file (like this one) will be
> prefixed with [BMRC]"
> [1] "[BMRC] You are running R on host
> with CPU "
> [1] "[BMRC] While running on this host, local R packages will be
> sourced from and installed to
> /well/combat/users/ifl143/R/4.0/ivybridge"
> /gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include
>
> I thought about using --vanilla but I use .Rprofile to set my library path,
> so ignoring that file completely defeats the point in my setup. Is anyone
> aware of either a more reliable way of getting the information I want
> (maybe suppressing messages, different mechanism entirely, etc)?
> Alternatively, is there anything definitive in WRE or the like that
> suggests printing messages Rprofile is a bad idea that I can pass on to the
> users?
>
> Cheers,
> Mike
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Suppressing messages from Rprofile
I have the following line in the configure.ac for rhdf5filters, which
returns the location of the HDF5 headers distributed with Rhdf5lib:
RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e
'cat(system.file("include", package="Rhdf5lib"))'`
For me the output is a path like
/mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets inserted into
the package Makevars file, and the package compilation works.
However I've had multiple reports (
https://github.com/grimbough/rhdf5filters/issues/11) where this doesn't
work, all of which seem to relate to messages printed when an Rprofile is
loaded. They have well intentioned messages like below, which don't work
so well when passed as compiler flags
[1] "[BMRC] You have sourced the BMRC Rprofile provided at
/apps/misc/R/bmrc-r-user-tools/Rprofile"
[1] "[BMRC] Messages coming from this file (like this one) will be
prefixed with [BMRC]"
[1] "[BMRC] You are running R on host
with CPU "
[1] "[BMRC] While running on this host, local R packages will be
sourced from and installed to
/well/combat/users/ifl143/R/4.0/ivybridge"
/gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include
I thought about using --vanilla but I use .Rprofile to set my library path,
so ignoring that file completely defeats the point in my setup. Is anyone
aware of either a more reliable way of getting the information I want
(maybe suppressing messages, different mechanism entirely, etc)?
Alternatively, is there anything definitive in WRE or the like that
suggests printing messages Rprofile is a bad idea that I can pass on to the
users?
Cheers,
Mike
[[alternative HTML version deleted]]
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