Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
Hi Uwe,
On 11-06-29 10:50 AM, Uwe Ligges wrote:
On 28.06.2011 23:11, Hervé Pagès wrote:
Simon,
On 11-06-28 01:44 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote:
Hi Simon,
On 11-06-28 12:19 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on
packages that don't strictly need it?
It does for two reasons: a) everything is built twice
That's exactly what I want when I do 'R CMD check --force-multiarch'
No, that's not what it does (and I assume you mean --force-biarch). It
builds the package just once, you're simply overriding the default
behavior of checking for configure.win, that's all. The two flags are
orthogonal, --force-biarch makes no sense with --merge-multiarch, they
are for all practical purposes mutually exclusive by definition of
what they do.
I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check'
has no --force-biarch option.
and b) package authors don't expect the necessity to support
--libs-only if the package doesn't require separate build runs.
When specifying --force-multiarch, the user really expects the
package to be installed for all sub-archs.
... with the assumption that the package supports it even though it
has a configure script which may to may not work unlike
--merge-multiarch which will always work.
Just to clarify:
--force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL'
option
--merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check'
option
Now you are saying that --merge-multiarch will always work (on Windows
of course, all this discussion is about how to achieve multiarch check
on Windows). Great, this is what I've been observing too so far!
It does not always work, unfortunately. We need force-biarch on CRAN for:
RGtk2
rgdal
rphast
SQLiteMap
On packages with or without native codes, with or without configure.win
scripts, etc... It always seems to work. So, again, why isn't
'R CMD check --force-multiarch' installing with --merge-multiarch?
Note that I'm not attached to that solution in particular, just trying
to suggest an easy fix for 'R CMD check --force-multiarch' (which right
now is broken on some packages).
Well, merge-multiarch will result in small overhead. It will try to
compile the code in ./src for the other architecture and merge that into
the same package. For packages without any compiled code, it does not
make sense to ask R to do that since the packages are identical under
32-bit and 64-bit, hence you don't want the overhead.
If the package doesn't contain any native code, then trying to compile
the native code for the other arch shouldn't result in a big overhead.
What's the overhead of an if statement like:
## add DLL for x64
if (file.exists(installation_folder/pkgname/libs)
!file.exists(installation_folder/pkgname/libs/x64)) {
...
## compile and install DLL for x64
...
}
## test if installed package can be loaded for x64
...
Note that the add DLL for x64 step is currently doing something
*very* useful, which is to make sure that the package can be loaded for
this arch:
D:\biocbld\bbs-2.9-bioc\meat..\R\bin\R CMD INSTALL --merge-multiarch
BSgenome_1.21.3.tar.gz
install for i386
* installing to library 'D:/biocbld/bbs-2.9-bioc/R/library'
* installing *source* package 'BSgenome' ...
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'BSgenomeForge.Rnw'
'GenomeSearching.Rnw'
** testing if installed package can be loaded
add DLL for x64
* installing to library 'D:/biocbld/bbs-2.9-bioc/R/library'
* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* DONE (BSgenome)
It's useful even for packages without compiled code since they can
depend on packages that do have compiled code but have been installed
only for 1 arch.
Unfortunately this is something that --force-biarch doesn't do
(it returns success even if compilation for x64 failed).
For packages that
include compiled code, you still do not want it, since R does it
automatically - unless there is a configure.win file.
I want to be able to use the same command for any package.
'R CMD check' looses *a lot* of value if people need to know what's
in a package in order
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On 28.06.2011 23:11, Hervé Pagès wrote: Simon, On 11-06-28 01:44 PM, Simon Urbanek wrote: On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote: Hi Simon, On 11-06-28 12:19 PM, Simon Urbanek wrote: On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote: Hi Uwe, On 11-06-28 01:44 AM, Uwe Ligges wrote: On 28.06.2011 01:31, Hervé Pagès wrote: Hi, Why isn't 'R CMD check --force-multiarch' installing the package for all the architectures that are going to be checked? Hervé, no, since it cannot know that that you need --merge-multiarch as an additional install flag for this particular package. Why not just use this flag anyway? Does it hurt to use it on packages that don't strictly need it? It does for two reasons: a) everything is built twice That's exactly what I want when I do 'R CMD check --force-multiarch' No, that's not what it does (and I assume you mean --force-biarch). It builds the package just once, you're simply overriding the default behavior of checking for configure.win, that's all. The two flags are orthogonal, --force-biarch makes no sense with --merge-multiarch, they are for all practical purposes mutually exclusive by definition of what they do. I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check' has no --force-biarch option. and b) package authors don't expect the necessity to support --libs-only if the package doesn't require separate build runs. When specifying --force-multiarch, the user really expects the package to be installed for all sub-archs. ... with the assumption that the package supports it even though it has a configure script which may to may not work unlike --merge-multiarch which will always work. Just to clarify: --force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL' option --merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check' option Now you are saying that --merge-multiarch will always work (on Windows of course, all this discussion is about how to achieve multiarch check on Windows). Great, this is what I've been observing too so far! It does not always work, unfortunately. We need force-biarch on CRAN for: RGtk2 rgdal rphast SQLiteMap On packages with or without native codes, with or without configure.win scripts, etc... It always seems to work. So, again, why isn't 'R CMD check --force-multiarch' installing with --merge-multiarch? Note that I'm not attached to that solution in particular, just trying to suggest an easy fix for 'R CMD check --force-multiarch' (which right now is broken on some packages). Well, merge-multiarch will result in small overhead. It will try to compile the code in ./src for the other architecture and merge that into the same package. For packages without any compiled code, it does not make sense to ask R to do that since the packages are identical under 32-bit and 64-bit, hence you don't want the overhead. For packages that include compiled code, you still do not want it, since R does it automatically - unless there is a configure.win file. Therefore, the option is just an add on that is necessary for only 18 out of roughly 3000 CRAN packages. So we have 4 packages that require --force-biarch and 18 requiring --merge-multiarch on CRAN. All the others build automatically for both architectures if they need to. So no reason to do that all the time. Best wishes, Uwe --force-biarch is just a way to flag packages that have configure.win that has no effect on the binary settings (flags etc.). It forces R to try multi-arch build in one flight, but it may or may not work depending on the package. It is a way to save time by not running --merge-multiarch (and thus building the package twice). --force-biarch is an 'R CMD INSTALL' option that I don't use. Why would I use something that might fail when I can use --merge-multiarch which always works. Thanks, H. Cheers, Simon The cross-platform way is to not use --merge-multiarch but use --libs-only instead as needed (easy to check after the first arch run which will tell you whether it's needed or not). I suspect that --merge-multiarch is just a convenience shortcut (and it's unclear to me why it's Windows-only...). A great convenience indeed as it allows to do the multiarch install in a single step. And it's unclear to me too why it's Windows-only but I would have hoped you would know... Thanks, H. Cheers, Simon You will have to check it in repository maintainer's mode (as the CRAN maintainers do everywhere). Essentially this is for me (when also producing WIndows binaries): Step 1: Installation R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch --library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21 (where the merge-multiarch part applies only to this package, of course) Step 2: Check (without installation, since that happened before already, using the install log from step 1) R CMD check --library=D:/path/to/library --force-multiarch
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command 'D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -ID:/biocbld/BBS-2˜1.9-B/R/include
-ID:/biocbld/BBS-2˜1.9-B/R/src/include -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-ID:/biocbld/BBS-2˜1.9-B/R/include -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR -o fabia.dll
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for plot from package graphics in
package fabia
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'fabia.Rnw'
** testing if installed package can be loaded
* DONE (fabia)
The source tarball for this package is available here:
http://bioconductor.org/packages/2.9/bioc/html/fabia.html
What command should be used to perform a multiarch check of this
package?
This is on a 64-bit Windows Server 2008 R2 Enterprise machine using a
recent combined Windows 32/64 bit binary of R-devel from CRAN.
Thanks!
H.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages
that don't strictly need it?
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command 'D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -ID:/biocbld/BBS-2˜1.9-B/R/include
-ID:/biocbld/BBS-2˜1.9-B/R/src/include -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-ID:/biocbld/BBS-2˜1.9-B/R/include -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR -o fabia.dll
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for plot from package graphics in
package fabia
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'fabia.Rnw'
** testing if installed package can be loaded
* DONE (fabia)
The source tarball for this package is available here:
http://bioconductor.org/packages/2.9/bioc/html/fabia.html
What command should be used to perform a multiarch check of this
package?
This is on a 64-bit Windows Server 2008 R2 Enterprise machine using a
recent combined Windows 32/64 bit binary of R-devel from CRAN.
Thanks!
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206)
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages that
don't strictly need it?
It does for two reasons: a) everything is built twice and b) package authors
don't expect the necessity to support --libs-only if the package doesn't
require separate build runs.
The cross-platform way is to not use --merge-multiarch but use --libs-only
instead as needed (easy to check after the first arch run which will tell you
whether it's needed or not). I suspect that --merge-multiarch is just a
convenience shortcut (and it's unclear to me why it's Windows-only...).
Cheers,
Simon
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command 'D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -ID:/biocbld/BBS-2˜1.9-B/R/include
-ID:/biocbld/BBS-2˜1.9-B/R/src/include -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-ID:/biocbld/BBS-2˜1.9-B/R/include -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR -o fabia.dll
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for plot from package graphics in
package fabia
** help
*** installing help indices
** building package indices ...
*** tangling vignette
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
Hi Simon,
On 11-06-28 12:19 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages that
don't strictly need it?
It does for two reasons: a) everything is built twice
That's exactly what I want when I do 'R CMD check --force-multiarch'
and b) package authors don't expect the necessity to support --libs-only if the
package doesn't require separate build runs.
When specifying --force-multiarch, the user really expects the package
to be installed for all sub-archs.
The cross-platform way is to not use --merge-multiarch but use --libs-only
instead as needed (easy to check after the first arch run which will tell you
whether it's needed or not). I suspect that --merge-multiarch is just a
convenience shortcut (and it's unclear to me why it's Windows-only...).
A great convenience indeed as it allows to do the multiarch install in
a single step. And it's unclear to me too why it's Windows-only but I
would have hoped you would know...
Thanks,
H.
Cheers,
Simon
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command 'D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -ID:/biocbld/BBS-2˜1.9-B/R/include
-ID:/biocbld/BBS-2˜1.9-B/R/src/include -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-ID:/biocbld/BBS-2˜1.9-B/R/include -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR -o fabia.dll
rm -f fabia.o *.a *.o
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote:
Hi Simon,
On 11-06-28 12:19 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages that
don't strictly need it?
It does for two reasons: a) everything is built twice
That's exactly what I want when I do 'R CMD check --force-multiarch'
No, that's not what it does (and I assume you mean --force-biarch). It builds
the package just once, you're simply overriding the default behavior of
checking for configure.win, that's all. The two flags are orthogonal,
--force-biarch makes no sense with --merge-multiarch, they are for all
practical purposes mutually exclusive by definition of what they do.
and b) package authors don't expect the necessity to support --libs-only if
the package doesn't require separate build runs.
When specifying --force-multiarch, the user really expects the package to be
installed for all sub-archs.
... with the assumption that the package supports it even though it has a
configure script which may to may not work unlike --merge-multiarch which will
always work. --force-biarch is just a way to flag packages that have
configure.win that has no effect on the binary settings (flags etc.). It forces
R to try multi-arch build in one flight, but it may or may not work depending
on the package. It is a way to save time by not running --merge-multiarch (and
thus building the package twice).
Cheers,
Simon
The cross-platform way is to not use --merge-multiarch but use --libs-only
instead as needed (easy to check after the first arch run which will tell
you whether it's needed or not). I suspect that --merge-multiarch is just a
convenience shortcut (and it's unclear to me why it's Windows-only...).
A great convenience indeed as it allows to do the multiarch install in
a single step. And it's unclear to me too why it's Windows-only but I
would have hoped you would know...
Thanks,
H.
Cheers,
Simon
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
Simon,
On 11-06-28 01:44 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote:
Hi Simon,
On 11-06-28 12:19 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages that
don't strictly need it?
It does for two reasons: a) everything is built twice
That's exactly what I want when I do 'R CMD check --force-multiarch'
No, that's not what it does (and I assume you mean --force-biarch). It builds
the package just once, you're simply overriding the default behavior of
checking for configure.win, that's all. The two flags are orthogonal,
--force-biarch makes no sense with --merge-multiarch, they are for all
practical purposes mutually exclusive by definition of what they do.
I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check'
has no --force-biarch option.
and b) package authors don't expect the necessity to support --libs-only if the
package doesn't require separate build runs.
When specifying --force-multiarch, the user really expects the package to be
installed for all sub-archs.
... with the assumption that the package supports it even though it has a
configure script which may to may not work unlike --merge-multiarch which will
always work.
Just to clarify:
--force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL'
option
--merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check'
option
Now you are saying that --merge-multiarch will always work (on Windows
of course, all this discussion is about how to achieve multiarch check
on Windows). Great, this is what I've been observing too so far!
On packages with or without native codes, with or without configure.win
scripts, etc... It always seems to work. So, again, why isn't
'R CMD check --force-multiarch' installing with --merge-multiarch?
Note that I'm not attached to that solution in particular, just trying
to suggest an easy fix for 'R CMD check --force-multiarch' (which right
now is broken on some packages).
--force-biarch is just a way to flag packages that have configure.win that has
no effect on the binary settings (flags etc.). It forces R to try multi-arch
build in one flight, but it may or may not work depending on the package. It is
a way to save time by not running --merge-multiarch (and thus building the
package twice).
--force-biarch is an 'R CMD INSTALL' option that I don't use. Why would
I use something that might fail when I can use --merge-multiarch which
always works.
Thanks,
H.
Cheers,
Simon
The cross-platform way is to not use --merge-multiarch but use --libs-only
instead as needed (easy to check after the first arch run which will tell you
whether it's needed or not). I suspect that --merge-multiarch is just a
convenience shortcut (and it's unclear to me why it's Windows-only...).
A great convenience indeed as it allows to do the multiarch install in
a single step. And it's unclear to me too why it's Windows-only but I
would have hoped you would know...
Thanks,
H.
Cheers,
Simon
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ...
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On Jun 28, 2011, at 5:11 PM, Hervé Pagès wrote:
Simon,
On 11-06-28 01:44 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote:
Hi Simon,
On 11-06-28 12:19 PM, Simon Urbanek wrote:
On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
On 28.06.2011 01:31, Hervé Pagès wrote:
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
Hervé,
no, since it cannot know that that you need
--merge-multiarch
as an additional install flag for this particular package.
Why not just use this flag anyway? Does it hurt to use it on packages
that don't strictly need it?
It does for two reasons: a) everything is built twice
That's exactly what I want when I do 'R CMD check --force-multiarch'
No, that's not what it does (and I assume you mean --force-biarch). It
builds the package just once, you're simply overriding the default behavior
of checking for configure.win, that's all. The two flags are orthogonal,
--force-biarch makes no sense with --merge-multiarch, they are for all
practical purposes mutually exclusive by definition of what they do.
I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check'
has no --force-biarch option.
and b) package authors don't expect the necessity to support --libs-only
if the package doesn't require separate build runs.
When specifying --force-multiarch, the user really expects the package to
be installed for all sub-archs.
... with the assumption that the package supports it even though it has a
configure script which may to may not work unlike --merge-multiarch which
will always work.
Just to clarify:
--force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL'
option
--merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check'
option
Now you are saying that --merge-multiarch will always work (on Windows
of course, all this discussion is about how to achieve multiarch check
on Windows). Great, this is what I've been observing too so far!
On packages with or without native codes, with or without configure.win
scripts, etc... It always seems to work. So, again, why isn't
'R CMD check --force-multiarch' installing with --merge-multiarch?
Note that I'm not attached to that solution in particular, just trying
to suggest an easy fix for 'R CMD check --force-multiarch' (which right
now is broken on some packages).
--force-biarch is just a way to flag packages that have configure.win that
has no effect on the binary settings (flags etc.). It forces R to try
multi-arch build in one flight, but it may or may not work depending on the
package. It is a way to save time by not running --merge-multiarch (and thus
building the package twice).
--force-biarch is an 'R CMD INSTALL' option that I don't use. Why would
I use something that might fail when I can use --merge-multiarch which
always works.
Ok, never mind then, I was talking exclusively about R CMD INSTALL.
Cheers,
Simon
Thanks,
H.
Cheers,
Simon
The cross-platform way is to not use --merge-multiarch but use --libs-only
instead as needed (easy to check after the first arch run which will tell
you whether it's needed or not). I suspect that --merge-multiarch is just
a convenience shortcut (and it's unclear to me why it's Windows-only...).
A great convenience indeed as it allows to do the multiarch install in
a single step. And it's unclear to me too why it's Windows-only but I
would have hoped you would know...
Thanks,
H.
Cheers,
Simon
You will have to check it in repository maintainer's mode (as the CRAN
maintainers do everywhere). Essentially this is for me (when also
producing WIndows binaries):
Step 1: Installation
R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch
--library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out
21
(where the merge-multiarch part applies only to this package, of course)
Step 2: Check (without installation, since that happened before already,
using the install log from step 1)
R CMD check --library=D:/path/to/library --force-multiarch
--install=check:fabia-install.out fabia
Wha! Would be nice if there was a plan to make 'R CMD check' also
usable by normal people (including the package developer), not just
by a few privileged people that know about those undocumented tricks.
Thanks,
H.
Best wishes,
Uwe
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30
r56020)
*
[Rd] R CMD check --force-multiarch does not install all the archs for testing
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
---
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command 'D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -ID:/biocbld/BBS-2˜1.9-B/R/include
-ID:/biocbld/BBS-2˜1.9-B/R/src/include -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-ID:/biocbld/BBS-2˜1.9-B/R/include -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR -o fabia.dll
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for plot from package graphics in
package fabia
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'fabia.Rnw'
** testing if installed package can be loaded
* DONE (fabia)
The source tarball for this package is available here:
http://bioconductor.org/packages/2.9/bioc/html/fabia.html
What command should be used to perform a multiarch check of this
package?
This is on a 64-bit Windows Server 2008 R2 Enterprise machine using a
recent combined Windows 32/64 bit binary of R-devel from CRAN.
Thanks!
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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