[Rd] config.status: error: cannot find input file: `po/Makefile.in'
Hi, Does anyone else see the following or is it just me? It usually works fine. I checked latest R-devel commits and couldn't see anything very recently changed or fixed w.r.t. po/ or Makefile. wget https://stat.ethz.ch/R/daily/R-devel.tar.gz tar xvf R-devel.tar.gz cd R-devel ./configure --without-recommended-packages ... config.status: error: cannot find input file: `po/Makefile.in' $ lsb_release -a Description:Ubuntu 18.04.1 LTS Release:18.04 Codename: bionic Best, Matt [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] config.status: error: cannot find input file: `po/Makefile.in'
Martin - many thanks, it's working now. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error in rbind(info, getNamespaceInfo(env, "S3methods"))
Dear all,
I'm experiencing an unusual installation error for one package. Could
anyone suggest how I can best investigate this from here please? I'm sorry
this isn't very much to go on. Hopefully someone can point me in the right
direction.
The problem seems to be my library. It is large (3,418 packages) and I'd
like to avoid rebuilding it, if possible. All packages are up to date
according to update.packages().
The error is :
** byte-compile and prepare package for lazy loading
Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
number of columns of matrices must match (see arg 2)
ERROR: lazy loading failed for package ‘staRdom’
* removing ‘/home/mdowle/build/revdeplib/staRdom’
This package (staRdom) has had a recent update but CRAN checks page is
showing OK, mostly:
https://cran.r-project.org/web/checks/check_results_staRdom.html. The two
errors there don't seem to be related.
The package installs no problem when I don't include my revdeplib. But
when I do include my revdeplib it fails with the error above.
I can reproduce as follows :
$ export R_LIBS=~/build/revdeplib/
$ R
> .libPaths()
[1] "/home/mdowle/build/revdeplib" "/usr/lib/R/library"
> install.packages("staRdom")
Installing package into ‘/home/mdowle/build/revdeplib’
(as ‘lib’ is unspecified)
trying URL 'http://cloud.r-project.org/src/contrib/staRdom_1.0.12.tar.gz'
Content type 'application/x-gzip' length 2669832 bytes (2.5 MB)
==
downloaded 2.5 MB
* installing *source* package ‘staRdom’ ...
** package ‘staRdom’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
number of columns of matrices must match (see arg 2)
ERROR: lazy loading failed for package ‘staRdom’
* removing ‘/home/mdowle/build/revdeplib/staRdom’
The downloaded source packages are in
‘/tmp/RtmprvTDCg/downloaded_packages’
Warning message:
In install.packages("staRdom") :
installation of package ‘staRdom’ had non-zero exit status
>
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
>
If I don't include my revdeplib library, it works fine :
$ R
> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
"/usr/lib/R/library"
> install.packages("staRdom")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cloud.r-project.org/src/contrib/staRdom_1.0.12.tar.gz'
Content type 'application/x-gzip' length 2669832 bytes (2.5 MB)
==
downloaded 2.5 MB
* installing *source* package ‘staRdom’ ...
** package ‘staRdom’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (staRdom)
The downloaded source packages are in
‘/tmp/RtmpmSiZLa/downloaded_packages’
>
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
>
I'm not sure how to debug this because both install.packages() and `R CMD
check` start a new instance of R. How do a get debugger() prompt at the
point of the error? All I can think of is inserting a browser() in my own
compile of R-devel. But that seems a big step. I thought I'd post here
first to see if anyone had any suggestions in how to proceed.
Thanks in advance,
Matt
[[alternative HTML version deleted]]
___
Re: [Rd] Error in rbind(info, getNamespaceInfo(env, "S3methods"))
Thanks, Duncan.
I took the approach you suggested and eventually found it was due to
R.matlab (staRdom imports R.matlab).
> require(R.matlab)
Loading required package: R.matlab
Error: package or namespace load failed for ‘R.matlab’ in rbind(info,
getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)
Warning message:
package ‘R.matlab’ was built under R version 3.6.0
> R.version.string
[1] "R version 3.5.2 (2018-12-20)"
At some point in the past I guess I used R-devel with this library and it
installed R.matlab using R-devel.
Reinstalling R.matlab did the trick and staRdom works fine now.
I checked that none of the other 2,643 packages in this library were built
using R>3.5.2. It was just R.matlab.
Thanks for your help!
Best, Matt
On Mon, Feb 18, 2019 at 1:28 PM Duncan Murdoch
wrote:
> On 18/02/2019 4:08 p.m., Matt Dowle wrote:
> > Dear all,
> >
> > I'm experiencing an unusual installation error for one package. Could
> > anyone suggest how I can best investigate this from here please? I'm
> sorry
> > this isn't very much to go on. Hopefully someone can point me in the
> right
> > direction.
>
> When packages are installed, a hidden environment is created called
> ".__NAMESPACE__.". It contains a number of objects; it looks as though
> one of yours called "S3methods" is corrupted. I can't guess whether it
> is one coming from staRdom or one already in your library, but it
> appears yours doesn't have the usual number of columns (which I think is
> 3).
>
> So you could get a list of all packages in your library, and run
>
> sapply(allpackages, function(x)
> ncol(asNamespace(x)$.__NAMESPACE__.$S3methods))
>
> to see which of them don't return 3 as the number of columns. (This
> will load all of them, so might need to be broken up into batches.)
>
> Duncan Murdoch
>
> >
> > The problem seems to be my library. It is large (3,418 packages) and I'd
> > like to avoid rebuilding it, if possible. All packages are up to date
> > according to update.packages().
> >
> > The error is :
> > ** byte-compile and prepare package for lazy loading
> > Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
> >number of columns of matrices must match (see arg 2)
> > ERROR: lazy loading failed for package ‘staRdom’
> > * removing ‘/home/mdowle/build/revdeplib/staRdom’
> >
> > This package (staRdom) has had a recent update but CRAN checks page is
> > showing OK, mostly:
> > https://cran.r-project.org/web/checks/check_results_staRdom.html. The
> two
> > errors there don't seem to be related.
> >
> > The package installs no problem when I don't include my revdeplib. But
> > when I do include my revdeplib it fails with the error above.
> >
> > I can reproduce as follows :
> >
> > $ export R_LIBS=~/build/revdeplib/
> > $ R
> >> .libPaths()
> > [1] "/home/mdowle/build/revdeplib" "/usr/lib/R/library"
> >> install.packages("staRdom")
> > Installing package into ‘/home/mdowle/build/revdeplib’
> > (as ‘lib’ is unspecified)
> > trying URL 'http://cloud.r-project.org/src/contrib/staRdom_1.0.12.tar.gz
> '
> > Content type 'application/x-gzip' length 2669832 bytes (2.5 MB)
> > ==
> > downloaded 2.5 MB
> > * installing *source* package ‘staRdom’ ...
> > ** package ‘staRdom’ successfully unpacked and MD5 sums checked
> > ** R
> > ** data
> > *** moving datasets to lazyload DB
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
> >number of columns of matrices must match (see arg 2)
> > ERROR: lazy loading failed for package ‘staRdom’
> > * removing ‘/home/mdowle/build/revdeplib/staRdom’
> > The downloaded source packages are in
> > ‘/tmp/RtmprvTDCg/downloaded_packages’
> > Warning message:
> > In install.packages("staRdom") :
> >installation of package ‘staRdom’ had non-zero exit status
> >>
> >> sessionInfo()
> > R version 3.5.2 (2018-12-20)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 18.04.2 LTS
> >
> > Matrix products: default
> > BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
> > LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-
Re: [Rd] Error generated by .Internal(nchar) disappears when debugging
Joris Meys gmail.com> writes: > > Hi all, > > I have a puzzling problem related to nchar. In R 3.2.1, the internal nchar > gained an extra argument (see > https://stat.ethz.ch/pipermail/r-announce/2015/000586.html) > > I've been testing code using the package copula, and at home I'm still > running R 3.2.0 (I know, I know...). When trying the following code, I got > an error: > > > library(copula) > > fgmCopula(0.8) > Error in substr(sc[i], 2, nchar(sc[i]) - 1) : > 4 arguments passed to .Internal(nchar) which requires 3 > > Cheers > Joris I'm seeing a similar problem. IIUC, the Windows binary .zip from CRAN of any package using base::nchar is affected. Could someone check my answer here is correct please : http://stackoverflow.com/a/32959306/403310 Matt __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error generated by .Internal(nchar) disappears when debugging
On Mon, Oct 5, 2015 at 4:57 PM, Duncan Murdoch wrote: > On 05/10/2015 7:24 PM, Matt Dowle wrote: > > Joris Meys gmail.com> writes: > > > >> > >> Hi all, > >> > >> I have a puzzling problem related to nchar. In R 3.2.1, the internal > > nchar > >> gained an extra argument (see > >> https://stat.ethz.ch/pipermail/r-announce/2015/000586.html) > >> > >> I've been testing code using the package copula, and at home I'm still > >> running R 3.2.0 (I know, I know...). When trying the following code, I > > got > >> an error: > >> > >>> library(copula) > >>> fgmCopula(0.8) > >> Error in substr(sc[i], 2, nchar(sc[i]) - 1) : > >> 4 arguments passed to .Internal(nchar) which requires 3 > >> > >> Cheers > >> Joris > > > > > > I'm seeing a similar problem. IIUC, the Windows binary .zip from CRAN of > > any package using base::nchar is affected. Could someone check my answer > > here is correct please : http://stackoverflow.com/a/32959306/403310 > > Nobody has posted a simple reproducible example here, so it's kind of > hard to say. > > I would have guessed that a change to the internal signature of the C > code underlying nchar() wouldn't have any effect on a package that > called the R nchar() function. > > When I put together my own example (a tiny package containing a function > calling nchar(), built to .zip using R 3.2.2, installed into R 3.2.0), > it confirmed my guess. > > On the other hand, if some package is calling the .Internal function > directly, I'd expect that to break. Packages shouldn't do that. > > So I'd say there's been no evidence posted of a problem in R here, > though there may be problems in some of the packages involved. I'd > welcome an example that provided some usable evidence. > > Duncan Murdoch > > I don't have Windows so am not able to test unfortunately. data.table makes no calls to .Internal(). Such calls are caught and prevented by R CMD check. Both data.table and copula contain "ByteCompile: yes" in their DESCRIPTION files. Does the toy package break with that setting? Matt [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.4 and mclapply assertion failure - is this a bug?
That's great news that OpenMP is now enabled in MacOS CRAN binaries! Thanks Simon. data.table is supposed to automatically switch down to single-threaded mode when explicitly parallelized via the fork mechanism. It does that via functions registered in init.c as follows : pthread_atfork(&when_fork, &when_fork_end, NULL) Tests 1705 and 1706 test this is working. Those tests are passing ok on CRAN currently including x86_64-apple-darwin15.6.0. I'll work with Yan off list to see what the difference is. Either the fork catch isn't working in that environment for some reason, the use case is different to the tests somehow or the fork catch is working but something somewhere is asserting its surprise at being single threaded. In the meantime setDTthreads(1) can be called manually before the explicit parallelism as a workaround. Matt On Tue, May 2, 2017 at 1:25 PM, Yan Alperovych wrote: > Dear Matt, > > I follow the Simon’s advice on this. Since R 3.4 the mclapply is producing > a strange error which was not present in R 3.3.3. Simon’s answer is below > and the relevant info (the console output, the code, and the sample data) > are all below. > > Thank you very much for helping, > Yan > > Begin forwarded message: > > *From: *Simon Urbanek > *Subject: **Re: [Rd] R 3.4 and mclapply assertion failure - is this a > bug?* > *Date: *May 2, 2017 at 7:09:36 PM GMT+2 > *To: *Yan Alperovych > *Cc: *"r-devel@r-project.org" > > Yan, > > this looks like an interaction of OpenMP in data.table and forking - you > may want to report that to Matt as he can shed more light on that. He has > been complaining that we didn't enable OpenMP before 3.4 so he probably > knows about the issue and how to fix it. > > Cheers, > Simon > > > On May 2, 2017, at 7:12 AM, Yan Alperovych via R-devel < > r-devel@r-project.org> wrote: > > Dear all, > > > I am not sure if this is a bug, so I prefer to post it here before filing. > > > After upgrading to 3.4 I encounter the following message with mclapply: > > > Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == > __null.OMP : Error #13: Assertion failure at kmp_runtime.cpp(6480).OMP: > Hint: Please submit a bug report with this message, compile and run > commands used, and machine configuration info including native compiler and > operating system versions. Faster response will be obtained by including > all program sources. For information on submitting this issue, please see > http://www.intel.com/software/products/support/. > > > The complete pdf of what console produces is here: > > https://www.dropbox.com/s/navugg28gqne14p/R%20Console.pdf?dl=0 > > > The batch with commands to (hopefully) reproduce it is here: > > https://www.dropbox.com/s/8pd0ij3kowigdlc/20170430%20-% > 20R%20mclapply%20bug%20report.r?dl=0 > > > The data for the reproducible example is here: > https://www.dropbox.com/s/2enoeapu7jgcxwd/z.Rdata?dl=0 > > > Note that this behavior was not present in R 3.3.3 on the same machine and > all the batch was working without any errors. > > > The sessionInfo(): > R version 3.4.0 (2017-04-21) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: macOS Sierra 10.12.4 > > > Matrix products: default > > > BLAS: /Library/Frameworks/R.framework/Versions/3.4/ > Resources/lib/libRblas.0.dylib > > LAPACK: /Library/Frameworks/R.framework/Versions/3.4/ > Resources/lib/libRlapack.dylib > > > *locale:* > *[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8* > > *attached base packages:* > *[1] parallel compiler stats graphics grDevices utils datasets > methods base * > > *other attached packages:* > * [1] data.table_1.10.4 numbers_0.6-6 microbenchmark_1.4-2.1 > zoo_1.8-0 doParallel_1.0.10 iterators_1.0.8 * > * [7] foreach_1.4.3 RSclient_0.7-3 stringi_1.1.5 > stringr_1.2.0 lubridate_1.6.0plyr_1.8.4* > > *loaded via a namespace (and not attached):* > * [1] Rcpp_0.12.10 lattice_0.20-35 codetools_0.2-15 grid_3.4.0 > gtable_0.2.0 magrittr_1.5 scales_0.4.1 ggplot2_2.2.1 * > * [9] lazyeval_0.2.0 tools_3.4.0 munsell_0.4.3colorspace_1.3-2 > tibble_1.3.0* > > > > Thank you in advance for help/hints, Yan > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] possible error in rdevel with --enable-strict-barrier?
Hi, With a fresh Rdevel r66690 (yesterday 26th) in ~/R/Rtrunk I get : ~/R/Rtrunk $ ./configure CC="gcc -std=gnu99 -fsanitize=address" CFLAGS="-fno-omit-frame-pointer -O0 -g -Wall -pedantic -mtune=native" --without-recommended-packages ~/R/Rtrunk $ make clean ~/R/Rtrunk $ make Works fine. Now adding --enable-strict-barrier to the end : ~/R/Rtrunk $ ./configure CC="gcc -std=gnu99 -fsanitize=address" CFLAGS="-fno-omit-frame-pointer -O0 -g -Wall -pedantic -mtune=native" --without-recommended-packages --enable-strict-barrier ~/R/Rtrunk $ make clean ~/R/Rtrunk $ make ... snip ... building package 'datasets' make[4]: Entering directory `/home/mdowle/R/Rtrunk/src/library/datasets' make[4]: Leaving directory `/home/mdowle/R/Rtrunk/src/library/datasets' Error in stats::ts(t(matrix(data = c(1628.75, 1678.1, 1772.8, 2443.6, : invalid time series parameters specified Calls: ... -> sys.source -> eval -> eval -> Execution halted I've done this with and without --enable-strict-barrier several times and it's repeatable, at least on my machine. Am I doing it right? Is it known? ~/R/Rtrunk $ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 4.8.2-1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --with-arch-32=i586 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 4.8.2 (Debian 4.8.2-1) I should mention that I've also installed gcc 4.9.1 to try combining ASAN and UBSAN i.e. -fsanitize=undefined,address. So it's possible that something in that install has upgraded a shared object somewhere else. In the command above I'm using just "gcc" in CC, though, not "gcc-4.9". The earlier snipped output confirms it is using gcc 4.8.2. Anyway, posting here to see if it's just me or if there's really a minor issue with Rdevel currently. Thanks, Matt __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
