Dear Joris,
indeed, the the data sets saved as R-files constituted the issue. As suggested
by you, saving them as *.rda helped.
Enormous thanks for your prompt and useful advice. The new version of the
R-package ddalpha (1.3.3, on CRAN now) causes no problems during the
byte-compilation phase.
Best regards,
Pavlo
On 30/04/2018 11:45, Joris Meys wrote:
Dear pavlo,
fwiw, the binary of ddalpha 1.3.2 installs just fine on Windows 10. When
building from source, I get a whole lot of warnings about uninitialized
variables, comparisons between signed and unsigned integers. The compilation of
the source code doesn't have a large impact on the memory. I can confirm that
the last step of the installation process (the byte compiling of the actual
package) requires at least 8 Gb. I have 8Gb DDR3 of which 2.5 Gb is used by
other processes. During the build process it fills up and at one point I have
another 3 Gb in swap. That works on Windows 10 (the installation process exits
successfully) but might well be the reason why on other systems you get the
errors you see.
One thing I noticed, is humongously huge code files (eg dataf.tecator.R is a
whopping 624 Kb). I would start with storing the data structures you include as
a .RDS file in a data folder (eg a file tefactor.rda containing a data
structure tefactor) , and rewrite the functions as
dataf.tefactor <- function() {return(tefactor) }
That will save in total several Mb of code files that need to be processed by
the byte compiler. Not sure this will solve the problem, but it's a low hanging
fruit ready to pick. If you're not sure what I'm talking about, you can link me
to the github repo (if you have one) and I'll take a look.
Cheers
Joris
On Mon, Apr 30, 2018 at 2:32 AM, MOZHAROVSKYI Pavlo
<pavlo.mozharovs...@ensai.fr<mailto:pavlo.mozharovs...@ensai.fr>> wrote:
After the R-update to version 3.5.0 there seems to be a problem with our
R-package ddalpha. As it seems that the problem is connected to the
newly introduced byte-compilation on installation, we feel unable to
locate its root cause and ask for your help.
During the byte-compilation of the package ddalpha (latest (CRAN)
version 1.3.2), an immense amount of memory (more than 4Gb) is consumed.
Further, byte-compilation takes at least several minutes to complete on
Windows and MacOS, while it throws an error on the Linux system where it
does not install at all:
Error message:
Error in system2(file.path(R.home("bin"), "R"), c(if (nzchar(arch))
paste0("--arch=", :
cannot popen ' '/usr/lib64/R/bin/R' --no-save --slave 2>&1 <
'/tmp/RtmpU4dXOt/file3fb5b89c507'', probable reason 'Cannot allocate memory'
We suspect a mistake in the design of our package and would appreciate
your advice. From our side, we are ready to undertake necessary actions
as soon as possible.
Here are the existing discussions on this topic:
- SO:
https://stackoverflow.com/questions/50028566/cannot-allocate-memory-while-re-installing-r-package-ddalpha-under-arch-linu
- Arch Linux: https://bbs.archlinux.org/viewtopic.php?id=236517
- RStudio Community:
https://community.rstudio.com/t/memory-allocation-problem-while-re-installing-ddalpha-package-after-upgrade-to-r-3-5-0/7663/3
Thank you a lot for your help!
Best regards,
Pavlo
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Ghent University
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------------------------------------------------------------
Pavlo Mozharovskyi
ENSAI - Campus de Ker-Lann
Rue Blaise Pascal - BP 37203
35172 Bruz cedex
FRANCE
Tel: +33 (0)2 99 05 32 55
Fax: +33 (0)2 99 05 32 05
Email: pavlo.mozharovs...@ensai.fr<mailto:pavlo.mozharovs...@ensai.fr>
http://www.ensai.fr/enseignant/alias/pavlo-mozharovskyi.html
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