On 5 December 2016 at 17:57, Gordon Ball wrote:
| On 01/12/16 09:46, Andreas Tille wrote:
| > However, yesterday I stumbled upon r-cran-yaml[1] which causes a problem
| > I was not able to solve quickly. Upstream has injected an additional
| > declaration to the code copy of libyaml which I injected via quilt patch
| > right into the C code which now enables building the code. Strangely
| > enough the resulting library does not end up in the target directory
| > location - or at least R can't find it there and the issue is hard to
| > debug since at the point when the build process gets control again and I
| > get a shell the files in questions are just removed by the Makefile:
| >
| > ** libs
| > make[1]: Entering directory '/build/r-cran-yaml-2.1.14+dfsg/src'
| > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g
-O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -
| > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g
-O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -
| > gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o yaml.so implicit.o
r-ext.o -lyaml -L/usr/lib/R/lib -lR
| > make[1]: Leaving directory '/build/r-cran-yaml-2.1.14+dfsg/src'
| > make[1]: Entering directory '/build/r-cran-yaml-2.1.14+dfsg/src'
| > make[1]: Leaving directory '/build/r-cran-yaml-2.1.14+dfsg/src'
| > installing to
/build/r-cran-yaml-2.1.14+dfsg/debian/r-cran-yaml/usr/lib/R/site-library/yaml/libs
| > ** R
| > ** inst
| > ** preparing package for lazy loading
| > ** help
| > *** installing help indices
| > ** building package indices
| > ** testing if installed package can be loaded
| > Error in dyn.load(file, DLLpath = DLLpath, ...) :.
| > unable to load shared object
'/build/r-cran-yaml-2.1.14+dfsg/debian/r-cran-yaml/usr/lib/R/site-library/yaml/libs/yaml.so':
| >
/build/r-cran-yaml-2.1.14+dfsg/debian/r-cran-yaml/usr/lib/R/site-library/yaml/libs/yaml.so:
undefined symbol: yaml_emitter_set_indent_mapping_sequence
| > Error: loading failed
| > Execution halted
| > ERROR: loading failed
| > * removing
'/build/r-cran-yaml-2.1.14+dfsg/debian/r-cran-yaml/usr/lib/R/site-library/yaml'
| >
| >
| > I admit my poor wisdom ends here. Any clue?
|
| Nothing from a quick look. I'll have a longer look tonight or tomorrow
| and see if I can spot anything.
Using (the command-line shorthand tool from my littler package)
$ install.r yaml
on a shell works fine in Ubuntu 16.04 (at work) as well as in a quickly
fired-up Docker container (using the official r-base image I co-maintaim)
based on Debian testing (see below).
So it looks like it is not the yaml CRAN package. No smoking gun here :-/
Dirk
$ docker run --rm -ti r-base /bin/bash
root@44037b347f37:/# apt-get update
Get:1 http://security.debian.org testing/updates InRelease [68.2 kB]
Get:3 http://deb.debian.org/debian testing InRelease [175 kB]
Get:2 http://debian.gtisc.gatech.edu/debian sid InRelease [223 kB]
Get:4 http://deb.debian.org/debian testing-updates InRelease [88.5 kB]
Get:5 http://deb.debian.org/debian testing/main amd64 Packages [9,327 kB]
Get:6 http://debian.gtisc.gatech.edu/debian sid/main amd64 Packages [9,877
kB]
Fetched 19.8 MB in 4s (4,847 kB/s)
Reading package lists... Done
root@44037b347f37:/# install.r yaml
trying URL 'https://cran.rstudio.com/src/contrib/yaml_2.1.14.tar.gz'
Content type 'application/x-gzip' length 81095 bytes (79 KB)
==================================================
downloaded 79 KB
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.c -o
*api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dumper.c -o
*dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c emitter.c -o
*emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c implicit.c -o
*implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loader.c -o
*loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parser.c -o
*parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-ext.c -o
*r-ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reader.c -o
*reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scanner.c -o
*scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2
*-fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat
*-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o
*writer.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o yaml.so api.o
*dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o
*writer.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
The downloaded source packages are in
‘/tmp/downloaded_packages’
root@44037b347f37:/#
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
