[R-pkg-devel] Compilation used the "non-portable flag"
edd @end|ng |rom deb|@n@org
Fri May 10 22:55:35 CEST 2019
On 10 May 2019 at 20:32, Goldfeld, Keith wrote:
| Good afternoon –
| I am submitting an update to my package ‘simstudy’, and the ran the rhub checks. I received a note from one of the four platforms (the other three passed). The Ubuntu Linux 16.04 objected to the compilation flags:
| * checking compilation flags used ... NOTE
| Compilation used the following non-portable flag(s):
| ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’
| I did some searching and someone suggested I create a ‘Makevars’ in the ~/.R directory (which is different from my package directory). This is what I included in the Makevars file:
| # Settings from /etc/R/Makeconf with "non-portable flag(s):"
| # ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ replaced by -Wall -pedantic
| # and without -fdebug-prefix-map=...
| CFLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 $(LTO)
| CXXFLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 $(LTO)
| CXX98FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
| CXX11FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
| CXX14FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
| I ran devtools::check(), and it seemed to find the Makevars file. However, when I reran devtools::check_rhub(), I still received a NOTE. Does anyone have any advice on what I might not be getting right?
"A change is gonna come."
This was arguably something I should have taken care of earlier. The long
story is that
- Debian (and thus Ubuntu) impose ‘-Wdate-time -Werror=format-security
-Wformat’ for security reasons, and have for a few years
- as an OS default these become active on Debian and Ubuntu when R is
compiled (see /etc/R/Makeconf)
- this confuses people, and what pushed me over the edge was that I had to
explain it to one of my STAT 430 students a week or two ago
As discussed on r-sig-debian we currently have another good reason to update
our R 3.6.0-1 package, and I will add this too. In the meantime try this on
local system (and I don't think you can influence the rhub build): just add
_R_CHECK_COMPILATION_FLAGS_KNOWN_=-Wformat -Werror=format-security -Wdate-time
to any one of $RHOME/etc/Renviron, $RHOME/etc/Renviron.site (and those two
can be accessed via /etc/R/ for convenience), your ~/.Renviron, your working
directory's .Renviron (if any), your ~/.R/check.Renviron.
Or wait a couple of days.
Hope this helps, Dirk
http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
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