Emmanuel Charpentier
2016-Dec-05 12:29 UTC
[R] Can't install or upgrade the "PKI" package on a Debian testing system
Dear list,
It seems that recent changes in openssl somehow broke the installation
or update of the PKI package. This is probably specific of my setup(s)
(Debian testing, updated frequently).
Copy of a mail to Simon Urbanek (PKI maintainer), sent 5 days ago
without reply nor acknowledgement so far :
=======================================================================
It seems that recent changes in openssl rendered the PKI package
uninstallable :
--------------------------------------------------------------------------
> install.packages("PKI")
essai de l'URL
'http://cran.univ-paris1.fr/src/contrib/PKI_0.1-3.tar.gz'
Content type 'application/x-gzip' length 31058 bytes (30 KB)
=================================================downloaded 30 KB
* installing *source* package ?PKI? ...
** package ?PKI? correctement d?compress? et sommes MD5 v?rifi?es
** libs
gcc -I/usr/local/sage-7/local/lib/R//include -DNDEBUG -fpic -g -O2
-c asn1.c -o asn1.o
gcc -I/usr/local/sage-7/local/lib/R//include -DNDEBUG -fpic -g -O2
-c init.c -o init.o
gcc -I/usr/local/sage-7/local/lib/R//include -DNDEBUG -fpic -g -O2
-c pki-x509.c -o pki-x509.o
pki-x509.c: In function ?PKI_extract_key?:
pki-x509.c:136:26: error: dereferencing pointer to incomplete type
?EVP_PKEY {aka struct evp_pkey_st}?
if (EVP_PKEY_type(key->type) != EVP_PKEY_RSA)
^~
pki-x509.c: In function ?get_cipher?:
pki-x509.c:244:40: error: dereferencing pointer to incomplete type
?EVP_CIPHER_CTX {aka struct evp_cipher_ctx_st}?
ctx = (EVP_CIPHER_CTX*) malloc(sizeof(*ctx));
^~~~
pki-x509.c: In function ?PKI_RSAkeygen?:
pki-x509.c:550:5: warning: ?RSA_generate_key? is deprecated
[-Wdeprecated-declarations]
rsa = RSA_generate_key(bits, 65537, 0, 0);
^~~
In file included from /usr/include/openssl/rsa.h:13:0,
from pki.h:13,
from pki-x509.c:1:
/usr/include/openssl/rsa.h:193:1: note: declared here
DEPRECATEDIN_0_9_8(RSA *RSA_generate_key(int bits, unsigned long e, void
^
/usr/local/sage-7/local/lib/R//etc/Makeconf:132 : la recette pour la
cible ? pki-x509.o ? a ?chou?e
make: *** [pki-x509.o] Erreur 1
ERROR: compilation failed for package ?PKI?
* removing ?/usr/local/sage-7/local/lib/R/library/PKI?
Les packages source t?l?charg?s sont dans
?/tmp/Rtmpnmt97E/downloaded_packages?
Warning message:
In install.packages("PKI") :
l'installation du package ?PKI? a eu un statut de sortie non nul
--------------------------------------------------------------------------
This problem blocks the installation of rstanarm, brms, rsconnect and
shinystan among others. Not exactly trivial.
As far as I know, my libssl libraries are all at 1.1.0c, as well as openssl.
=======================================================================
New data point : it turns out that this problem also impedes the update
of PKI : my running R installatin still has PKI 1.3, which seems enough
for rstanarm, brms, rsconnect and shinystan to run and install/upgrade.
However, on a new installation of R (installed in Sage), PKI can't be
installed. I tried to install PKI 1.3 fro Rforge, with no success.
- Did someone already had this problem ?
- Has he/she been able to work around it ? If so, How ?
- Is my mail to Simon Urbanek sufficient as a bug report ? If not, what
should I do ?
Sincerely yours,
Emanuel Charpentier
PS : If possible, I'd appreciate to be CC'd of your answers : I'm
not on
the list and have had trouble subscribing "reasonably". I'm
following it
through the mail archives.