Hi Ivan, Thanks for the suggestion.
I found that libpqwalreceiver.so, which is part of pgsql-15.1, made for a simpler example of my issue. So, using your advice, I ran the following in my shell: LD_DEBUG=libs R -e 'dyn.load("/stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so", now=FALSE)' I have attached the relevant part of the output from this command below. The gist of it is that, indeed, R starts to look for dependent libraries even if now=FALSE. Maybe it is the case that, as Duncan suggests, this is intended behaviour? But I think it's not ideal behaviour because otherwise it requires you to topologically sort all library dependencies and load them in the optimal order, which is very difficult to do. Is there someone involved in R development who can explain this behaviour to me? Cheers. *** > dyn.load("/stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so", now=FALSE) 1655: find library=libpq.so.5 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libpq.so.5 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libpq.so.5 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libpq.so.5 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libpq.so.5 1655: trying file=/usr/local/lib64/libpq.so.5 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libpq.so.5 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libpq.so.5 1655: search path=/usr/pgsql-15/lib/tls/x86_64:/usr/pgsql-15/lib/tls:/usr/pgsql-15/lib/x86_64:/usr/pgsql-15/lib (RUNPATH from file /stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so) 1655: trying file=/usr/pgsql-15/lib/tls/x86_64/libpq.so.5 1655: trying file=/usr/pgsql-15/lib/tls/libpq.so.5 1655: trying file=/usr/pgsql-15/lib/x86_64/libpq.so.5 1655: trying file=/usr/pgsql-15/lib/libpq.so.5 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libpq.so.5 1655: 1655: find library=libssl.so.10 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libssl.so.10 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libssl.so.10 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libssl.so.10 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libssl.so.10 1655: trying file=/usr/local/lib64/libssl.so.10 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libssl.so.10 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libssl.so.10 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libssl.so.10 1655: 1655: find library=libcrypto.so.10 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libcrypto.so.10 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libcrypto.so.10 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libcrypto.so.10 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libcrypto.so.10 1655: trying file=/usr/local/lib64/libcrypto.so.10 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libcrypto.so.10 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libcrypto.so.10 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libcrypto.so.10 1655: 1655: find library=libkrb5.so.3 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libkrb5.so.3 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libkrb5.so.3 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libkrb5.so.3 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libkrb5.so.3 1655: trying file=/usr/local/lib64/libkrb5.so.3 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libkrb5.so.3 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libkrb5.so.3 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libkrb5.so.3 1655: 1655: find library=libcom_err.so.2 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libcom_err.so.2 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libcom_err.so.2 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libcom_err.so.2 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libcom_err.so.2 1655: trying file=/usr/local/lib64/libcom_err.so.2 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libcom_err.so.2 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libcom_err.so.2 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libcom_err.so.2 1655: 1655: find library=libgssapi_krb5.so.2 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libgssapi_krb5.so.2 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libgssapi_krb5.so.2 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libgssapi_krb5.so.2 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libgssapi_krb5.so.2 1655: trying file=/usr/local/lib64/libgssapi_krb5.so.2 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libgssapi_krb5.so.2 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libgssapi_krb5.so.2 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libgssapi_krb5.so.2 1655: 1655: find library=libldap_r-2.4.so.2 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libldap_r-2.4.so.2 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libldap_r-2.4.so.2 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libldap_r-2.4.so.2 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libldap_r-2.4.so.2 1655: trying file=/usr/local/lib64/libldap_r-2.4.so.2 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libldap_r-2.4.so.2 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libldap_r-2.4.so.2 D_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libplc4.so 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libplc4.so 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libplc4.so 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libplc4.so 1655: trying file=/usr/local/lib64/libplc4.so 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libplc4.so 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libplc4.so 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libplc4.so 1655: 1655: find library=libnspr4.so [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libnspr4.so 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libnspr4.so 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libnspr4.so 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libnspr4.so 1655: trying file=/usr/local/lib64/libnspr4.so 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libnspr4.so 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libnspr4.so 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libnspr4.so 1655: 1655: find library=libselinux.so.1 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libselinux.so.1 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libselinux.so.1 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libselinux.so.1 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libselinux.so.1 1655: trying file=/usr/local/lib64/libselinux.so.1 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libselinux.so.1 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libselinux.so.1 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libselinux.so.1 1655: 1655: find library=libpcre.so.1 [0]; searching 1655: search path=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64:/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib:/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib:/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib:/usr/local/lib64:/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server:/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib (LD_LIBRARY_PATH) 1655: trying file=/stornext/System/data/apps/gcc/gcc-11.1.0/lib64/libpcre.so.1 1655: trying file=/stornext/System/data/apps/pcre2/pcre2-10.36-gcc-11.1.0/lib/libpcre.so.1 1655: trying file=/stornext/System/data/tools/openSSL/openSSL-1.1.1n/lib/libpcre.so.1 1655: trying file=/stornext/System/data/apps/R/R-4.2.1/lib64/R/lib/libpcre.so.1 1655: trying file=/usr/local/lib64/libpcre.so.1 1655: trying file=/stornext/System/data/tools/openjdk/openjdk-13.0.2/lib/server/libpcre.so.1 1655: trying file=/stornext/System/data/apps/hdf5/hdf5-1.8.20/lib/libpcre.so.1 1655: search cache=/etc/ld.so.cache 1655: trying file=/lib64/libpcre.so.1 1655: 1655: /stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so: error: symbol lookup error: undefined symbol: work_mem (fatal) Error in dyn.load("/stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so", : unable to load shared object '/stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so': /stornext/System/data/tools/pgsql/pgsql-15.1/lib/libpqwalreceiver.so: undefined symbol: work_mem Execution halted On Wed, Feb 1, 2023 at 9:05 PM Ivan Krylov <krylov.r...@gmail.com> wrote: > В Wed, 1 Feb 2023 14:16:54 +1100 > Michael Milton <ttmigue...@gmail.com> пишет: > > > Is this a bug in the `dyn.load` implementation for R? If not, why is > > it behaving like this? What should I do about it? > > On Unix-like systems, dyn.load forwards its arguments to dlopen(). It > should be possible to confirm with a debugger that R passes RTLD_NOW to > dlopen() when calling dyn.load(now = TRUE) and RTLD_LAZY when calling > dyn.load(now = FALSE). > > I don't know for sure why the symbols are being resolved despite you > asked the linker not to. Did something in the system set the > LD_BIND_NOW environment variable? Do any of the libraries in the > dependency tree have any constructors (C++ or > __attribute__((constructor)) or otherwise mentioned in .ini* sections) > that rely on MKL being available at initialisation time? > > If you launch R with the environment variable LD_DEBUG=libs set, the > debugging output may shine some light on the problem. > > -- > Best regards, > Ivan > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.