`Hi,
our cluster is running Ubuntu-22.04. Due to packages that require specific versions of R, I need to have R-3.6.1 available on the nodes.
Through the package manager the oldest version of R that can be installed is 3.6.3-2:
apt-cache madison r-base
r-base | 4.3.1-4.2204.0 jammy-cran40/ Packages r-base | 4.3.1-3.2204.0 jammy-cran40/ Packages r-base | 4.3.1-2.2204.0 jammy-cran40/ Packages r-base | 4.3.1-1.2204.0 jammy-cran40/ Packages r-base | 4.3.0-1.2204.0 jammy-cran40/ Packages r-base | 4.2.3-1.2204.0 jammy-cran40/ Packages r-base | 4.2.2.20221110-1.2204.0 jammy-cran40/ Packages r-base | 4.2.2-1.2204.0 jammy-cran40/ Packages r-base | 4.2.1-3.2204.0 jammy-cran40/ Packages r-base | 4.2.1-2.2204.0 jammy-cran40/ Packages r-base | 4.2.1-1.2204.0 jammy-cran40/ Packages r-base | 4.2.0-1.2204.0 jammy-cran40/ Packages r-base | 4.1.2-1ubuntu2 amd64 Packages r-base | 4.1.2-1ubuntu2 i386 Packages r-base | 3.6.3-2 | http://de.archive.ubuntu.com/ubuntu focal/universe Sources
In a common software directory I keep compiled versions of R that can be accessed on all nodes. This is the added to the path, so that it can be found by bash scripts.
Compilation of R-3.6.3 works using these configuration options:
./configure --with-blas --with-lapack --with-readline --with-readline --with-cairo --with-libpng --with-jpeglib --with-libtiff --enable-R-shlib --with-x --with-recommended-packages --enable-R-shlib --enable-BLAS-shlib --enable-shared=lapack --enable-shared=blas --with-tcltk --with-tcl-config=/usr/lib/x86_64-linux-gnu/tcl8.6/tclConfig.sh --with-tk-config=/usr/lib/x86_64-linux-gnu/tk8.6/tkConfig.sh --prefix=$(pwd)
The gcc compiler is installed through the package manager and version 11.4.0:
gcc --version
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
But I fail to build R-3.6.1, because it runs into a linker error with "tools.so":
installing 'sysdata.rda'
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/storage1/Software/ubuntu/R/R-3.6.1/library/tools/libs/tools.so':
> /storage1/Software/ubuntu/R/R-3.6.1/library/tools/libs/tools.so: undefined symbol: yyllocL
Error: unable to load R code in package 'tools'
Execution halted
make[4]: *** [../../../share/make/basepkg.mk:151: sysdata] Error 1
make[4]: Leaving directory '/storage1/Software/ubuntu/R/R-3.6.1/src/library/tools'
make[3]: *** [Makefile:36: all] Error 2
make[3]: Leaving directory '/storage1/Software/ubuntu/R/R-3.6.1/src/library/tools'
make[2]: *** [Makefile:37: R] Error 1
make[2]: Leaving directory '/storage1/Software/ubuntu/R/R-3.6.1/src/library'
make[1]: *** [Makefile:28: R] Error 1
make[1]: Leaving directory '/storage1/Software/ubuntu/R/R-3.6.1/src'
make: *** [Makefile:61: R] Error 1
I am confused why this occurs only for R-3.6.1 - after all this is only a minor version change.
I could not find "yyllocL" through:
apt-cache search yylloc
or
apt-file search yyllocL
but
apt-file search yyloc
libmailutils-dev: /usr/include/mailutils/yyloc.h
I then installed this package:
apt-get install libmailutils-dev
but that did not help either, as that seems only to install the above mentioned include file:
/usr/include/mailutils/yyloc.h
But I managed to find this forum post, which mentions the yy-lexer.
I then installed these packages:
apt-get install flex flexc++ yydebug r-cran-isoweek
where the latter will probably only relate to the R-versions of the package manager, but flex and yydebug seemed good candidates.
After a complete cycle of:
make clean
./configure --with-blas --with-lapack --with-readline --with-readline --with-cairo --with-libpng --with-jpeglib --with-libtiff --enable-R-shlib --with-x --with-recommended-packages --enable-R-shlib --enable-BLAS-shlib --enable-shared=lapack --enable-shared=blas --with-tcltk --with-tcl-config=/usr/lib/x86_64-linux-gnu/tcl8.6/tclConfig.sh --with-tk-config=/usr/lib/x86_64-linux-gnu/tk8.6/tkConfig.sh --prefix=$(pwd)
and
make -j4
to rebuild it, I ran into the same error, though.
Using R-3.6.3 is only partially an option, as - to my dismay - all packages do not only a recompilation in spite of the minor version upgrade, but also partially fail entirely, because they seem to be badly maintained.
In order to keep our analysis workflows reproducible, we need R-3.6.1 on the cluster nodes.
Using docker/rocker might be a workaround, but requires adaption in all analysis scripts that the scientists use.
Could the error be due to a newer version of gcc compared to Ubuntu-20.04? Maybe using "alternatives" with gcc and using an older version could help? But I would only expect that with compilation problems, while this is clearly a linker problem.
I would set LD_LIBRARY_PATH, if I knew the location of the "yylocL"-library; provided it got installed with the yydebug package?
export LDFLAGS=-L/storage1/Software/ubuntu/R/R-3.6.1/library/
export LD_LIBRARY_PATH=/storage1/Software/ubuntu/R/R-3.6.1/library
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/storage1/Software/ubuntu/R/R-3.6.1/lib
export LDFLAGS=-L/storage1/Software/ubuntu/R/R-3.6.1/lib
Checking with nm shows more undefined symbols in tools.so:
nm -u /storage1/Software/ubuntu/R/R-3.6.1/library/tools/libs/tools.so
U ALTREP_LENGTH
U ALTSTRING_ELT
U ALTVEC_DATAPTR
U chmod@GLIBC_2.2.5
U closedir@GLIBC_2.2.5
U __ctype_b_loc@GLIBC_2.3
U __ctype_get_mb_cur_max@GLIBC_2.2.5
w __cxa_finalize@GLIBC_2.2.5
U dcgettext@GLIBC_2.2.5
U __errno_location@GLIBC_2.2.5
U extR_HTTPDCreate
U extR_HTTPDStop
U fclose@GLIBC_2.2.5
U ferror@GLIBC_2.2.5
U fopen@GLIBC_2.2.5
U fread@GLIBC_2.2.5
U free@GLIBC_2.2.5
U fwrite@GLIBC_2.2.5
U getConnection
U getpriority@GLIBC_2.2.5
w __gmon_start__
U INTEGER
w _ITM_deregisterTMCloneTable
w _ITM_registerTMCloneTable
U kill@GLIBC_2.2.5
U LENGTH
U malloc@GLIBC_2.2.5
U mbcslocale
U __memcpy_chk@GLIBC_2.3.4
U memcpy@GLIBC_2.14
U __memmove_chk@GLIBC_2.3.4
U memmove@GLIBC_2.2.5
U opendir@GLIBC_2.2.5
U parseError
U R_alloc
U R_BadLongVector
U R_BaseEnv
U RC_fopen
U R_CHAR
U R_chk_calloc
U R_chk_free
U R_chk_realloc
U R_ClassSymbol
U Rconn_fgetc
U readdir@GLIBC_2.2.5
U realloc@GLIBC_2.2.5
U R_EmptyEnv
U Rf_allocVector
U Rf_allocVector3
U Rf_asInteger
U Rf_asLogical
U Rf_begincontext
U Rf_coerceVector
U Rf_cons
U Rf_defineVar
U Rf_duplicate
U Rf_endcontext
U Rf_envlength
U Rf_error
U Rf_findVar
U Rf_getAttrib
U Rf_getCharCE
U R_FileExists
U Rf_imax2
U Rf_install
U Rf_installTrChar
U Rf_isString
U Rf_length
U Rf_lengthgets
U Rf_mbrtowc
U Rf_mkChar
U Rf_mkCharCE
U Rf_mkCharLen
U Rf_mkCharLenCE
U R_forceSymbols
U Rf_PairToVectorList
U Rf_protect
U Rf_ScalarInteger
U Rf_ScalarLogical
U Rf_ScalarString
U Rf_setAttrib
U Rf_strchr
U Rf_translateChar
U Rf_translateCharUTF8
U Rf_unprotect
U Rf_warning
U Rf_warningcall
U Rf_xlengthgets
U R_NaInt
U R_NaString
U R_NewHashedEnv
U R_NewPreciousMSet
U R_NilValue
U R_ParseContext
U R_ParseContextLast
U R_ParseContextLine
U R_ParseError
U R_ParseErrorMsg
U R_PPStack
U R_PPStackSize
U R_PPStackTop
U R_PreserveInMSet
U Rprintf
U R_registerRoutines
U R_ReleaseFromMSet
U R_signal_protect_error
U R_SrcfileSymbol
U R_SrcrefSymbol
U R_UnboundValue
U R_useDynamicSymbols
U SETCAR
U SETCDR
U setpriority@GLIBC_2.2.5
U SET_STRING_ELT
U SET_VECTOR_ELT
U __snprintf_chk@GLIBC_2.3.4
U snprintf@GLIBC_2.2.5
U __sprintf_chk@GLIBC_2.3.4
U __stack_chk_fail@GLIBC_2.4
U stat@GLIBC_2.33
U __stpcpy_chk@GLIBC_2.3.4
U stpcpy@GLIBC_2.2.5
U __strcat_chk@GLIBC_2.3.4
U strchr@GLIBC_2.2.5
U strcmp@GLIBC_2.2.5
U __strcpy_chk@GLIBC_2.3.4
U strcspn@GLIBC_2.2.5
U STRING_ELT
U strlen@GLIBC_2.2.5
U strncmp@GLIBC_2.2.5
U __strncpy_chk@GLIBC_2.3.4
U strncpy@GLIBC_2.2.5
U strstr@GLIBC_2.2.5
U TYPEOF
U vmaxget
U vmaxset
U yyllocL
Has anyone successfully built R-3.6.1 from sources on Ubuntu 22.04? Any suggestions on how to get R-3.6.1 built on Ubuntu-22.04 are highly appreciated.
Best regards,
Dr_Soong
