[R-sig-Debian] Failed to install RQuantLib in Ubuntu machine
Christofer Bogaso
bog@@o@chri@tofer @ending from gm@il@com
Sun Jan 6 18:36:03 CET 2019
Hi,
<This issue was previously posted in R-help, but advised to post here as a
more relevant group>
I was trying to install RQuantLib in my Ubuntu machine which failed with
below information :
*> install.packages('RQuantLib', repos='http://cran.rstudio.com/
<http://cran.rstudio.com/>', INSTALL_opts = c('--no-lock'))*
*Installing package into ‘/usr/local/lib/R/site-library’*
*(as ‘lib’ is unspecified)*
*trying URL 'http://cran.rstudio.com/src/contrib/RQuantLib_0.4.7.tar.gz
<http://cran.rstudio.com/src/contrib/RQuantLib_0.4.7.tar.gz>'*
*Content type 'application/x-gzip' length 189726 bytes (185 KB)*
*==================================================*
*downloaded 185 KB*
** installing *source* package ‘RQuantLib’ ...*
*** package ‘RQuantLib’ successfully unpacked and MD5 sums checked*
*checking whether the C++ compiler works... yes*
*checking for C++ compiler default output file name... a.out*
*checking for suffix of executables... *
*checking whether we are cross compiling... no*
*checking for suffix of object files... o*
*checking whether we are using the GNU C++ compiler... yes*
*checking whether g++ accepts -g... yes*
*checking how to run the C++ preprocessor... g++ -E*
*checking whether we are using the GNU C++ compiler... (cached) yes*
*checking whether g++ accepts -g... (cached) yes*
*checking for R... yes*
*checking for quantlib-config... yes*
*checking for Boost development files... yes*
*checking for minimal Boost version... yes*
*configure: creating ./config.status*
*config.status: creating src/Makevars*
*Completed configuration and ready to build.*
*** libs*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
RcppExports.cpp -o RcppExports.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
affine.cpp -o affine.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
asian.cpp -o asian.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
barrier_binary.cpp -o barrier_binary.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
bermudan.cpp -o bermudan.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
bonds.cpp -o bonds.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
calendars.cpp -o calendars.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
curves.cpp -o curves.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
dates.cpp -o dates.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
daycounter.cpp -o daycounter.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
discount.cpp -o discount.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
hullwhite.cpp -o hullwhite.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
implieds.cpp -o implieds.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
modules.cpp -o modules.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
sabr.cpp -o sabr.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
schedule.cpp -o schedule.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
utils.cpp -o utils.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
vanilla.cpp -o vanilla.o*
*g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include
-I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
zero.cpp -o zero.o*
*g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions
-Wl,-z,relro -o RQuantLib.so RcppExports.o affine.o asian.o
barrier_binary.o bermudan.o bonds.o calendars.o curves.o dates.o
daycounter.o discount.o hullwhite.o implieds.o modules.o sabr.o schedule.o
utils.o vanilla.o zero.o -L/usr/local/lib -lQuantLib -fopenmp
-L/usr/lib/R/lib -lR*
*installing to /usr/local/lib/R/site-library/RQuantLib/libs*
*** R*
*** data*
*** demo*
*** inst*
*** preparing package for lazy loading*
*** help*
**** installing help indices*
*** building package indices*
*** testing if installed package can be loaded*
* *** caught segfault ****
*address 0x7f255e91a9a0, cause 'invalid permissions'*
*Traceback:*
* 1: dyn.load(file, DLLpath = DLLpath, ...)*
* 2: library.dynam(lib, package, package.lib)*
* 3: loadNamespace(package, lib.loc)*
* 4: doTryCatch(return(expr), name, parentenv, handler)*
* 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])*
* 6: tryCatchList(expr, classes, parentenv, handlers)*
* 7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <-
loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos,
deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L]) else "" msg <-
gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e)) if (logical.return)
message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE,
domain = NA)})*
* 8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return
= TRUE)*
* 9: withCallingHandlers(expr, packageStartupMessage = function(c)
invokeRestart("muffleMessage"))*
*10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))*
*11: doTryCatch(return(expr), name, parentenv, handler)*
*12: tryCatchOne(expr, names, parentenv, handlers[[1L]])*
*13: tryCatchList(expr, classes, parentenv, handlers)*
*14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <-
conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L
+ nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na
<http://is.na>(w)) w <- 14L + nchar(dcall, type = "b") +
nchar(sm[1L], type = "b") if (w > LONG)
prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg
<- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = outFile) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))})*
*15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE)))*
*16: tools:::.test_load_package("RQuantLib",
"/usr/local/lib/R/site-library")*
*An irrecoverable exception occurred. R is aborting now ...*
*Segmentation fault (core dumped)*
*ERROR: loading failed*
** removing ‘/usr/local/lib/R/site-library/RQuantLib’*
*The downloaded source packages are in*
* ‘/tmp/RtmpKTXorW/downloaded_packages’*
*Warning message:*
*In install.packages("RQuantLib", repos = "http://cran.rstudio.com/
<http://cran.rstudio.com/>", :*
* installation of package ‘RQuantLib’ had non-zero exit status*
Next I tried with Dirk Eddelbuettel's advice as follows
sudo apt-get install r-cran-rquantlib
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer
required:
grub-pc-bin libgsasl7 libkyotocabinet16v5 libntlm0
linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic
linux-headers-4.4.0-119 linux-headers-4.4.0-119-generic
linux-headers-4.4.0-121 linux-headers-4.4.0-121-generic
linux-headers-4.4.0-124
linux-headers-4.4.0-124-generic linux-headers-4.4.0-127
linux-headers-4.4.0-127-generic linux-headers-4.4.0-128
linux-headers-4.4.0-128-generic linux-headers-4.4.0-130
linux-headers-4.4.0-130-generic linux-headers-4.4.0-134
linux-headers-4.4.0-134-generic
linux-headers-4.4.0-137 linux-headers-4.4.0-137-generic
linux-headers-4.4.0-138 linux-headers-4.4.0-138-generic
linux-image-4.4.0-116-generic linux-image-4.4.0-119-generic
linux-image-4.4.0-121-generic linux-image-4.4.0-124-generic
linux-image-4.4.0-127-generic
linux-image-4.4.0-128-generic linux-image-4.4.0-130-generic
linux-image-4.4.0-134-generic linux-image-4.4.0-137-generic
linux-image-4.4.0-138-generic mailutils-common
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
libquantlib0v5 littler r-cran-littler r-cran-pkgkitten r-cran-rcpp
Suggested packages:
r-cran-getopt r-cran-inline
The following NEW packages will be installed:
libquantlib0v5 littler r-cran-littler r-cran-pkgkitten r-cran-rcpp
r-cran-rquantlib
0 upgraded, 6 newly installed, 0 to remove and 177 not upgraded.
Need to get 11.2 MB of archives.
After this operation, 52.9 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:2 http://ppa.launchpad.net/edd/misc/ubuntu xenial/main amd64
libquantlib0v5 amd64 1.10-1xenial1 [7,966 kB]
Get:3 http://cran.rstudio.com/bin/linux/ubuntu xenial/ r-cran-littler
0.3.3-1xenial0 [336 kB]
Get:1 http://sgp1.mirrors.digitalocean.com/ubuntu xenial/universe amd64
r-cran-pkgkitten all 0.1.3-1 [17.7 kB]
Get:4 http://sgp1.mirrors.digitalocean.com/ubuntu xenial/universe amd64
r-cran-rcpp amd64 0.12.3-1 [2,073 kB]
Get:6 http://cran.rstudio.com/bin/linux/ubuntu xenial/ littler
0.3.3-1xenial0 [12.5 kB]
Get:5 http://sgp1.mirrors.digitalocean.com/ubuntu xenial/universe amd64
r-cran-rquantlib amd64 0.4.2-1 [805 kB]
Fetched 11.2 MB in 8s (1,321 kB/s)
Selecting previously unselected package libquantlib0v5.
(Reading database ... 552387 files and directories currently installed.)
Preparing to unpack .../libquantlib0v5_1.10-1xenial1_amd64.deb ...
Unpacking libquantlib0v5 (1.10-1xenial1) ...
Selecting previously unselected package r-cran-littler.
Preparing to unpack .../r-cran-littler_0.3.3-1xenial0_amd64.deb ...
Unpacking r-cran-littler (0.3.3-1xenial0) ...
Selecting previously unselected package littler.
Preparing to unpack .../littler_0.3.3-1xenial0_all.deb ...
Unpacking littler (0.3.3-1xenial0) ...
Selecting previously unselected package r-cran-pkgkitten.
Preparing to unpack .../r-cran-pkgkitten_0.1.3-1_all.deb ...
Unpacking r-cran-pkgkitten (0.1.3-1) ...
Selecting previously unselected package r-cran-rcpp.
Preparing to unpack .../r-cran-rcpp_0.12.3-1_amd64.deb ...
Unpacking r-cran-rcpp (0.12.3-1) ...
Selecting previously unselected package r-cran-rquantlib.
Preparing to unpack .../r-cran-rquantlib_0.4.2-1_amd64.deb ...
Unpacking r-cran-rquantlib (0.4.2-1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libquantlib0v5 (1.10-1xenial1) ...
Setting up r-cran-littler (0.3.3-1xenial0) ...
Setting up littler (0.3.3-1xenial0) ...
Setting up r-cran-pkgkitten (0.1.3-1) ...
Setting up r-cran-rcpp (0.12.3-1) ...
Setting up r-cran-rquantlib (0.4.2-1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
But it also failed when I tried to load the package in R console.
*> library(RQuantLib)*
*Error: package or namespace load failed for ‘RQuantLib’ in dyn.load(file,
DLLpath = DLLpath, ...):*
* unable to load shared object
'/usr/lib/R/site-library/RQuantLib/libs/RQuantLib.so':*
* /usr/lib/R/site-library/RQuantLib/libs/RQuantLib.so: undefined symbol:
_ZN8QuantLib11daysBetweenERKNS_4DateES2_*
*> ls('package:RQuantLib')*
*Error in as.environment(pos) : *
* no item called "package:RQuantLib" on the search list*
Any advice on how to correctly install it will be highly helpful. Relevant
R info:
*> sessionInfo()*
*R version 3.4.4 (2018-03-15)*
*Platform: x86_64-pc-linux-gnu (64-bit)*
*Running under: Ubuntu 16.04.4 LTS*
*Matrix products: default*
*BLAS: /usr/lib/libblas/libblas.so.3.6.0*
*LAPACK: /usr/lib/lapack/liblapack.so.3.6.0*
*locale:*
* [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C *
* [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 *
* [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 *
* [7] LC_PAPER=en_US.UTF-8 LC_NAME=C *
* [9] LC_ADDRESS=C LC_TELEPHONE=C *
*[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C *
*attached base packages:*
*[1] stats graphics grDevices utils datasets methods base *
*loaded via a namespace (and not attached):*
*[1] compiler_3.4.4 Rcpp_0.12.19 *
Thanks,
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