[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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