sgaure/chebpol

Source code for R package chebpol on CRAN

chebpol's Issues

must build fftw3 library with '--enable-shared' flag to install `chebpol`

I had some difficulty installing chebpol in R 4.0.3
.
I was able to solve the problem and thought I would share the problem and solution here for everyone's sake.

Perhaps you can put a note about this in the documentation or a new installation guide for future reference.

---

I tried to install chebpol from CRAN and it failed:

> install.packages("chebpol")

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)  
trying URL 'https://cloud.r-project.org/src/contrib/chebpol_2.1-2.tar.gz' 
Content type 'application/x-gzip' length 2349391 bytes (2.2 MB)
==================================================                                             downloaded 2.2 MB                                                                              
* installing *source* package ‘chebpol’ ...
** package ‘chebpol’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc -std=gnu99
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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for FFTW... yes
checking for GSL... yes
checking for working fftw_plan_r2r in R... Error in dyn.load("conftest.so") :
checking for working fftw_plan_r2r in R... Error in dyn.load("conftest.so") :
  unable to load shared object '/tmp/Rtmpnqg7uw/R.INSTALL24b26868b96a/chebpol/conftest.so':
  /tmp/Rtmpnqg7uw/R.INSTALL24b26868b96a/chebpol/conftest.so: cannot open shared object file: No
 such file or directory
Execution halted
yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden   -fopenmp -fpic  -g -
O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -We
rror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chebpol.c -o chebpol.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden   -fopenmp -fpic  -g -
O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -We
rror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stalker.c -o stalker.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o chebpol.so che
bpol.o stalker.o -L/usr/local/lib -lfftw3 -lgsl -lgslcblas -lm -llapack -lblas -lgfortran -lm -
lquadmath -fopenmp -fopenmp -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32 against symbol `stdo
ut@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: chebpol.so] Error 1
ERROR: compilation failed for package ‘chebpol’
* removing ‘/usr/local/lib/R/site-library/chebpol’

The downloaded source packages are in
        ‘/tmp/RtmpbkIO5x/downloaded_packages’
Warning message:
In install.packages("chebpol") :
  installation of package ‘chebpol’ had non-zero exit status

The function fftw_plan_r2r referred to in the error message is from the fftw package.

I found a github issue from another repository with a similar error message. There, it was suggested to provide the flag --enable-shared when building the FFTW package.

This therefore requires us to download and build the FFTW package from source, not from a package manager like apt-get.

I did this as follows:

wget https://www.fftw.org/fftw-3.3.9.tar.gz
tar zxvf fftw-3.3.9.tar.gz
cd fftw-3.3.9
./configure   --enable-shared
make
sudo make install

and then when I tried to install chebpol in R again, it worked!

install.packages("chebpol")

For reference, here is some session info:

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13     magrittr_2.0.1      usethis_2.0.1
 [4] devtools_2.4.2      pkgload_1.2.1       R6_2.5.0
 [7] rlang_0.4.11        fastmap_1.0.1       tools_4.0.3
[10] pkgbuild_1.2.0      sessioninfo_1.1.1   cli_3.0.1
[13] withr_2.4.2         ellipsis_0.3.2      remotes_2.3.0
[16] rprojroot_2.0.2     lifecycle_1.0.0     crayon_1.4.1
[19] processx_3.5.2      BiocManager_1.30.16 purrr_0.3.4
[22] callr_3.7.0         fs_1.5.0            ps_1.4.0
[25] testthat_3.0.3      curl_4.3            memoise_2.0.0
[28] glue_1.4.2          cachem_1.0.4        compiler_4.0.3
[31] desc_1.3.0          prettyunits_1.1.1