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Failing to install sf on a CentoOS machine with R 3.5.1 #815

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matteodefelice opened this issue Aug 9, 2018 · 9 comments
Closed

Failing to install sf on a CentoOS machine with R 3.5.1 #815

matteodefelice opened this issue Aug 9, 2018 · 9 comments

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@matteodefelice
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Hi everybody, I have just spent 3 hours trying to install sf on my machine without any success (I am just now switching to anaconda).

I have a Linux machine with a CentOS 7.15 distribution and with R 3.5.1 installed. I have tried to install sf but nothing, in the repository you can only find gdal 1.11 and not gdal 2.2. Then, this is what happened:

  1. I have installed gdal-2.3.1 from sources but it required c++11 that apparently is not available with the version of gcc I have (4.8.5)
  2. Then I have installed gdal-2.2 from sources
  3. I have installed geos 3.6.2 from sources
  4. I have installed proj-5.1.0 from sources
    However, if I install sf (any version, even the latest from github) this is what happens:
> devtools::install_github("r-spatial/sf")
Downloading GitHub repo r-spatial/sf@master
from URL https://api.github.com/repos/r-spatial/sf/zipball/master
Installing sf
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5'  \
  --library='/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5' --install-tests 

* installing *source* package ‘sf’ ...
configure: CC: gcc -m64 -std=gnu99
configure: CXX: g++ -m64 -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.4
checking GDAL version >= 2.0.0... yes
checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
configure: PROJ: 4.8.0
checking for pj_init_plus in -lproj... yes
/tmp/cc3nT6Mc.o: In function `main':
/tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/proj_conf_test.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 3808: ./proj_conf_test: No such file or directory
checking PROJ: epsg found and readable... yes
/tmp/ccxztagi.o: In function `main':
/tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/proj_conf_test.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 3867: ./proj_conf_test: No such file or directory
checking PROJ: conus found and readable... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.6.2
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/local/lib -lgeos_c... yes
configure: Package CPP flags:    -I/usr/local/include -I/usr/local/include
configure: Package LIBS: -lproj     -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c bbox.cpp -o bbox.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal.cpp -o gdal.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal_geom.cpp -o gdal_geom.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal_read.cpp -o gdal_read.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal_utils.cpp -o gdal_utils.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal_write.cpp -o gdal_write.o
gdal_write.cpp: In function ‘int CPL_write_ogr(Rcpp::List, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::List, Rcpp::CharacterVector, bool, bool, bool, bool)’:
gdal_write.cpp:275:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (names.size() > i)
                      ^
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c geos.cpp -o geos.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c hex.cpp -o hex.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c proj.cpp -o proj.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c raster2sf.cpp -o raster2sf.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c sfg.cpp -o sfg.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c signed_area.cpp -o signed_area.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c stars.cpp -o stars.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c wkb.cpp -o wkb.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_utils.o gdal_write.o geos.o hex.o proj.o raster2sf.o sfg.o signed_area.o stars.o wkb.o -lproj -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c -L/usr/lib64/R/lib -lR
installing to /home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf/libs
** R
** data
** demo
** inst
** tests
** byte-compile and prepare package for lazy loading
in method for ‘dbWriteTable’ with signature ‘"PostgreSQLConnection","character","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘dbDataType’ with signature ‘"PostgreSQLConnection","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘coerce’ with signature ‘"Spatial","sf"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"Spatial","sfc"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sf","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sfc","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"XY","Spatial"’: no definition for class “Spatial”
** help
*** installing help indices
  converting help for package ‘sf’
    finding HTML links ... done
    Ops                                     html  
    aggregate.sf                            html  
    bgMap                                   html  
    bind                                    html  
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/bind.Rd:21: file link ‘rbind’ in package ‘base’ does not exist and so has been treated as a topic
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/bind.Rd:36: file link ‘bind_cols’ in package ‘dplyr’ does not exist and so has been treated as a topic
    coerce-methods                          html  
    dbDataType                              html  
    db_drivers                              html  
    extension_map                           html  
    gdal                                    html  
    gdal_utils                              html  
    geos_binary_ops                         html  
    geos_binary_pred                        html  
    geos_combine                            html  
    geos_measures                           html  
    geos_query                              html  
    geos_unary                              html  
    internal                                html  
    is_driver_available                     html  
    is_driver_can                           html  
    is_geometry_column                      html  
    merge.sf                                html  
    plot                                    html  
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/plot.Rd:86: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
    prefix_map                              html  
    rawToHex                                html  
    reexports                               html  
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
    sf-deprecated                           html  
    sf                                      html  
    sf_extSoftVersion                       html  
    sf_project                              html  
    sfc                                     html  
    sgbp                                    html  
    st                                      html  
    st_agr                                  html  
    st_as_binary                            html  
    st_as_grob                              html  
    st_as_sf                                html  
    st_as_sfc                               html  
    st_as_text                              html  
    st_bbox                                 html  
    st_cast                                 html  
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/st_cast.Rd:89: file link ‘aggregate’ in package ‘sf’ does not exist and so has been treated as a topic
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/st_cast.Rd:89: file link ‘summarise’ in package ‘sf’ does not exist and so has been treated as a topic
    st_cast_sfc_default                     html  
    st_collection_extract                   html  
    st_coordinates                          html  
    st_crop                                 html  
    st_crs                                  html  
    st_drivers                              html  
    st_geometry                             html  
    st_geometry_type                        html  
    st_graticule                            html  
    st_interpolate_aw                       html  
    st_is                                   html  
    st_is_longlat                           html  
    st_jitter                               html  
    st_join                                 html  
Rd warning: /tmp/Rtmpfet4gW/devtools4f76b2e442/r-spatial-sf-bafc5b5/man/st_join.Rd:24: file link ‘left_join’ in package ‘dplyr’ does not exist and so has been treated as a topic
    st_layers                               html  
    st_line_sample                          html  
    st_make_grid                            html  
    st_nearest_feature                      html  
    st_nearest_points                       html  
    st_precision                            html  
    st_read                                 html  
    st_relate                               html  
    st_sample                               html  
    st_transform                            html  
    st_viewport                             html  
    st_write                                html  
    finding level-2 HTML links ... done

    st_zm                                   html  
    stars                                   html  
    summary.sfc                             html  
    tibble                                  html  
    tidyverse                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf/libs/sf.so':
  /home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf/libs/sf.so: undefined symbol: _ZN10OGRFeature20GetFieldAsDoubleListEiPi
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf’
Installation failed: Command failed (1)
@matteodefelice matteodefelice mentioned this issue Aug 9, 2018
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@edzer
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edzer commented Aug 28, 2018

I would check whether

ldd /home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf/libs/sf.so | grep -i gdal

indeed shows that the shared library tries to link against shared libraries in /usr/local/lib. Your PROJ.5 is not being picked up by install, but that doesn't seem a problem.

@matteodefelice
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Do you know if there is a way to avoid to have the installation directory deleted after the fail?

@edzer
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edzer commented Aug 29, 2018

Hang on, it said

  • removing ‘/home/felicma/R/x86_64-redhat-linux-gnu-library/3.5/sf’

so the .so I pointed to shouldn't be available after all.

@matteodefelice
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The same with the latest version of sf from CRAN.

@edzer
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edzer commented Oct 29, 2018

See the README section on Multiple GDAL, GEOS and/or PROJ versions on your system and #844 for the issue leading up to it.

@matteodefelice
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Thanks for that information, actually I had two version of libproj. Unfortunately, I have the same issue now that I have removed all the libraries that were under /usr/local/lib (and no more duplicates on ldconfig -p). I still can't install the package.

@edzer
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edzer commented Oct 29, 2018

If you provide me with a docker file that replicates your system, I can have a look at it.

@edzer edzer closed this as completed Nov 16, 2018
@rsbivand rsbivand mentioned this issue Jan 16, 2019
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@nuest
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nuest commented Jul 20, 2019 •
edited
Loading

Just want to document how I solved the undefined symbol: _ZN10OGRFeature20GetFieldAsDoubleListEiPi problem on my machine:

I did have two libgdal20.so binaries flying around, one probably from an old source install of GDAL that I forgot I did a year ago. I identified this by running

daniel@gin-nuest:/usr/share/proj$ ldconfig -p | grep gdal
	libgdal.so.20 (libc6,x86-64) => /usr/local/lib/libgdal.so.20
	libgdal.so.20 (libc6,x86-64) => /usr/lib/libgdal.so.20
	libgdal.so (libc6,x86-64) => /usr/local/lib/libgdal.so
	libgdal.so (libc6,x86-64) => /usr/lib/libgdal.so

So, two libgdal.so. After uninstalling GDAL (libgdal20) with apt and then running the same command again I got

daniel@gin-nuest:/usr/share/proj$ ldconfig -p | grep gdal
	libgdal.so.20 (libc6,x86-64) => /usr/local/lib/libgdal.so.20
	libgdal.so (libc6,x86-64) => /usr/local/lib/libgdal.so

So I manually removed the files (daniel@gin-nuest:/usr/local/lib$ sudo rm libgdal.*), updated the cache (rm /etc/ld.so.cache; ldconfig) and then installed GDAL from Ubuntu sources (not UbuntuGIS unstable). Installation of sf works again:

> library("sf")
Linking to GEOS 3.7.1, GDAL 2.2.3, PROJ 4.9.3

@leungi
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leungi commented May 18, 2020

To add to @nuest workflow:

  • the troublemaker for me was running echo "/usr/local/lib" /etc/ld.so.conf.d/libgdal-x86_64.conf based on this SO post; this was what created the duplicated libgdal.so* in /usr/local/lib, as per @nuest post above.
(base) bash-4.2$ ldconfig -p | grep gdal
        libgdal.so.20 (libc6,x86-64) => /usr/local/lib/libgdal.so.20
        libgdal.so.20 (libc6,x86-64) => /lib64/libgdal.so.20
        libgdal.so.1 (libc6,x86-64) => /lib64/libgdal.so.1
        libgdal.so (libc6,x86-64) => /usr/local/lib/libgdal.so
        libgdal.so (libc6,x86-64) => /lib64/libgdal.so

  • so I went into /etc/ld.so.conf.d/, and did sudo rm libgdal-x86_64.conf

  • then sudo ldconfig to commit

  • my final ldconfig

(base) bash-4.2$ ldconfig -p | grep gdal
        libgdal.so.20 (libc6,x86-64) => /lib64/libgdal.so.20
        libgdal.so.1 (libc6,x86-64) => /lib64/libgdal.so.1
        libgdal.so (libc6,x86-64) => /lib64/libgdal.so

  • install sf pointing to the gdal-config of choice; in the case of RHEL7, since we need to build GDAL >2.0 from source, point to path of compilation - e.g., install.packages('sf',configure.args='--with-gdal-config=/home/leungi/gdal-compile/bin/gdal-config'

  • then do the happy 🕺

Thank you both for the guidance.

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4 participants
@edzer @nuest @matteodefelice @leungi