Error installing on R4.2.2 running on CentOS 7
ytakemon opened this issue · 10 comments
ytakemon commented
Hello,
I am getting the error below when trying to install Magick. I have also verified with our IT department that we have the following ImageMagick installed, but it seems to run into issues at the -c options.cpp -o options.o step. What can I try next to troubleshoot this?
Thanks in advance!
-Yuka
[root@marrahost02 avi]# yum list installed | grep Image
ImageMagick.x86_64 6.7.8.9-16.el7_6 @GSC-Update
ImageMagick-c++.x86_64 6.7.8.9-16.el7_6 @GSC-Update
ImageMagick-c++-devel.x86_64 6.7.8.9-16.el7_6 @GSC-Update
ImageMagick-devel.x86_64 6.7.8.9-16.el7_6 @GSC-Update
Error:
> install.packages("magick")
Installing package into ‘/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/magick_2.7.4.tar.gz'
Content type 'application/x-gzip' length 4754217 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package ‘magick’ ...
** package ‘magick’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-fopenmp -I/usr/include/ImageMagick
Using PKG_LIBS=-lMagick++ -lMagickCore
** libs
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c animation.cpp -o animation.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c attributes.cpp -o attributes.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base.cpp -o base.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c color.cpp -o color.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c composite.cpp -o composite.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.cc -o config.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c convolve.cpp -o convolve.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c device.cpp -o device.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edges.cpp -o edges.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edit.cpp -o edit.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fonts.cpp -o fonts.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fonts.cpp -o fonts.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14 -I"/gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/include" -DNDEBUG -fopenmp -I/usr/include/ImageMagick -I'/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.cpp -o options.o
options.cpp: In function ‘void set_magick_seed(long unsigned int)’:
options.cpp:45:11: error: ‘SetRandomSeed’ is not a member of ‘Magick’
Magick::SetRandomSeed(seed);
^~~~~~~~~~~~~
make: *** [options.o] Error 1
ERROR: compilation failed for package ‘magick’
* removing ‘/home/ytakemon/R/x86_64-pc-linux-gnu-library/4.2/magick’
Warning in install.packages :
installation of package ‘magick’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpOFPb6E/downloaded_packages’
My SessionInfo:
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /gsc/software/linux-x86_64-centos7/R-4.2.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.7.3 formatR_1.14
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 BiocManager_1.30.19 pillar_1.8.1
[4] compiler_4.2.2 later_1.3.0 tools_4.2.2
[7] digest_0.6.30 lifecycle_1.0.3 tibble_3.1.8
[10] gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6
[13] DBI_1.1.3 cli_3.4.1 ggrepel_0.9.2
[16] fastmap_1.1.0 withr_2.5.0 dplyr_1.0.10
[19] generics_0.1.3 vctrs_0.5.1 grid_4.2.2
[22] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1
[25] fansi_1.0.3 tcltk_4.2.2 ggplot2_3.4.0
[28] magrittr_2.0.3 scales_1.2.1 promises_1.2.0.1
[31] htmltools_0.5.3 ellipsis_0.3.2 assertthat_0.2.1
[34] mime_0.12 colorspace_2.0-3 xtable_1.8-4
[37] httpuv_1.6.6 ggsignif_0.6.4 utf8_1.2.2
[40] munsell_0.5.0 cachem_1.0.6
paulstretenowich commented
Hi Yuka,
I guess you solved your issue as you closed it. I run into a very similar issue that led me here so I'm wondering how you solved it.
Thanks in advance,
Paul
jeroen commented
This probably indicates you have manually installed conflicting or older versions of imagemagick on your server. What do you see for pkg-config --cflags Magick++ ?
paulstretenowich commented
Thanks for the quick reply. Here is what I have when running pkg-config --cflags Magick++:
-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6
jeroen commented
Which linux distribution are you on? Can you show your sessionInfo() and the full log of trying to install magick?
For reference, if you are on centos-7 and have installed ImageMagick-c++-devel the output should be this:
## pkg-config --cflags Magick++
-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6So I am guessing you either have a non standard imagemagick, or perhaps are using a weird R installation?
paulstretenowich commented
I'm on Ubuntu 16.04 and the full error message is:
* installing *source* package ‘magick’ ...
** package ‘magick’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6
Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16
** libs
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c animation.cpp -o animation.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c attributes.cpp -o attributes.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base.cpp -o base.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c color.cpp -o color.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c composite.cpp -o composite.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.cc -o config.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c convolve.cpp -o convolve.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c device.cpp -o device.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edges.cpp -o edges.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edit.cpp -o edit.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fonts.cpp -o fonts.o
g++ -std=gnu++14 -I"/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.cpp -o options.o
options.cpp: In function ‘void set_magick_seed(long unsigned int)’:
options.cpp:45:3: error: ‘SetRandomSeed’ is not a member of ‘Magick’
Magick::SetRandomSeed(seed);
^
/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/etc/Makeconf:178: recipe for target 'options.o' failed
make: *** [options.o] Error 1
ERROR: compilation failed for package ‘magick’
* removing ‘/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/magick’
* restoring previous ‘/cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/library/magick’
To draft you a bit more the context. I'm inside a proot session because I'm in an HPC environment and I'm creating modules to share to users.
There is indeed a version already installed but I try to re-install/update as I have an error message with a tool (linx) using ImageMagick.
sessionInfo() gives:
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
Matrix products: default
BLAS: /cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/lib/libRblas.so
LAPACK: /cvmfs/soft.mugqic/root/software/R_Bioconductor/R_Bioconductor-4.2.2_3.16/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=C LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.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_4.2.2
jeroen commented
Ah well you probably know that ubuntu 16.04 is EOL. But so which version of ImageMagick are you using? Did you build it from source? It must be really old?
Maybe can you try pkg-config --modversion Magick++
paulstretenowich commented
I'm using 16.04 because the former person in charge installed our R module in this one. If you suggest switching to at newer I could give a try with 20.04.
I see pkg-config --modversion Magick++ being 6.8.9. But within the linx tool I mentioned the error is about Linking to ImageMagick 6.9.10.23
jeroen commented
Yes your problems will disappear if you update to ubuntu 20.04, that is by far the easiest solution.
paulstretenowich commented
Ok thanks a lot for your responsiveness! I'll do the switch then.
jjesusfilho commented
I am using Ubuntu 16.04 and I can't upgrade it. With the fix, I was able to install the development of magick. Thank you.