"FAILED to install circlize" when install " java -jar vdjtools-1.2.1.jar Rinstall"

[yueli8]

Hello mikessh,

Thank you for developing so nice software!

I tried to install vdjtools in my ubuntu 18.04.5. My R version is 4.1.3.

It said: "FAILED to install circlize"

Thank yo in advance for your great help!

Best,

Yue

`<Inspiron-3670:~/vdjtools-1.2.1$ java -jar vdjtools-1.2.1.jar Rinstall WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.codehaus.groovy.vmplugin.v7.Java7$1 (file:/home/jing/vdjtools-1.2.1/vdjtools-1.2.1.jar) to constructor java.lang.invoke.MethodHandles$Lookup(java.lang.Class,int) WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.vmplugin.v7.Java7$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Executing com.antigenomics.vdjtools.misc.RInstall [RInstall] Opening resources stream [RInstall] Scanning for dependencies [RInstall] Scanning rscripts/rarefaction_curve.r reshape ggplot2 gridExtra FField grid [RInstall] Scanning rscripts/tracking_similarity_map.r ggplot2 reshape gridExtra grid [RInstall] Scanning rscripts/install.r [RInstall] Scanning rscripts/cluster_permutations_plot.r ggplot2 [RInstall] Scanning rscripts/tracking_stackplot.r ggplot2 reshape gridExtra grid [RInstall] Scanning rscripts/test.r [RInstall] Scanning rscripts/tracking_heatcourse.r gplots [RInstall] Scanning rscripts/vj_pairing_plot.r circlize RColorBrewer [RInstall] Scanning rscripts/cdr3aa_profile.r ggplot2 [RInstall] Scanning rscripts/plot_time_series.r ggplot2 reshape [RInstall] Scanning rscripts/fancy_spectratype.r ggplot2 reshape RColorBrewer [RInstall] Scanning rscripts/vexpr_plot.r gplots RColorBrewer ggplot2 plotrix [RInstall] Scanning rscripts/intersect_pair_scatter.r ggplot2 grid gridExtra reshape grid [RInstall] Scanning rscripts/quantile_stats.r ggplot2 RColorBrewer [RInstall] Scanning rscripts/cluster_samples.r ape reshape2 ggplot2 MASS plotrix RColorBrewer scales [RInstall] Scanning rscripts/intersect_pair_area.r ggplot2 RColorBrewer [RInstall] Scanning rscripts/join_venn.r VennDiagram RColorBrewer [RInstall] Scanning rscripts/pairwise_distance_plot.r circlize reshape2 RColorBrewer [RInstall] Scanning rscripts/intersect_pair_area_v2.r ggplot2 reshape RColorBrewer FField [RInstall] Full list of dependencies to be installed: reshape2 FField reshape gplots gridExtra circlize ggplot2 grid VennDiagram RColorBrewer plotrix ape MASS scales [RUtil] Executing Rscript install.r /home/jing/vdjtools-1.2.1/Rpackages/ reshape2 FField reshape gplots gridExtra circlize ggplot2 grid VennDiagram RColorBrewer plotrix ape MASS scales g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c melt.cpp -o melt.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o reshape2.so RcppExports.o melt.o -L/usr/lib/R/lib -lR gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BIONJ.c -o BIONJ.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NNI.c -o NNI.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SPR.c -o SPR.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c additive.c -o additive.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ape.c -o ape.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bNNI.c -o bNNI.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bionjs.c -o bionjs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bipartition.c -o bipartition.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bitsplits.c -o bitsplits.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c delta_plot.c -o delta_plot.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dist_dna.c -o dist_dna.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dist_nodes.c -o dist_nodes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ewLasso.c -o ewLasso.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c heap.c -o heap.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mat_expo.c -o mat_expo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c me.c -o me.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c me_balanced.c -o me_balanced.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c me_ols.c -o me_ols.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mvr.c -o mvr.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mvrs.c -o mvrs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nj.c -o nj.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c njs.c -o njs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pic.c -o pic.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prop_part.cpp -o prop_part.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rTrait.c -o rTrait.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_dna.c -o read_dna.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reorder_phylo.c -o reorder_phylo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c treePop.c -o treePop.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tree_build.c -o tree_build.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tree_phylo.c -o tree_phylo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c triangMtd.c -o triangMtd.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c triangMtds.c -o triangMtds.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/jing/vdjtools-1.2.1/Rpackages/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ultrametric.c -o ultrametric.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MASS.c -o MASS.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lqs.c -o lqs.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/usr/lib/R/lib -lR [RInstall] Testing [RUtil] Executing Rscript test.r reshape2 FField reshape gplots gridExtra circlize ggplot2 grid VennDiagram RColorBrewer plotrix ape MASS scales [1] "FAILED to install circlize" [RInstall] Finished

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