Hello,
I tried to install vdjtools in my ubuntu 18.04.5. My R version is 4.1.3.
It said: "FAILED to install circlize". I only find "-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c triangMtd.c -o triangMtd.o". I have no idea how to fix it.
Thank you 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
