[R-pkg-team] install ape error
Richard Cadenillas
cadenillasordinola at gmail.com
Mon Nov 19 15:47:38 GMT 2018
Dear APE team,
May name is Richard Cadenillas, today I try to install APE, but I have
this problem, please let me know how to fix it.
I use Ubuntu 18.04
Error : object ‘warnErrList’ is not exported by 'namespace:utils'
ERROR: lazy loading failed for package ‘BPEC’
> install.packages("ape", dependencies = TRUE)
Installing package into ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ape_5.2.tar.gz'
Content type 'application/x-gzip' length 790069 bytes (771 KB)
==================================================
downloaded 771 KB
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c BIONJ.c -o BIONJ.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c NNI.c -o NNI.o
g++ -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c SPR.c -o SPR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c TBR.c -o TBR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c additive.c -o additive.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ape.c -o ape.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c bNNI.c -o bNNI.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c bionjs.c -o bionjs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c bipartition.c -o bipartition.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c bitsplits.c -o bitsplits.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c delta_plot.c -o delta_plot.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c dist_dna.c -o dist_dna.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c dist_nodes.c -o dist_nodes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ewLasso.c -o ewLasso.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c heap.c -o heap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c mat_expo.c -o mat_expo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c me.c -o me.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c me_balanced.c -o me_balanced.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c me_ols.c -o me_ols.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c mvr.c -o mvr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c mvrs.c -o mvrs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c nj.c -o nj.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c njs.c -o njs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c pic.c -o pic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c plot_phylo.c -o plot_phylo.o
g++ -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c prop_part.cpp -o prop_part.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c rTrait.c -o rTrait.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c read_dna.c -o read_dna.o
g++ -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c reorder_phylo.c -o reorder_phylo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c treePop.c -o treePop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c tree_build.c -o tree_build.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c tree_phylo.c -o tree_phylo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c triangMtd.c -o triangMtd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c triangMtds.c -o triangMtds.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/richard/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic
-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ultrametric.c -o ultrametric.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o
ape.so BIONJ.o NNI.o RcppExports.o SPR.o TBR.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
installing to /home/richard/R/x86_64-pc-linux-gnu-library/3.4/ape/libs
** R
** data
** inst
** preparing package for lazy loading
Error : object ‘warnErrList’ is not exported by 'namespace:utils'
ERROR: lazy loading failed for package ‘ape’
* removing ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.4/ape’
* restoring previous ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.4/ape’
Warning in install.packages :
installation of package ‘ape’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpn6tuhY/downloaded_packages’
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