installation of package ‘sp’ had non-zero exit status

[zhonglinma]

I met this error when i install R package qiime2R, and I install it with Rstudio server, with R version of 4.0.3. What happened? please help

[edzer]

Maybe remove it first?

[zhonglinma]

Still can't after I remove the old package and this is what I got :

install.packages("sp")
Installing package into ‘/home/mzl/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sp_1.4-4.tar.gz'
Content type 'application/x-gzip' length 1137296 bytes (1.1 MB)

downloaded 1.1 MB

• installing source package ‘sp’ ...
  ** package ‘sp’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcentroid.c -o Rcentroid.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gcdist.c -o gcdist.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip.c -o pip.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip2.c -o pip2.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sp_xports.c -o sp_xports.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c surfaceArea.c -o surfaceArea.o
  gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zerodist.c -o zerodist.o
  gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR
  installing to /home/mzl/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-sp/00new/sp/libs
  ** R
  ** data
  ** demo
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: package ‘lattice’ was installed before R 4.0.0: please re-install it
  Execution halted
  ERROR: lazy loading failed for package ‘sp’
• removing ‘/home/mzl/R/x86_64-pc-linux-gnu-library/3.6/sp’
  Warning in install.packages :
  installation of package ‘sp’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpd4XeU8/downloaded_packages’

[bniebuhr]

@zhonglinma It seems you need to reinstall the package lattice here, because it was installed before you updated R to version 4.
Maybe you can do this before installing sp.

install.packages("lattice", dependencies = T)
install.packages("sp", dependencies = T)