roma
April 30, 2023
206 views
0 votes
2 Answers

I’m on LMDE
(that is, on a Debian-based OS like Ubuntu):

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: LMDE 5 (elsie)

and keep getting an error installing libraries.
Sometimes I come across local solutions,
but usually they don’t work for me
(like installing dependent packages,
installing later versions,
installing from github,
etc.).
For package rms I tried the following with the following results.

Attempts

Attempt 1:

if (!require("pacman"))
  install.packages("pacman")

pacman::p_install(rms)

Logs 1:

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependency ‘Hmisc’

"download"

* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Hmisc/00new/Hmisc/libs
** R
Error in parse(outFile) : 
  /tmp/Rtmp2kS6VC/R.INSTALL3a165bca1f38/Hmisc/R/movStats.r:398:43: unexpected '>'
397:             else
398:               info <- knitr::kable(info) |>
                                               ^
ERROR: unable to collate and parse R files for package ‘Hmisc’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/Hmisc’
* installing *source* package ‘rms’ ...
** package ‘rms’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c lrmfit.f -o lrmfit.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c mlmats.f -o mlmats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c ormuv.f -o ormuv.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c robcovf.f -o robcovf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rms.so init.o lrmfit.o mlmats.o ormuv.o robcovf.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-rms/00new/rms/libs
** R
Error in parse(outFile) : 
  /tmp/RtmpsUMuRd/R.INSTALL3a5392a2cc/rms/R/latex.cph.s:56:49: unexpected '>'
55:       knitr::kable(s, format='html',
56:                    align='r', row.names=FALSE) |>
                                                    ^
ERROR: unable to collate and parse R files for package ‘rms’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/rms’

The downloaded source packages are in
    ‘/tmp/RtmpUQQ6Hn/downloaded_packages’
Warning messages:
1: In utils::install.packages(package, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
2: In utils::install.packages(package, ...) :
  installation of package ‘rms’ had non-zero exit status
3: In pacman::p_install(rms) :

Attempt 2:

install.packages("rms")

Logs 2:

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rvest’, ‘svglite’, ‘Hmisc’, ‘kableExtra’

trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz'

"download"

* installing *source* package ‘rvest’ ...
** package ‘rvest’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rvest)
* installing *source* package ‘svglite’ ...
** package ‘svglite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/r/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I'/usr/lib/R/site-library/systemfonts/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/r/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I'/usr/lib/R/site-library/systemfonts/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c devSVG.cpp -o devSVG.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o svglite.so cpp11.o devSVG.o -lpng -lz -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-svglite/00new/svglite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (svglite)
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Hmisc/00new/Hmisc/libs
** R
Error in parse(outFile) : 
  /tmp/RtmpZwFrAl/R.INSTALL2fd8571b94db/Hmisc/R/movStats.r:398:43: unexpected '>'
397:             else
398:               info <- knitr::kable(info) |>
                                               ^
ERROR: unable to collate and parse R files for package ‘Hmisc’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/Hmisc’
Warning in install.packages :
  installation of package ‘Hmisc’ had non-zero exit status
* installing *source* package ‘kableExtra’ ...
** package ‘kableExtra’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (kableExtra)
* installing *source* package ‘rms’ ...
** package ‘rms’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c lrmfit.f -o lrmfit.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c mlmats.f -o mlmats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c ormuv.f -o ormuv.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c robcovf.f -o robcovf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rms.so init.o lrmfit.o mlmats.o ormuv.o robcovf.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-rms/00new/rms/libs
** R
Error in parse(outFile) : 
  /tmp/Rtmpg5dNg6/R.INSTALL304c1b431630/rms/R/latex.cph.s:56:49: unexpected '>'
55:       knitr::kable(s, format='html',
56:                    align='r', row.names=FALSE) |>
                                                    ^
ERROR: unable to collate and parse R files for package ‘rms’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/rms’
Warning in install.packages :
  installation of package ‘rms’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpUQQ6Hn/downloaded_packages’

Attempt 3:

install.packages("rms", dependencies = T, Ncpus = 12)

Logs 3:

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘Hmisc’, ‘rmsb’

trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_5.0-1.tar.gz'

"download"

trying URL 'https://cloud.r-project.org/src/contrib/rms_6.6-0.tar.gz'

"download"

begin installing package ‘Hmisc’
make: *** [Makefile:4: Hmisc.ts] Error 1
make: Target 'all' not remade because of errors.
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpryJGgV/R.INSTALL3110717eb705/Hmisc/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpryJGgV/R.INSTALL3110717eb705/Hmisc/src'
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Hmisc/00new/Hmisc/libs
** R
Error in parse(outFile) : 
  /tmp/RtmpryJGgV/R.INSTALL3110717eb705/Hmisc/R/movStats.r:398:43: unexpected '>'
397:             else
398:               info <- knitr::kable(info) |>
                                               ^
ERROR: unable to collate and parse R files for package ‘Hmisc’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/Hmisc’
cat: rms.out: No such file or directory
cat: rmsb.out: No such file or directory
Warning in install.packages :
  installation of one or more packages failed,
  probably ‘Hmisc’, ‘rms’, ‘rmsb’

The downloaded source packages are in
    ‘/tmp/RtmpUQQ6Hn/downloaded_packages’

Attempt 4:

packageurl <- "https://cran.r-project.org/src/contrib/Archive/rms/rms_6.5-0.tar.gz"
install.packages(packageurl, repos = NULL, type = "source", Ncpus = 12)

Logs 4:

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/rms/rms_6.5-0.tar.gz'

"download"

* installing *source* package ‘rms’ ...
** package ‘rms’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c lrmfit.f -o lrmfit.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c mlmats.f -o mlmats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c ormuv.f -o ormuv.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c robcovf.f -o robcovf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rms.so init.o lrmfit.o mlmats.o ormuv.o robcovf.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-rms/00new/rms/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘Hmisc’ 4.5.0 was found, but >= 4.8.0 is required by ‘rms’
Execution halted
ERROR: lazy loading failed for package ‘rms’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/rms’
Warning in install.packages :
  installation of package ‘/tmp/RtmpUQQ6Hn/downloaded_packages/rms_6.5-0.tar.gz’ had non-zero exit status

Error with Hmisc hence try install this:

install.packages("Hmisc", dependencies = T, Ncpus = 12)

Logs:

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘qreport’, ‘rms’

trying URL 'https://cloud.r-project.org/src/contrib/qreport_0.1.0.tar.gz'

"download"

trying URL 'https://cloud.r-project.org/src/contrib/rms_6.6-0.tar.gz'

"download"

trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_5.0-1.tar.gz'

"download"

begin installing package ‘Hmisc’
make: *** [Makefile:4: Hmisc.ts] Error 1
make: Target 'all' not remade because of errors.
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpH728Mq/R.INSTALL35046481c0f2/Hmisc/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpH728Mq/R.INSTALL35046481c0f2/Hmisc/src'
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Hmisc/00new/Hmisc/libs
** R
Error in parse(outFile) : 
  /tmp/RtmpH728Mq/R.INSTALL35046481c0f2/Hmisc/R/movStats.r:398:43: unexpected '>'
397:             else
398:               info <- knitr::kable(info) |>
                                               ^
ERROR: unable to collate and parse R files for package ‘Hmisc’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/Hmisc’
cat: rms.out: No such file or directory
cat: qreport.out: No such file or directory
Warning in install.packages :
  installation of one or more packages failed,
  probably ‘Hmisc’, ‘rms’, ‘qreport’

The downloaded source packages are in
    ‘/tmp/RtmpUQQ6Hn/downloaded_packages’

Installing packages ggplot2 and colorspace didn’t help either.

There were still errors related to fonts and maybe some more,
but after reinstalling I didn’t see them anymore.

I didn’t find anything else on the following links:
1
2
3

So how do I install this package and in general,
how do I install packages painlessly?

Tags: install.packages r rms

Answers

Chosen as BEST ANSWER

Try a "terminal" install like this:

sudo apt install r-cran-rms

In the terminal:

r@ma:~$ sudo apt install r-cran-rms
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  r-cran-polspline
The following NEW packages will be installed:
  r-cran-polspline r-cran-rms
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 2,670 kB of archives.
After this operation, 3,242 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 https://deb.debian.org/debian bullseye/main amd64 r-cran-polspline amd64 1.1.19-1 [567 kB]
Get:2 https://deb.debian.org/debian bullseye/main amd64 r-cran-rms amd64 6.1-1-1 [2,103 kB]
Fetched 2,670 kB in 1s (3,210 kB/s)
Selecting previously unselected package r-cran-polspline.
(Reading database ... 366788 files and directories currently installed.)
Preparing to unpack .../r-cran-polspline_1.1.19-1_amd64.deb ...
Unpacking r-cran-polspline (1.1.19-1) ...
Selecting previously unselected package r-cran-rms.
Preparing to unpack .../r-cran-rms_6.1-1-1_amd64.deb ...
Unpacking r-cran-rms (6.1-1-1) ...
Setting up r-cran-polspline (1.1.19-1) ...
Setting up r-cran-rms (6.1-1-1) ...
r@ma:~$

(the first time there was more text)

Check:

packageVersion("rms")
[1] ‘6.1.1’

The current CRAN version of the package is 6.6.0

Remark --- delete only in terminal accordingly like this:

sudo apt --purge remove r-cran-rms
sudo apt autoremove

If this method doesn't work, try installing your package in R and read the installation log. Most of all, there will be an advice to install packages, so do that.

If it's something to do with the versions, try updating the packages (be careful, updating R requires reinstalling the required libraries). If that didn't work, try BACKPORTS

(Edit)

- BenBolker
- May 2, 2023 at 2:56 pm
- 0 votes
0
tl;dr the current version of these packages won’t work with versions of R earlier than 4.1. This is arguably a bug in these packages: their DESCRIPTION files ought to mandate R >= 4.1.0 (in which case you would get a slightly more informative message telling you that the package was unavailable for your version of R); see here.

To resolve the issue you could:
- update your version of R
- look on the archive pages for Hmisc and rms and use remotes::install_version() to install earlier versions. In particular, since R 4.1 was released in May 2018, any version of Hmisc/rms dated before that should work. More generally, I suspect that there are versions more recent than May 2018 that don’t use the native pipe, but it’s hard to track down when the changes were made.
- as you suggest, install via apt from a Debian-style repository that provides an older version of the package, as in this answer
The key is the errors of the form
```
Error in parse(outFile) : 
  /tmp/RtmpsUMuRd/R.INSTALL3a5392a2cc/rms/R/latex.cph.s:56:49: unexpected '>'
55:       knitr::kable(s, format='html',
56:                    align='r', row.names=FALSE) |>
```
or
```
Error in parse(outFile) : 
  /tmp/Rtmp2kS6VC/R.INSTALL3a165bca1f38/Hmisc/R/movStats.r:398:43: unexpected '>'
```
which occur because your version of R is failing to parse the "native pipe" |>, which wasn’t added until R 4.1.
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Ubuntu – Parse error when installing packages from source (on the example of package rms)

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Answers