[R] Errors in R package installation

David Stevens
Fri, 13 Dec 2019 14:21:06 -0000

I started a new session and entered

> rm(list=ls())
> install.packages(
+  c('lmerTest', 'quantreg', 'rmarkdown',
'SparseM'),
+  lib = .libPaths()[1L],
+  destdir = 'c:/myRLib'
+ )

And this is the result:

  There are binary versions available but the
  source versions are later:
          binary source needs_compilation
lmerTest   3.1-0  3.1-1             FALSE
quantreg    5.52   5.54              TRUE
rmarkdown   1.18    2.0             FALSE
SparseM     1.77   1.78              TRUE

installing the source packages ?lmerTest?, ?quantreg?, ?rmarkdown?, ?SparseM?

trying URL
'https://cloud.r-project.org/src/contrib/lmerTest_3.1-1.tar.gz'
Content type 'application/x-gzip' length 194447 bytes (189 KB)
downloaded 189 KB

trying URL
'https://cloud.r-project.org/src/contrib/quantreg_5.54.tar.gz'
Content type 'application/x-gzip' length 995368 bytes (972 KB)
downloaded 972 KB

trying URL
'https://cloud.r-project.org/src/contrib/rmarkdown_2.0.tar.gz'
Content type 'application/x-gzip' length 3186667 bytes (3.0 MB)
downloaded 3.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/SparseM_1.78.tar.gz'
Content type 'application/x-gzip' length 735024 bytes (717 KB)
downloaded 717 KB

* installing *source* package 'lmerTest' ...
** package 'lmerTest' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Fatal error: cannot open file 'C:\Users\David': No such file or
directory

ERROR: lazy loading failed for package 'lmerTest'
* removing 'C:/myRLib/lmerTest'
Warning in install.packages :
  installation of package ?lmerTest? had non-zero exit status
* installing *source* package 'rmarkdown' ...
** package 'rmarkdown' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Fatal error: cannot open file 'C:\Users\David': No such file or
directory

ERROR: lazy loading failed for package 'rmarkdown'
* removing 'C:/myRLib/rmarkdown'
Warning in install.packages :
  installation of package ?rmarkdown? had non-zero exit status
* installing *source* package 'SparseM' ...
** package 'SparseM' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c bckslv.f -o bckslv.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c chol.f -o chol.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c chol2csr.f -o
chol2csr.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c cholesky.f -o
cholesky.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c csr.f -o csr.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c extract.f -o
extract.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c sparskit.f -o
sparskit.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c subscr.f -o subscr.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SparseM.dll tmp.def
bckslv.o chol.o chol2csr.o cholesky.o csr.o extract.o init.o sparskit.o subscr.o
-lgfortran -lm -lquadmath -LC:/PROGRA~1/R/R-3.6.2/bin/i386 -lR
installing to C:/myRLib/00LOCK-SparseM/00new/SparseM/libs/i386

*** arch - x64
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c bckslv.f -o bckslv.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c chol.f -o chol.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c chol2csr.f -o
chol2csr.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c cholesky.f -o
cholesky.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c csr.f -o csr.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c extract.f -o
extract.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sparskit.f -o
sparskit.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c subscr.f -o subscr.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SparseM.dll tmp.def
bckslv.o chol.o chol2csr.o cholesky.o csr.o extract.o init.o sparskit.o subscr.o
-lgfortran -lm -lquadmath -LC:/PROGRA~1/R/R-3.6.2/bin/x64 -lR
installing to C:/myRLib/00LOCK-SparseM/00new/SparseM/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Fatal error: cannot open file 'C:\Users\David': No such file or
directory

ERROR: lazy loading failed for package 'SparseM'
* removing 'C:/myRLib/SparseM'
Warning in install.packages :
  installation of package ?SparseM? had non-zero exit status
* installing *source* package 'quantreg' ...
** package 'quantreg' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c boot.f -o boot.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c bound.f -o bound.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c boundc.f -o boundc.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c brute.f -o brute.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c chlfct.f -o chlfct.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c cholesky.f -o
cholesky.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c combos.f -o combos.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c crqf.f -o crqf.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c crqfnb.f -o crqfnb.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c dsel05.f -o dsel05.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c etime.f -o etime.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c extract.f -o
extract.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c idmin.f -o idmin.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c iswap.f -o iswap.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c kuantiles.f -o
kuantiles.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c linpack.f -o
linpack.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O3 -Wall  -std=gnu99 -mtune=generic -c mcmb.c -o mcmb.o
mcmb.c: In function 'func':
mcmb.c:176:32: warning: variable 'large' set but not used
[-Wunused-but-set-variable]
   double taustar, pwtsum, ans, large;
                                ^
mcmb.c:175:16: warning: variable 'mm' set but not used
[-Wunused-but-set-variable]
   unsigned int mm;
                ^
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c penalty.f -o
penalty.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c powell.f -o powell.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O3 -Wall  -std=gnu99 -mtune=generic -c quantreg_init.c -o quantreg_init.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rls.f -o rls.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rq0.f -o rq0.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rq1.f -o rq1.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rqbr.f -o rqbr.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rqfn.f -o rqfn.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rqfnb.f -o rqfnb.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rqfnc.f -o rqfnc.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c rqs.f -o rqs.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c sakj.f -o sakj.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c sparskit2.f -o
sparskit2.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c srqfn.f -o srqfn.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c srqfnc.f -o srqfnc.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c srtpai.f -o srtpai.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o quantreg.dll tmp.def
boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o
dsel05.o etime.o extract.o idmin.o iswap.o kuantiles.o linpack.o mcmb.o
penalty.o powell.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o
rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o
-LC:/PROGRA~1/R/R-3.6.2/bin/i386 -lRlapack -LC:/PROGRA~1/R/R-3.6.2/bin/i386
-lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
-LC:/PROGRA~1/R/R-3.6.2/bin/i386 -lR
installing to C:/myRLib/00LOCK-quantreg/00new/quantreg/libs/i386

*** arch - x64
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c boot.f -o boot.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c bound.f -o bound.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c boundc.f -o boundc.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c brute.f -o brute.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c chlfct.f -o chlfct.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c cholesky.f -o
cholesky.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c combos.f -o combos.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c crqf.f -o crqf.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c crqfnb.f -o crqfnb.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dsel05.f -o dsel05.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c etime.f -o etime.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c extract.f -o
extract.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c idmin.f -o idmin.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c iswap.f -o iswap.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c kuantiles.f -o
kuantiles.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c linpack.f -o
linpack.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O2 -Wall  -std=gnu99 -mtune=generic -c mcmb.c -o mcmb.o
mcmb.c: In function 'func':
mcmb.c:176:32: warning: variable 'large' set but not used
[-Wunused-but-set-variable]
   double taustar, pwtsum, ans, large;
                                ^
mcmb.c:175:16: warning: variable 'mm' set but not used
[-Wunused-but-set-variable]
   unsigned int mm;
                ^
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c penalty.f -o
penalty.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c powell.f -o powell.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-3.6.2/include" -DNDEBUG
-O2 -Wall  -std=gnu99 -mtune=generic -c quantreg_init.c -o quantreg_init.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rls.f -o rls.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rq0.f -o rq0.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rq1.f -o rq1.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rqbr.f -o rqbr.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rqfn.f -o rqfn.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rqfnb.f -o rqfnb.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rqfnc.f -o rqfnc.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rqs.f -o rqs.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sakj.f -o sakj.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sparskit2.f -o
sparskit2.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c srqfn.f -o srqfn.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c srqfnc.f -o srqfnc.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c srtpai.f -o srtpai.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o quantreg.dll tmp.def
boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o
dsel05.o etime.o extract.o idmin.o iswap.o kuantiles.o linpack.o mcmb.o
penalty.o powell.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o
rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o
-LC:/PROGRA~1/R/R-3.6.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-3.6.2/bin/x64
-lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath
-LC:/PROGRA~1/R/R-3.6.2/bin/x64 -lR
installing to C:/myRLib/00LOCK-quantreg/00new/quantreg/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Fatal error: cannot open file 'C:\Users\David': No such file or
directory

ERROR: lazy loading failed for package 'quantreg'
* removing 'C:/myRLib/quantreg'
Warning in install.packages :
  installation of package ?quantreg? had non-zero exit status

On 12/13/2019 7:12 AM, Ivan Krylov wrote:

install.packages(
 c('lmerTest', 'quantreg', 'rmarkdown',
'SparseM'),
 lib = .libPaths()[1L],
 destdir = 'c:/myRLib'
)

--
David K Stevens, PhD, PE
Environmental Engineering Division
Civil and Environmental Engineering
Utah State University
8200 Old Main Hill
Logan, UT 83200-8200
(435) 797-3229
david.stevens at usu.edu<mailto:david.stevens at usu.edu>

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