Блог

Я пытаюсь установить пакет, но по какой-то причине он отказывается устанавливаться? Ошибка, которую я получаю, заключается в

 ERROR: compilation failed for package 'methylclock.'

    install_github("isglobal-brge/methylclock")

Downloading GitHub repo isglobal-brge/methylclock@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
     Which would you like to update?

     1: All                                  
     2: CRAN packages only                   
     3: None                                 
     4: matrixStats (0.58.0 -> 0.59.0) [CRAN]
     5: fansi       (0.4.2  -> 0.5.0 ) [CRAN]
     6: tibble      (3.1.1  -> 3.1.2 ) [CRAN]
     7: cachem      (1.0.4  -> 1.0.5 ) [CRAN]
     8: stringi     (1.5.3  -> 1.6.2 ) [CRAN]
     9: rtracklayer (1.49.5 -> 1.50.0) [CRAN]
     10: zip         (2.1.1  -> 2.2.0 ) [CRAN]

    Enter one or more numbers, or an empty line to skip updates: 1
    matrixStats (0.58.0 -> 0.59.0) [CRAN]
    fansi       (0.4.2  -> 0.5.0 ) [CRAN]
    tibble      (3.1.1  -> 3.1.2 ) [CRAN]
    cachem      (1.0.4  -> 1.0.5 ) [CRAN] 
    stringi     (1.5.3  -> 1.6.2 ) [CRAN]
    rtracklayer (1.49.5 -> 1.50.0) [CRAN]
    zip         (2.1.1  -> 2.2.0 ) [CRAN]
    Installing 7 packages: matrixStats, fansi, tibble, cachem, stringi, rtracklayer, zip
Warning: package ‘matrixStats’ is in use and will not be installed
Installing packages into ‘C:/Users/saeed/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)

  There are binary versions available but the source versions are later:
            binary source needs_compilation
stringi      1.5.3  1.6.2              TRUE
rtracklayer 1.49.5 1.50.0              TRUE
zip          2.1.1  2.2.0              TRUE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.5.0.zip'
Content type 'application/zip' length 248461 bytes (242 KB)
downloaded 242 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/tibble_3.1.2.zip'
Content type 'application/zip' length 825073 bytes (805 KB)
downloaded 805 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cachem_1.0.5.zip'
Content type 'application/zip' length 78389 bytes (76 KB)
downloaded 76 KB

package ‘fansi’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘fansi’
Warning: restored ‘fansi’
package ‘tibble’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘tibble’
Warning: restored ‘tibble’
package ‘cachem’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘cachem’
Warning: restored ‘cachem’

The downloaded binary packages are in
    C:UserssaeedAppDataLocalTempRtmpcBVi0vdownloaded_packages
installing the source packages ‘stringi’, ‘rtracklayer’, ‘zip’

trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.6.2.tar.gz'
Content type 'application/x-gzip' length 7575370 bytes (7.2 MB)
downloaded 7.2 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/rtracklayer_1.50.0.tar.gz'
Content type 'application/x-gzip' length 6369416 bytes (6.1 MB)
downloaded 6.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/zip_2.2.0.tar.gz'
Content type 'application/x-gzip' length 114391 bytes (111 KB)
downloaded 111 KB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: cannot remove earlier installation, is it in use?
* removing 'C:/Users/saeed/Documents/R/win-library/4.0/stringi'
* restoring previous 'C:/Users/saeed/Documents/R/win-library/4.0/stringi'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCK-stringistringilibsicudt61l.dat to C:UserssaeedDocumentsRwin-library4.0stringilibsicudt61l.dat: Invalid argument
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCK-stringistringilibsx64stringi.dll to C:UserssaeedDocumentsRwin-library4.0stringilibsx64stringi.dll: Permission denied
* installing *source* package 'rtracklayer' ...
ERROR: cannot remove earlier installation, is it in use?
* removing 'C:/Users/saeed/Documents/R/win-library/4.0/rtracklayer'
* restoring previous 'C:/Users/saeed/Documents/R/win-library/4.0/rtracklayer'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCK-rtracklayerrtracklayerlibsx64rtracklayer.dll to C:UserssaeedDocumentsRwin-library4.0rtracklayerlibsx64rtracklayer.dll: Permission denied
* installing *source* package 'zip' ...
** package 'zip' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
"c:/rtools40/mingw32/bin/"gcc  -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -DCMDZIP miniz.c zip.c winutils.c tools/cmdzip.c 
-municode -o tools/cmdzip.exe
sh: c:/rtools40/mingw32/bin/gcc: No such file or directory
make: *** [Makevars.win:9: tools/cmdzip.exe] Error 127
ERROR: compilation failed for package 'zip'
* removing 'C:/Users/saeed/Documents/R/win-library/4.0/zip'
* restoring previous 'C:/Users/saeed/Documents/R/win-library/4.0/zip'

The downloaded source packages are in
    ‘C:UserssaeedAppDataLocalTempRtmpcBVi0vdownloaded_packages’
√  checking for file 'C:UserssaeedAppDataLocalTempRtmpcBVi0vremotes4c682cb429e7isglobal-brge-methylclock-6f8c69a/DESCRIPTION' ...
-  preparing 'methylclock': (1.3s)
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'methylclock_0.7.5.tar.gz'
   
Installing package into ‘C:/Users/saeed/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'methylclock' ...
** using staged installation
** libs

*** arch - i386
"c:/rtools40/mingw32/bin/"g   -std=gnu  11  -I"C:/PROGRA~1/R/R-40~1.5/include" -DNDEBUG  -I'C:/Users/saeed/Documents/R/win-library/4.0/Rcpp/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c NewModel1Clean.cpp -o NewModel1Clean.o
sh: c:/rtools40/mingw32/bin/g  : No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.5/etc/i386/Makeconf:229: NewModel1Clean.o] Error 127
ERROR: compilation failed for package 'methylclock'
* removing 'C:/Users/saeed/Documents/R/win-library/4.0/methylclock'
Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCKfansilibsx64fansi.dll to C:UserssaeedDocumentsRwin-library4.0fansilibsx64fansi.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCKtibblelibsx64tibble.dll to C:UserssaeedDocumentsRwin-library4.0tibblelibsx64tibble.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:UserssaeedDocumentsRwin-library4.00LOCKcachemlibsx64cachem.dll to C:UserssaeedDocumentsRwin-library4.0cachemlibsx64cachem.dll: Permission denied
4: In i.p(...) :
  installation of package ‘stringi’ had non-zero exit status
5: In i.p(...) :
  installation of package ‘rtracklayer’ had non-zero exit status
6: In i.p(...) : installation of package ‘zip’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘C:/Users/saeed/AppData/Local/Temp/RtmpcBVi0v/file4c68a8c1be0/methylclock_0.7.5.tar.gz’ had non-zero exit status