installation of package 'rmarkdown' had non-zero exit status
1
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Entering edit mode
@tarekmohamed-9489
Last seen 2.7 years ago

 

I had problems installing rmarkdown updated version in Rstudio

Rstudio can not open a new rmarkdown file and it requests an updated version. However, when I tried to install one , it did not work.

**Here is what I got:**

Installing package into 'C:/Users/tmm447/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependencies 'base64enc', 'jsonlite'

trying URL 'https://cran.rstudio.com/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/x-gzip' length 7833 bytes
==================================================
downloaded 7833 bytes

trying URL 'https://cran.rstudio.com/src/contrib/jsonlite_1.0.tar.gz'
Content type 'application/x-gzip' length 1057732 bytes (1.0 MB)==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_1.0.tar.gz'
Content type 'application/x-gzip' length 2049183 bytes (2.0 MB)==================================================
downloaded 2.0 MB

* installing *source* package 'base64enc' ...
** package 'base64enc' successfully unpacked and MD5 sums checked
** libs

*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-33~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.1/share/make/winshlib.mk" SHLIB="base64enc.dll" OBJECTS="base64.o uriencode.o utf8.o"' had status 127
ERROR: compilation failed for package 'base64enc'
* removing 'C:/Users/tmm447/Documents/R/win-library/3.3/base64enc'
* installing *source* package 'jsonlite' ...
** package 'jsonlite' successfully unpacked and MD5 sums checked
** libs

*** arch - i386
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-33~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.1/share/make/winshlib.mk" SHLIB="jsonlite.dll" OBJECTS="base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o row_collapse.o validate.o"' had status 127
ERROR: compilation failed for package 'jsonlite'
* removing 'C:/Users/tmm447/Documents/R/win-library/3.3/jsonlite'
ERROR: dependencies 'base64enc', 'jsonlite' are not available for package 'rmarkdown'
* removing 'C:/Users/tmm447/Documents/R/win-library/3.3/rmarkdown'

The downloaded source packages are in
    'C:\Users\tmm447\AppData\Local\Temp\RtmpQXU8qH\downloaded_packages'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\tmm447\Documents\R\win-library\3.3" C:\Users\tmm447\AppData\Local\Temp\RtmpQXU8qH/downloaded_packages/base64enc_0.1-3.tar.gz' had status 1 
2: In utils::install.packages(c("rmarkdown"), repos = "https://cran.rstudio.com/",  :
  installation of package 'base64enc' had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\tmm447\Documents\R\win-library\3.3" C:\Users\tmm447\AppData\Local\Temp\RtmpQXU8qH/downloaded_packages/jsonlite_1.0.tar.gz' had status 1 
4: In utils::install.packages(c("rmarkdown"), repos = "https://cran.rstudio.com/",  :
  installation of package 'jsonlite' had non-zero exit status
5: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\tmm447\Documents\R\win-library\3.3" C:\Users\tmm447\AppData\Local\Temp\RtmpQXU8qH/downloaded_packages/rmarkdown_1.0.tar.gz' had status 1 
6: In utils::install.packages(c("rmarkdown"), repos = "https://cran.rstudio.com/",  :
  installation of package 'rmarkdown' had non-zero exit status


Thanks
Tarek

rmarkdown package updates • 2.4k views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

Neither of these things (Rstudio, rmarkdown) is affiliated in any way with Bioconductor. If you are having problems with either, the correct people to ask would be the Rstudio folks.

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Entering edit mode

...though it looks like the poster is trying to install source packages, when they probably want binary, options(pkgType="win.binary").

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