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3.0 years ago
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Following this script for meta data analysis- while I am using R-4.0.5, rtools40 and RStudio-1.4.1106 then shiny package got installed but while running this script-
shiny::runApp('metaOmics', port=9987, launch.browser=T)
It is showing error in-
Warning in install.packages : package ‘DMwR’ is not available for this version of R
A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages Downloading package from url: https://github.com/metaOmics/preproc/archive/master.zip √ checking for file 'C:\Users\AppData\Local\Temp\RtmpcDwams\remotes8e05c3224ec\preproc-master/DESCRIPTION' (358ms)
ERROR: dependency 'DMwR' is not available for package 'preproc'
* removing 'C:/R/R-4.0.5/library/preproc' Warning in i.p(...) : installation of package ‘C:/Users/kiit1/AppData/Local/Temp/RtmpcDwams/file8e01ccc285f/preproc_1.2-4.tar.gz’ had non-zero exit status Error in library(preproc) : there is no package called ‘preproc
As these packages are not available for R4.0.5
When I use the lower version(R3.3.1 with rtools34 and RStudio-0.99.903) then some package of same script are not working-
> install.packages('shiny')
It is showing error like this-
* installing *source* package 'magrittr' ...
** package 'magrittr' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pipe.c -o pipe.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [pipe.o] Error 127
Warning: running command 'make -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="magrittr.dll" OBJECTS="pipe.o utils.o"' had status 2
ERROR: compilation failed for package 'magrittr'
* removing 'C:/Users/3.3/magrittr'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/magrittr_2.0.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘magrittr’ had non-zero exit status
* installing *source* package 'digest' ...
** package 'digest' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/R/R-33~1.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c SpookyV2.cpp -o SpookyV2.o
c:/Rtools/mingw_32/bin/g++: not found
make: *** [SpookyV2.o] Error 127
Warning: running command 'make -f "Makevars" -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="digest.dll" OBJECTS="SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o"' had status 2
ERROR: compilation failed for package 'digest'
* removing 'C:/Users/3.3/digest'
* restoring previous 'C:/Users/3.3/digest'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/digest_0.6.27.tar.gz' had status 1
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
* installing *source* package 'rlang' ...
** package 'rlang' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -I./lib/ -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c capture.c -o capture.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [capture.o] Error 127
Warning: running command 'make -f "Makevars" -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="rlang.dll" OBJECTS="capture.o export.o internal.o lib.o version.o"' had status 2
ERROR: compilation failed for package 'rlang'
* removing 'C:/Users/3.3/rlang'
* restoring previous 'C:/Users/3.3/rlang'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/rlang_0.4.11.tar.gz' had status 1
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
* installing *source* package 'fastmap' ...
** package 'fastmap' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/R/R-33~1.1/include" -DNDEBUG -Ilib/ -I"d:/Compiler/gcc-4.9.3/local330/include" -DR_NO_REMAP -O2 -Wall -mtune=core2 -c fastmap.cpp -o fastmap.o
c:/Rtools/mingw_32/bin/g++: not found
make: *** [fastmap.o] Error 127
Warning: running command 'make -f "Makevars.win" -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="fastmap.dll" OBJECTS="fastmap.o init.o"' had status 2
ERROR: compilation failed for package 'fastmap'
* removing 'C:/Users/3.3/fastmap'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/fastmap_1.1.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘fastmap’ had non-zero exit status
* installing *source* package 'commonmark' ...
** package 'commonmark' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/html.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions.o init.o wrapper.o commonmark.dll cmark/libstatcmark.a
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c extensions.c -o extensions.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [extensions.o] Error 127
Warning: running command 'make -f "Makevars" -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="commonmark.dll" OBJECTS="extensions.o init.o wrapper.o"' had status 2
ERROR: compilation failed for package 'commonmark'
* removing 'C:/Users/3.3/commonmark'
* restoring previous 'C:/Users/3.3/commonmark'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/commonmark_1.7.tar.gz' had status 1
Warning in install.packages :
installation of package ‘commonmark’ had non-zero exit status
* installing *source* package 'glue' ...
** package 'glue' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c glue.c -o glue.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [glue.o] Error 127
Warning: running command 'make -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="glue.dll" OBJECTS="glue.o init.o trim.o"' had status 2
ERROR: compilation failed for package 'glue'
* removing 'C:/Users/3.3/glue'
* restoring previous 'C:/Users/3.3/glue'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/glue_1.4.2.tar.gz' had status 1
Warning in install.packages :
installation of package ‘glue’ had non-zero exit status
* installing *source* package 'htmltools' ...
** package 'htmltools' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [init.o] Error 127
Warning: running command 'make -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="htmltools.dll" OBJECTS="init.o template.o"' had status 2
ERROR: compilation failed for package 'htmltools'
* removing 'C:/Users/3.3/htmltools'
* restoring previous 'C:/Users/3.3/htmltools'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/htmltools_0.5.1.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘htmltools’ had non-zero exit status
* installing *source* package 'later' ...
** package 'later' successfully unpacked and MD5 sums checked
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/R/R-33~1.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I"C:/Users/3.3/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++: not found
make: *** [RcppExports.o] Error 127
Warning: running command 'make -f "Makevars.win" -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="later.dll" OBJECTS="RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o"' had status 2
ERROR: compilation failed for package 'later'
* removing 'C:/Users/3.3/later'
* restoring previous 'C:/Users/3.3/later'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/later_1.2.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘later’ had non-zero exit status
ERROR: dependency 'fastmap' is not available for package 'cachem'
* removing 'C:/Users/3.3/cachem'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/cachem_1.0.4.tar.gz' had status 1
Warning in install.packages :
installation of package ‘cachem’ had non-zero exit status
* installing *source* package 'ellipsis' ...
** package 'ellipsis' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/R/R-33~1.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dots.c -o dots.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [dots.o] Error 127
Warning: running command 'make -f "C:/R/R-33~1.1/etc/i386/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" SHLIB="ellipsis.dll" OBJECTS="dots.o init.o"' had status 2
ERROR: compilation failed for package 'ellipsis'
* removing 'C:/Users/3.3/ellipsis'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/ellipsis_0.3.2.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ellipsis’ had non-zero exit status
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.2.0 is being loaded, but >= 0.4.10 is required
ERROR: lazy loading failed for package 'lifecycle'
* removing 'C:/Users/3.3/lifecycle'
Warning in install.packages :
installation of package ‘bslib’ had non-zero exit status
ERROR: dependencies 'httpuv', 'promises', 'fastmap', 'bslib', 'cachem', 'ellipsis', 'lifecycle' are not available for package 'shiny'
* removing 'C:/Users/3.3/shiny'
Warning in install.packages :
running command '"C:/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\RtmpAVqPmw/downloaded_packages/shiny_1.6.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\AppData\Local\Temp\RtmpAVqPmw\downloaded_packages’
How to solve this issue?
