unable to install snpStats
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@amirfartash-22610
Last seen 4.4 years ago

Hello

I am trying to install snpStats in Rstudio. but at the end i have an error which mentioned

"ERROR: compilation failed for package ‘bibtex’ "

what can i do to et ride of these error? ( i even deleted "bibtex" folder but again i had the same error.

the R version i am using is 3.6.1 and i am using mac

does anybody have any idea how can i solve this problem ?

Best Regards Amir

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software error • 571 views
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It seems like the problem is actually with installing bibtex. Can you show us more of the output of attempting to install that package -- I have

> BiocManager::install("bibtex")
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable)
  (2019-12-20 r77608)
Installing package(s) 'bibtex'
trying URL 'https://cran.rstudio.com/src/contrib/bibtex_0.4.2.1.tar.gz'
Content type 'application/x-gzip' length 90932 bytes (88 KB)
==================================================
downloaded 88 KB

* installing *source* package ‘bibtex’ ...
** package ‘bibtex’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/Users/ma38727/bin/R-devel/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -g -O0  -c biblex.c -o biblex.o
gcc -I"/Users/ma38727/bin/R-devel/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -g -O0  -c bibparse.c -o bibparse.o
gcc -I"/Users/ma38727/bin/R-devel/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -g -O0  -c init.c -o init.o
gcc -I"/Users/ma38727/bin/R-devel/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -g -O0  -c stretchyList.c -o stretchyList.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/ma38727/bin/R-devel/lib -L/usr/local/lib -o bibtex.so biblex.o bibparse.o init.o stretchyList.o -L/Users/ma38727/bin/R-devel/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/ma38727/Library/R/4.0/Bioc/3.11/library/00LOCK-bibtex/00new/bibtex/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (bibtex)
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