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Question: Problem installing Repitools package
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gravatar for sumudu_rangika
2.1 years ago by
sumudu_rangika20 wrote:

Hi,

I installed Qualimap software and when I try to load it a warning issued saying Repitools package missing.

Then I tried to install Repitools but failed. Below is the error I received. Appreciate if someone can help me solve this issue.

 

 

> biocLite("Repitools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘Repitools’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/Repitools_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1692218 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -D R_NO_REMAP -I. -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c const.c -o const.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -D R_NO_REMAP -I. -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hyp2f1.c -o hyp2f1.o
In file included from /usr/share/R/include/Rmath.h:48:0,
                 from hyp2f1.c:82:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘extern’
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘extern’
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘extern’
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/lib/R/etc/Makeconf:132: recipe for target 'hyp2f1.o' failed
make: *** [hyp2f1.o] Error 1
ERROR: compilation failed for package ‘Repitools’
* removing ‘/home/parasit/R/x86_64-pc-linux-gnu-library/3.3/Repitools’

The downloaded source packages are in
    ‘/tmp/RtmpeTPTnC/downloaded_packages’
Old packages: 'ggplot2', 'Rcpp', 'stringi', 'stringr', 'boot', 'cluster',
  'codetools', 'foreign', 'lattice', 'Matrix', 'mgcv', 'nlme', 'survival'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Repitools’ had non-zero exit status
>

---------------------------------------------------------------------------------------------------------------

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=si_LK          
 [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=si_LK       LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=si_LK          LC_NAME=C               LC_ADDRESS=C           
[10] LC_TELEPHONE=C          LC_MEASUREMENT=si_LK    LC_IDENTIFICATION=C    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

Best Regards

Rangika

ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 22k • written 2.1 years ago by sumudu_rangika20

Two years later and I have the exact same issue!!! Weirdly enough no other mention of this anywhere.

ADD REPLYlink written 4 months ago by pimlists0

According to the thread here https://gtalug.org/pipermail/talk/2016-August/003917.html it might be related to having libc6-dev

ADD REPLYlink written 4 months ago by pimlists0

hmm no progress so far... my error message is slightly different

* installing *source* package 'Repitools' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -D R_NO_REMAP -I. -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c const.c -o const.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -D R_NO_REMAP -I. -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hyp2f1.c -o hyp2f1.o
In file included from /usr/share/R/include/Rmath.h:38:0,
                 from hyp2f1.c:82:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'extern'
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'extern'
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'extern'
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
 ^
/usr/lib/R/etc/Makeconf:134: recipe for target 'hyp2f1.o' failed
make: *** [hyp2f1.o] Error 1
ERROR: compilation failed for package 'Repitools'
* removing '/usr/local/lib/R/site-library/Repitools'

 

 

ADD REPLYlink written 4 months ago by pimlists0

did you install R with one gcc compiler, then update your gcc compiler, then try to install Repitools? My guess is that the compiler R thinks it's using (based on configure at install time) is different from the compiler it is using.

ADD REPLYlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 22k
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