ExomeDepth installation fail

[Leelouh]

Hello, I am trying to install ExomeDepth (install_github("vplagnol/ExomeDepth")) in order to install and use DECoN but unfortunately, it is not working.
I use the R version 4.2.1

Does anyone already has this issue? Thank you in advance.
Sincerely,
Lou

> install_github("vplagnol/ExomeDepth")
Downloading GitHub repo vplagnol/ExomeDepth@HEAD
Skipping 5 packages not available: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, Biostrings
v  checking for file '/tmp/RtmpZeBznm/remotes1179f51e5699a/vplagnol-ExomeDepth-80da0cb/DESCRIPTION' ...
-  preparing 'ExomeDepth':
v  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
-  looking to see if a 'data/datalist' file should be added
-  building 'ExomeDepth_1.1.15.tar.gz'
   
Installing package into '/DECoN/Linux/renv/library/R-4.2/x86_64-pc-linux-gnu'
(as 'lib' is unspecified)
* installing *source* package 'ExomeDepth' ...
** using staged installation
** libs
** arch - 
R CMD SHLIB hmm.cpp fdiv.c stream.c hypot.c error.c ldfrexp.c VP_infnan.c elementary.c invhyp.c log1p.c VP_log.c exp.c math.c VP_zeta.c VP_trig.c VP_psi.c VP_gamma.c beta.c CNV_estimate.cpp -o ExomeDepth.so 
make[1]: Entering directory '/tmp/RtmpSq3pBX/R.INSTALL133fd341b3e96/ExomeDepth/src'
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wSz8CH/r-base-4.2.1=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c hmm.cpp -o hmm.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wSz8CH/r-base-4.2.1=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c fdiv.c -o fdiv.o
In file included from fdiv.c:21:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:168: fdiv.o] Error 1
make[1]: Leaving directory '/tmp/RtmpSq3pBX/R.INSTALL133fd341b3e96/ExomeDepth/src'
make: *** [Makefile:15: CNV_estimate.so] Error 1
ERROR: compilation failed for package 'ExomeDepth'
* removing '/DECoN/Linux/renv/library/R-4.2/x86_64-pc-linux-gnu/ExomeDepth'
Warning message:
In i.p(...) :
  installation of package '/tmp/RtmpZeBznm/file1179f56ce92d5/ExomeDepth_1.1.15.tar.gz' had non-zero exit status

[vplagnol]

Thanks I am looking into this now. That issue is now keeping ExomeDepth out of CRAN so I need to work it out.

[vplagnol]

OK I think it's sorted. The explanation came from this post:
https://stat.ethz.ch/pipermail/r-package-devel/2022q4/008580.html

ExomeDepth should be back in CRAN shortly (or so I hope).

[vplagnol]

And @Leelouh if you can give the latest version of the repo a try, it would be a good confirmation that the issue is fixed.

[laetitiarialland]

Hello !
Do you know if Exome Depth is back in the CRAN now ? And if not, when it will be done ?
Actually, I am also trying to install Exome Depth on R 3.6.3 and it appears that ExomeDepth can't be downloaded from the CRAN...

Thanks for help !!

Kind regards,

Laëtitia

[jiangldu]

today i have try this command:
devtools::install_github("vplagnol/ExomeDepth")
the package can be successfully installed.