install issue

[xueweic]

Hi,

I would like to install the package "seqminer" in HPC where I did not have the manager permisson.
The R version is 3.2.5 in HPC.
When I installed it, it showed the following error message.
Could you help me to solve this issue? Thank you.

install.packages("seqminer", lib = "..../library", repos = "http://cran.us.r-project.org")
Error in readRDS(file) :
cannot read workspace version 3 written by R 3.6.0; need R 3.5.0 or newer
Error in readRDS(file) :
cannot read workspace version 3 written by R 3.6.0; need R 3.5.0 or newer
Error in readRDS(file) :
cannot read workspace version 3 written by R 3.6.0; need R 3.5.0 or newer
Error in readRDS(file) :
cannot read workspace version 3 written by R 3.6.0; need R 3.5.0 or newer
trying URL 'http://cran.us.r-project.org/src/contrib/seqminer_8.0.tar.gz'
Content type 'application/x-gzip' length 4055251 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

• installing source package 'seqminer' ...
  ** package 'seqminer' successfully unpacked and MD5 sums checked
  configure: CC = icc -std=gnu99
  configure: CFLAGS = -g -O2 -std=c99
  configure: CXX = ERROR: no information for variable 'CXX11' ERROR: no information for variable 'CXX11STD'
  configure: CXXFLAGS = ERROR: no information for variable 'CXX11FLAGS'
  checking whether the C++ compiler works... no
  configure: error: in /tmp/2967577.1.long.q/RtmpXlvYqd/R.INSTALL1ee473a5617c6/seqminer': configure: error: C++ compiler cannot create executables See config.log' for more details
  ERROR: configuration failed for package 'seqminer'
• removing '.../library/seqminer'

The downloaded source packages are in
'/tmp/2967577.1.long.q/RtmpJkxLe0/downloaded_packages'
Warning message:
In install.packages("seqminer", lib = ".../library", :
installation of package 'seqminer' had non-zero exit status

[ahstram]

I'm experiencing similar issues with R-3.3.0...

if you type

/path/to/R CMD config

it appears that the relevant variables used to be known as:

CXX1X compiler command for C++11 code
CXX1XSTD flag used with CXX1X to enable C++11 support
CXX1XFLAGS further compiler flags for CXX1X
CXX1XPICFLAGS special flags for compiling C++11 code to be included in a shared library

So, it appears you should either update your version of R to one which uses the CXX11 variables, or modify the configure script in this package's source code to point at CXX1X instead of CXX11, etc.

Here's an example patch:

index 8097f58..a22a183 100755
--- a/configure
+++ b/configure
@@ -2045,9 +2045,9 @@ fi

 CC=`"${R_HOME}/bin/R" CMD config CC`
 CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CXX11=`"${R_HOME}/bin/R" CMD config CXX11`
-CXX11STD=`"${R_HOME}/bin/R" CMD config CXX11STD`
-CXX11FLAGS=`"${R_HOME}/bin/R" CMD config CXX11FLAGS`
+CXX11=`"${R_HOME}/bin/R" CMD config CXX1X`
+CXX11STD=`"${R_HOME}/bin/R" CMD config CXX1XSTD`
+CXX11FLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
 CXX="${CXX11} ${CXX11STD}"

 { $as_echo "$as_me:${as_lineno-$LINENO}: CC = $CC" >&5