Failed to compile on Linux

[giantwhale]

I am not familiar with the R build system. When I tried to install this package either through install.packages or R CMD INSTALL, I got the following message:

* installing to library ‘/myownpath/R/xxx-main/build’
* installing *source* package ‘RcppBDT’ ...
** libs
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppBDTdd.cpp -o RcppBDTdd.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppBDTdd.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppBDTdt.cpp -o RcppBDTdt.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppBDTdt.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppBDTdu.cpp -o RcppBDTdu.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppBDTdu.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppBDTpt.cpp -o RcppBDTpt.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppBDTpt.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppBDTtz.cpp -o RcppBDTtz.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppBDTtz.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c RcppExports.cpp -o RcppExports.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [RcppExports.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/myownpath/R/xxx-main/build/Rcpp/include" -I"/myownpath/R/xxx-main/build/BH/include"      -c toPOSIXct.cpp -o toPOSIXct.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
make: [toPOSIXct.o] Error 127 (ignored)
-shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o RcppBDT.so RcppBDTdd.o RcppBDTdt.o RcppBDTdu.o RcppBDTpt.o RcppBDTtz.o RcppExports.o toPOSIXct.o -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR
sh: line 2: -shared: command not found
make: *** [RcppBDT.so] Error 127
ERROR: compilation failed for package ‘RcppBDT’
* removing ‘/myownpath/R/xxx-main/build/RcppBDT’

Instead of compiling cpp sources through:

g++ -I/usr/lib64/microsoft-r/3.3/lib64/R/include

it used the wrong command with g++ - missing:

I/usr/lib64/microsoft-r/3.3/lib64/R/include

I tried to install Rcpp and it succeeded. Do you know what's going on here?

---

My temporary workaround is to cd into the src directory and manually compile all cpp files by:

g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppBDTdd.cpp -o RcppBDTdd.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppBDTdt.cpp -o RcppBDTdt.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppBDTdu.cpp -o RcppBDTdu.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppBDTpt.cpp -o RcppBDTpt.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppBDTtz.cpp -o RcppBDTtz.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c RcppExports.cpp -o RcppExports.o
g++ -fPIC -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I../inst/include/ -DU_STATIC_IMPLEMENTATION -I"/xxx/build/Rcpp/include" -I"/xxx/build/BH/include"      -c toPOSIXct.cpp -o toPOSIXct.o
g++ -fPIC -shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o RcppBDT.so RcppBDTdd.o RcppBDTdt.o RcppBDTdu.o RcppBDTpt.o RcppBDTtz.o RcppExports.o toPOSIXct.o -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR

I also have to manually add -fPIC to build the shared library.

[eddelbuettel]

Briefly:

• I don't have Microsoft R so I cannot help you with particulars
• RcppBDT itself works just fine on Linux, see
  • Travis CI build history
  • CRAN check results
• You should never have gotten RcppBDT without Rcpp as the latter is a declared dependency

So in short there is no reproducible issue here, beyond make something you may need to report to Microsoft,

[giantwhale]

thank you, confirmed this is a bug in Microsoft-R-Open

microsoft/microsoft-r-open#17

[eddelbuettel]

Thanks for the follow-up, and the reference! I left a message in their threads microsoft/microsoft-r-open#11 and microsoft/microsoft-r-open#17 too.

In a nutshell, 9000+ CRAN package are built with a set of assumptions about how things are going to work at install time, and "they" violated that contract here. Which leaves you in the hole they dug :-/