Whenever I try to install HTSeqGenie for using the markduplicate function in R, I failed to compile gmapR (Rtools version 35 installed), error message shown below:

> if (!requireNamespace("BiocManager", quietly = TRUE))  
> install.packages("BiocManager")    BiocManager::install("HTSeqGenie") 
> Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
> Installing package(s) 'HTSeqGenie' also installing the dependency
> ‘gmapR’
> 
> Package which is only available in source form, and may need
> compilation of C/C++/Fortran: ‘gmapR’ installing the source packages
> ‘gmapR’, ‘HTSeqGenie’
> 
> trying URL
> 'https://bioconductor.org/packages/3.10/bioc/src/contrib/gmapR_1.28.0.tar.gz'
> Content type 'application/x-gzip' length 30568711 bytes (29.2 MB)
> downloaded 29.2 MB
> 
> trying URL
> 'https://bioconductor.org/packages/3.10/bioc/src/contrib/HTSeqGenie_4.16.0.tar.gz'
> Content type 'application/x-gzip' length 3242888 bytes (3.1 MB)
> downloaded 3.1 MB
> 
> * installing *source* package 'gmapR' ...
> ** using staged installation
> ** libs
> 
> *** arch - i386 c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_gmapR.c -o R_init_gmapR.o c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-36~1.1/include"
> -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c bamreader.c -o bamreader.o bamreader.c:2:29: fatal error: gstruct/bamread.h: No such file or directory  #include <gstruct bamread.h="">
>                              ^ compilation terminated. make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:208: bamreader.o] Error 1
> ERROR: compilation failed for package 'gmapR'
> * removing 'C:/Users/erik.huang/Documents/R/win-library/3.6/gmapR' ERROR: dependency 'gmapR' is not available for package 'HTSeqGenie'
> * removing 'C:/Users/erik.huang/Documents/R/win-library/3.6/HTSeqGenie'
> 
> The downloaded source packages are in
>   ‘C:\Users\erik.huang\AppData\Local\Temp\RtmpktWIrT\downloaded_packages’
> Warning messages: 1: In install.packages(...) :   installation of
> package ‘gmapR’ had non-zero exit status 2: In install.packages(...) :
> installation of package ‘HTSeqGenie’ had non-zero exit status

I don't know why it couldn't compile bamreader.h nor where to get it, would be really appreciate if anyone knows how to solve the problem.

Your package is failing to install because of problems with compiling gmapR:

> *** arch - i386 c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_gmapR.c -o R_init_gmapR.o c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-36~1.1/include"
> -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c bamreader.c -o bamreader.o bamreader.c:2:29: fatal error: gstruct/bamread.h: No such file or directory  #include <gstruct bamread.h="">
>                              ^ compilation terminated. make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:208: bamreader.o] Error 1
> ERROR: compilation failed for package 'gmapR'

you can see from the 'platforms' badge at the top of the 'landing page' http://bioconductor.org/packages/gmapR that this package is only available on 'some' platforms, and by clicking on the badge to navigate to the bottom of the page that this package is not available as a Windows binary.

If it's intentionally not available as a binary, then it means that the Bioc core team and developer were not able to build it; this is usually a good (though not infallible, sign that the user will not be able to install it on that platform either.

So likely this means that you cannot use gmapR or any package that depends on it on Windows; the best option is to use a different platfoorm.

One option for using a different platform is to use the 'bioconductor_docker' image, with some guidance at http://bioconductor.org/help/docker/ ; frankly I do not have experience with the success of this approach on Windows.