Whenever I try to install HTSeqGenie for using the markduplicate function in R, I failed to compile gmapR (Rtools installed, version 35), 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 ^ 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.