hpages
commented
5 years ago Hi,
The Rhtslib package doesn't use a configure script because it is assumed that R "knows" where to find the libbz2 library and its header files. This is why using configure.vars=... when installing the package has no effect.
More precisely, the Makefile used to compile Rhtslib on Linux or Mac (Rhtslib/src/htslib-1.7/Makefile.Rhtslib) re-uses the LDFLAGS and CPPFLAGS values set by R itself. This is why they are commented out in Makefile.Rhtslib. You can see the values set by R for these variables by running R CMD config LDFLAGS and R CMD config CPPFLAGS on your system. Here is what I get on my system (64-bit Ubuntu Linux 16.04):
hpages@spectre:~$ R CMD config LDFLAGS
-L/usr/local/lib
hpages@spectre:~$ R CMD config CPPFLAGS
-I/usr/local/includeIf R was configured properly, you should be able to use these flags to compile/link the following simple program that uses libbz2:
test.c file
#include <bzlib.h>
int main() {
BZFILE *file;
char buf[5];
file = BZ2_bzopen("some/path", "rb");
BZ2_bzread(file, buf, 1);
return 0;
}Try to compile/link test.c using the LDFLAGS and CPPFLAGS set by R
gcc -Wall `R CMD config CPPFLAGS` test.c `R CMD config LDFLAGS` -lbz2On my system the a.out executable produced by the above command is linked to the following dynamic libraries:
hpages@spectre:~$ ldd a.out
linux-vdso.so.1 => (0x00007fffdafad000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f200ec6f000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f200e8a5000)
/lib64/ld-linux-x86-64.so.2 (0x00007f200ee7f000)As you can see, in my case libbz2 is in a standard location so adding the CPPFLAGS and LDFLAGS to the command I used to compile/link test.c was not necessary (i.e. gcc -Wall test.c -lbz2 also works fine). However, on systems where libbz2 is NOT in a standard location, R should "know" where to find the library and its header files and this should be reflected in the output of R CMD config LDFLAGS and R CMD config CPPFLAGS. If trying to compile/link test.c using the LDFLAGS and CPPFLAGS set by R doesn't work for you, it probably means that R was not configured properly, or that libbz2 was installed to a non-standard location after R was configured.
Could the problem be related to the way R got installed on your system? I know nothing about Spack or installing R via Spack.
H.
jessepharrison
Hello,
I am running R 3.6.1 installed via spack on Linux, with both zlib and bzip2 installed (the necessary header files are present, although in non-standard locations). There have been some reports of missing files / libraries for previous Rhtslib versions and I am running into similar problems when trying to install Rhtslib 1.16.2 or the devel version (1.17.6).
If I run the regular BiocManager installation command:
BiocManager::install("Rhtslib", lib = libpath, update = FALSE)... I get an error concerning bzlib.h:cram/cram_io.c:57:10: fatal error: bzlib.h: No such file or directoryThis is not fixed by specifying CPPFLAGS, CFLAGS or LDFLAGS in the above installation command by using
configure.vars=....If I manually change the flags in Makefile and Makefile.Rhtslib, repackage the source files and install using
R CMD INSTALL, that fixes the bzlib.h issue but I still run into a further missing library problem. The changes I made consisted of:It then is able to find bzlib.h but gives the following error:
cannot find -lbz2So far I've found no solution to this problem. I've also tried setting flags directly as part of the
R CMD INSTALLcommand. Would anyone have suggestions as to fixing the issue? The relevant bzip2 directories are also included in my LD_LIBRARY_PATH and PATH.Aside from problems with installing the R package, I am able to install HTSlib as follows... so it must be something about the R package installation itself.
CFLAGS="-I/path/to/include/" LIBS="-L/path/to/lib -lz -lm -lbz2 -llzma -lcurl" ./configure --prefix=/destination/directory --enable-libcurl... followed by
make && make install.Best wishes, Jesse Harrison