I get the error "cannot find -lz". Do you have any insight into that? I think I have zlib version 1.2.11 installed, it is in the directory /home/josephe/miniconda3/envs/dada2pipeline/lib, and my LD_LIBRARY_PATH is set to that directory.

configure:2897: checking for gzeof in -lz
configure:2922: /home/josephe/miniconda3/envs/dada2pipeline/bin/x86_64-conda_cos6-linux-gnu-cc -o conftest -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now conftest.c -lz   >&5
/home/josephe/miniconda3/envs/dada2pipeline/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
configure:2922: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char gzeof ();
| int
| main ()
| {
| return gzeof ();
|   ;
|   return 0;
| }
configure:2931: result: no
configure:2941: error: zlib not found

Hi Martin,

I have the same problem with the same versions etc. I tried your troubleshooting method, but it just gives the same error that I get in the R console, the one posted above. This is also using conda. Installing ShortRead via conda will unfortuately downgrade R and some other things as I guess they don't have the current version yet.

For what it's worth and in an attempt at a reproducible example, I did

sh ~/Downloads/Miniconda3-latest-Linux-x86_64.sh
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda create -n bioconductor bioconductor-biocinstaller
conda activate bioconductor
conda install bioconductor-shortread

and had no trouble.

 

In the failing configuration, if you clone the ShortRead package

git clone https://git.bioconductor.org/packages/ShortRead
cd ShortRead

and run

./configure

it should fail. Does it also report, in the config.log file that should now exist, a line like the one above, 

...gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status

? If so, can you further simplify the problem by creating a file conftest.c

/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.  */
#ifdef __cplusplus
extern "C"
#endif
char gzeof ();
int
main ()
{
return gzeof ();
  ;
  return 0;
}

and have it fail with

gcc conftest.c -lz

If so can you investigate the paths where libz is being sought

gcc -Wl,--verbose conftest.c -lz > conftest.log 2>&1
grep "libz.so" conftest.log

and compare these to where libz.so is found in the working environment. It is not, to my understanding, an issue about the library version, but rather how it  is installed and discovered by conda.

 

In case anyone else comes along here searching for an answer:

I've played around with this a bit. It turns out that the problem is not with zlib at all; requiring zlib=1.2.8 ends up meaning that you need r-base<=3.4.1=1. Installing ShortRead also works with no problems in r-base=3.4.1=2, which requires zlib=1.2.11. At some point after that, they introduced changes in r-base which break installing packages with external dependencies.

I filed an issue at Conda-Forge with my findings.

Thank you for this, it was very helpful and worked wonderfully (I'm also using r-base=3.5.1). I'm glad I looked at the thread gain, two days ago, when I bumped into this issue, you had not shared your solution!

Thans, it works!

Or we can still use following command after setting LDFLAGS:

> library(BiocManager)
> BiocManager::install("ShortRead")

This is my R and bioconductor version:

> BiocManager::install()
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)