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Question: Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
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gravatar for joseph.elsherbini
10 weeks ago by
joseph.elsherbini30 wrote:
I am unable to install ShortRead which I need for dada2
R version 3.4.3 (2017-11-30)

biocLite(c("ShortRead"))

...

checking for gzeof in -lz... no
configure: error: zlib not found
ERROR: configuration failed for package ‘ShortRead’
However, I do have libz available:
Sys.getenv()

...

LD_LIBRARY_PATH         /home/josephe/miniconda3/envs/dada2pipeline/lib/R/lib:/builddir/vendor/build/lib:/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.111.x86_64/jre/lib/amd64/server:/home/josephe/miniconda3/envs/dada2pipeline/lib

ls -l ~/miniconda3/envs/dada2pipeline/lib/libz*
-rw-rw-r-- 4 josephe josephe 153418 Jan 23  2017 /home/josephe/miniconda3/envs/dada2pipeline/lib/libz.a
lrwxrwxrwx 2 josephe josephe     14 May 11 12:30 /home/josephe/miniconda3/envs/dada2pipeline/lib/libz.so -> libz.so.1.2.11
lrwxrwxrwx 2 josephe josephe     14 May 11 12:30 /home/josephe/miniconda3/envs/dada2pipeline/lib/libz.so.1 -> libz.so.1.2.11
ADD COMMENTlink modified 24 days ago by pandit.aridaman0 • written 10 weeks ago by joseph.elsherbini30
1
gravatar for Martin Morgan
10 weeks ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I'd ensure that this was seen by R, and that the header for libz (typically, installing the '-dev' version of the library) are available.

As a next step, if from the command line and with the unpacked source tarball available you try to install the package

> download.packages("ShortRead", ".", repos = BiocInstaller::biocinstallRepos())
> quit()
$ tar xzf ShortRead_*gz
$ cd ShortRead
ShortRead$ R CMD INSTALL .

and then look for config.log you'll see something like

configure:2897: checking for gzeof in -lz
configure:2922: gcc -o conftest -g -O2   conftest.c -lz   >&5
configure:2922: $? = 0
configure:2931: result: yes

except that you won't get that result, and there'll be a conftest.c file and perhaps informative messages. I'd also look on the mailing list / support site for whatever 'conda' manager you're using for similar messages.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Martin Morgan ♦♦ 22k
1
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
ADD REPLYlink written 9 weeks ago by joseph.elsherbini30

You can see the command begin run (the stuff after the line configure:2922:) on the file echoed in the | comment. I'd guess it is that the LD_LIBRARY_PATH is either incorrect or not forwarded to the process that does the compilation and installation. You could edit the configure.ac file to echo what configure is seeing

AC_INIT("DESCRIPTION")
echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
AC_CHECK_LIB([z], [gzeof], , AC_ERROR([zlib not found]))
AC_CHECK_SIZEOF([unsigned long]) AC_OUTPUT(src/Makevars)

then use autoconf and R CMD INSTALL; I have

ShortRead master$ autoconf
ShortRead master$ bioc-dev CMD INSTALL .
* installing to library '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.8'
* installing *source* package 'ShortRead' ... 
LD_LIBRARY_PATH: /home/mtmorgan/bin/R-3-5-branch/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-9-openjdk-amd64/lib/amd64/server:/home/mtmorgan/bin/R-3-5-branch/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-9-openjdk-amd64/lib/amd64/server

If LD_LIBRARY_PATH is not correct, then I'm not really sure what to do -- I think it is really a conda problem.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Martin Morgan ♦♦ 22k

I am also facing the same issue with R version 3.4.3 installed via anaconda3.5.2. Did you find any solution for this problem? 
Thanks!

ADD REPLYlink modified 25 days ago • written 25 days ago by amalthomas1110

did you try to troubleshoot as above? what were the results?

ADD REPLYlink written 25 days ago by Martin Morgan ♦♦ 22k

Yes. No luck with that!  Echoing LD_LIBRARY_PATH shows that anaconda lib is included. I am not sure why the package still can't find zlib.
checking for gzeof in -lz... no
configure: error: zlib not found

 

ADD REPLYlink modified 15 days ago • written 15 days ago by amalthomas1110

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.

ADD REPLYlink written 7 days ago by Till10
1

I finally figured out setting CPPFLAGS and LDFLAGS works:

CPPFLAGS='-I/home/till/miniconda2/envs/dada2/include' LDFLAGS='-L/home/till/miniconda2/miniconda2/envs/dada2/lib'

What does NOT work however is

R CMD INSTALL --configure-args='--with-zlib-include=home/till//miniconda2/envs/dada2/include --with-zlib-lib=/home/till/miniconda2/envs/dada2/lib' .

ADD REPLYlink modified 7 days ago • written 7 days ago by Till10

Thanks for working on this. It sounds like a bioconda issue (I guess -- is that what creates the 'miniconda2' directory?), and that somehow R should know to look in the paths you indicate for the include and lib files. Can you pursue this 'upstream' with the bioconda team?

ADD REPLYlink written 5 days ago by Martin Morgan ♦♦ 22k

 Could you please tell us what exactly you did?
This didn't work for me.

export CPPFLAGS="-I~/panases_soft/anaconda3.5.2/include"
export LDFLAGS="-L~/panases_soft/anaconda3.5.2/lib"

 

ADD REPLYlink modified 5 days ago • written 5 days ago by amalthomas1110
0
gravatar for pandit.aridaman
24 days ago by
pandit.aridaman0 wrote:

I had the same error for the past week. I made it to work by installing ShortRead in R (not in conda) and then add the core R's library when I ran R in conda environment. I just made it to work, so I am sure there might be a better solution. I think this is because of conflict in the zlib conda and core library.

Also posted the solution for the same question here:
https://stackoverflow.com/questions/51017495/zlib-not-found-when-installing-shortread/51042014#51042014

 

ADD COMMENTlink written 24 days ago by pandit.aridaman0
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