Problem with the installation of Zinba(peak caller) on R

Question

[anais1396]

Hi everyone !!

I tried to install Zinba, a tool for peak calling used in the analysis of ATAC-seq datas.

• Operating system that I am using : Linux (computing cluster) and R (version 3.4.3)

• Error message : compilation aborted for bed2vector.cc (code 2) make: * [bed2vector.o] Error 2 ERROR: compilation failed for package ‘zinba’

• Command used : install.packages("zinba_2.02.03.tar.gz", repos=NULL) But I've also tried to install zinba_2.03.1.tar.gz and zinba_2.02.04.tar.gz and I have the same error message.

• Copy of the output :

  install.packages("zinba_2.03.1.tar.gz")

Installing package into ‘/sulb2/amontois/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified) inferring 'repos = NULL' from 'pkgs' * installing source package ‘zinba’ ... ** libs

icc -I/apps/brussel/CO7/magnycours-ib/software/R/3.4.3-intel-2017b-X11-20171023/lib64/R/include -DNDEBUG   -I/apps/brussel/CO7/magnycours-ib/software/imkl/2017.3.196-iimpi-2017b/mkl/include -I/apps/brussel/CO7/magnycours-ib/software/X11/20171023-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/Mesa/17.2.4-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libGLU/9.0.0-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/cairo/1.14.10-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libreadline/7.0-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/ncurses/6.0-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/XZ/5.2.3-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/zlib/1.2.11-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/SQLite/3.20.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/PCRE/8.41-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libpng/1.6.32-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libjpeg-turbo/1.5.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/LibTIFF/4.0.8-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/Java/1.8.0_152/include -I/apps/brussel/CO7/magnycours-ib/software/Tcl/8.6.7-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/Tk/8.6.7-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/cURL/7.56.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libxml2/2.9.4-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/GDAL/2.2.2-intel-2017b-Python-2.7.14/include -I/apps/brussel/CO7/magnycours-ib/software/PROJ/4.9.3-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/GMP/6.1.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/NLopt/2.4.2-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/FFTW/3.3.6-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libsndfile/1.0.28-GCCcore-6.4.0/include   -fpic  -O2 -xHost -ftz -fp-speculation=safe -fp-model source  -c aliType.c -o aliType.o
ire/SQLite/3.20.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/PCRE/8.41-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libpng/1.6.32-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libjpeg-turbo/1.5.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/LibTIFF/4.0.8-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/Java/1.8.0_152/include -I/apps/brussel/CO7/magnycours-ib/software/Tcl/8.6.7-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/Tk/8.6.7-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/cURL/7.56.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libxml2/2.9.4-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/GDAL/2.2.2-intel-2017b-Python-2.7.14/include -I/apps/brussel/CO7/magnycours-ib/software/PROJ/4.9.3-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/GMP/6.1.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/NLopt/2.4.2-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/FFTW/3.3.6-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libsndfile/1.0.28-GCCcore-6.4.0/include   -fpic  -O2 -xHost -ftz -fp-speculation=safe -fp-model source  -c alignAdjust.cc -o alignAdjust.o

[...]

icpc  -I/apps/brussel/CO7/magnycours-ib/software/R/3.4.3-intel-2017b-X11-20171023/lib64/R/include -DNDEBUG   -I/apps/brussel/CO7/magnycours-ib/software/imkl/2017.3.196-iimpi-2017b/mkl/include -I/apps/brussel/CO7/magnycours-ib/software/X11/20171023-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/Mesa/17.2.4-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libGLU/9.0.0-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/cairo/1.14.10-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libreadline/7.0-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/ncurses/6.0-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/XZ/5.2.3-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/zlib/1.2.11-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/SQLite/3.20.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/PCRE/8.41-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libpng/1.6.32-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libjpeg-turbo/1.5.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/LibTIFF/4.0.8-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/Java/1.8.0_152/include -I/apps/brussel/CO7/magnycours-ib/software/Tcl/8.6.7-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/Tk/8.6.7-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/cURL/7.56.1-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/libxml2/2.9.4-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/GDAL/2.2.2-intel-2017b-Python-2.7.14/include -I/apps/brussel/CO7/magnycours-ib/software/PROJ/4.9.3-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/GMP/6.1.2-GCCcore-6.4.0/include -I/apps/brussel/CO7/magnycours-ib/software/NLopt/2.4.2-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/FFTW/3.3.6-intel-2017b/include -I/apps/brussel/CO7/magnycours-ib/software/libsndfile/1.0.28-GCCcore-6.4.0/include   -fpic  -O2 -xHost -ftz -fp-speculation=safe -fp-model source  -c bed2vector.cc -o bed2vector.o
In file included from /gpfs/software/CO7/magnycours-ib/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/ext/hash_set(60),
                 from pc.h(5),
                 from bed2vector.cc(1):
/gpfs/software/CO7/magnycours-ib/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header which   may be removed without further notice at a future date. Please use a   non-deprecated interface with equivalent functionality instead. For a   listing of replacement headers and interfaces, consult the file   backward_warning.h. To disable this warning use -Wno-deprecated.
  #warning \
   ^

bed2vector.cc(41): error: "hash" is ambiguous
        hash_map<string, int, hash<string>,equal_to<string> > cind_map;
                              ^

bed2vector.cc(111): error: "hash" is ambiguous
                        hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
                                              ^

compilation aborted for bed2vector.cc (code 2)
make: *** [bed2vector.o] Error 2
ERROR: compilation failed for package ‘zinba’
* removing ‘/sulb2/amontois/R/x86_64-pc-linux-gnu-library/3.4/zinba’
Warning message:
In install.packages("zinba_2.03.1.tar.gz") :
  installation of package ‘zinba_2.03.1.tar.gz’ had non-zero exit status

• It seems to have an error with the installation of bed2vector... But I don't really understand what's wrong... Can you help me to solve this problem of installation please ?? Thank you in advance !

Anais

[ATpoint]

Gave it a try and had the same error. Do you really need this peak caller? Except the original ATAC-seq paper, no one seems to use it for ATAC peak calling anymore. Even the first author said in the ATAC community once that they used it only because the second author was involved in Zinba development and therefore had expertise with it. After he left, they started using MACS (like everyone else now) because it is more straight-forward, still maintained and performs well.

Given that you have a typical paired-end dataset in bam format that has already been deduplicated, use:

macs2 callpeak -t sample.bam --nomodel --keep-dup=all -f BAMPE

[anais1396]

Thank you for your answer. Actually I need Zinba to make a comparison between few peak calkers on my data set. But I also use MACS in my study. So I need to install Zinba...

[anicet.ebou]

Hello @anais1386, can you run systemInfo() in your R terminal and paste the output to help us understand the issue ? Thanks you in advance.

[anais1396]

Sys.info()

sysname : release

"Linux" : "3.10.0-693.17.1.el7.x86_64

version : nodename

"#1 SMP Thu Jan 25 20:13:58 UTC 2018" : "nic50"

machine: login

"x86_64" : "amontois"

user : effective_user

"amontois" : "amontois"

[Yang]

Hi anais1396，

I has come across the same problem as yours and tried the "Quick Fix" method. Unfortunately, the error keeps the same:

 /usr/include/c++/5/cmath:926:3: error: template with C linkage
   template<typename _Tp>
   ^
/usr/include/c++/5/cmath:935:3: error: template with C linkage
   template<typename _Tp>
   ^
/usr/lib/R/etc/Makeconf:166: recipe for target 'bed2vector.o' failed
make: *** [bed2vector.o] Error 1
ERROR: compilation failed for package ‘zinba’
* removing ‘/usr/local/lib/R/site-library/zinba’
Warning message:
In install.packages("zinba_2.02.03.tar.gz", repos = NULL) :
  installation of package ‘zinba_2.02.03.tar.gz’ had non-zero exit status

My R version is 3.5.0.

How can I solve this problem? Thanks in advance.

[mmfansler]

Could you include some of the lines before the error? Specifically, it is useful to see the call to the compiler that generated the error and not just the error. This would help to both verify that the -std=gnu++98 is properly included and provide us insight into what compiler you're using and the associated includes.

Also, do you get the same error when trying to install zinba_2.03.1.tar.gz? I think that is the version @anais1396 got working.

[Yang]

Thanks for your reply. I changed my R to version 3.2.3. Finally, it works.

Answer 1

[mmfansler]

The ZINBA code was written before C++11, which is when hash was added to the standard library, and so the authors used the g++ extension instead. Based on your output, the compiler is using C++11 (or later), so it has two versions of the class hash available and can't figure out which to use.

Quick Fix

You can temporarily direct the compiler to use a specific C++ version for installation using withr::makevars. Try

library(withr)
with_makevars(c(CXXFLAGS = "-std=gnu++98"), install.packages("zinba_2.03.1.tar.gz", repos = NULL))

Long Game

I hit different errors than you on both OS X (clang) and Linux (g++), so expect to hack on the code to get it working (I started to last year, but had other priorities). A more permanent workaround for your issue is to untar/zip the archive and add a Makevars file to the zinba/src directory containing the line:

PKG_CXXFLAGS = -std=gnu++98

Leave the source unzipped and install with install.packages("your/path/to/zinba", repos = NULL, type = "source").

[anais1396]

Thank you !! you save me !! It works with the quick fix !!!

I succeeded in installing zinba on R. I think it is difficult because zinba has no update until 2012 and it is not working with current version of R...

But with your commands, it works !!

Thank you mmfandler !!