Could not install spp

[rt...@nyu.edu]

Hi guys,

I ran into some problems while installing spp package. Does any one know what went wrong?

I want to get the estimated fragment length for my data. Any alternative tool for this?

I installed the following packages:

R3.3.1

boost 

samtools

caTools, snow, snowfall, bitops, Rsamtools

install.packages("spp-1.14.tar.gz")

Installing package into '/home/rt/R/x86_64-centos-linux-gnu-library/3.3'

(as 'lib' is unspecified)

inferring 'repos = NULL' from 'pkgs'

Warning in untar2(tarfile, files, list, exdir, restore_times) :

  skipping pax global extended headers

* installing *source* package 'spp' ...

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for BZ2_bzDecompressInit in -lbz2... yes

checking for g++... g++

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking for grep that handles long lines and -e... /bin/grep

checking how to run the C++ preprocessor... g++ -E

checking for a sed that does not truncate output... /bin/sed

configure: Detected BOOST_ROOT; continuing with --with-boost=/share/apps/boost/1.58.0/gnu

checking for Boost headers version >= 1.41.0... /share/apps/boost/1.58.0/gnu/include

checking for Boost's header version... 1_58

configure: creating ./config.status

config.status: creating src/Makevars

** libs

icpc -I/share/apps/r/3.3.1/intel/lib64/R/include -DNDEBUG  -I/share/apps/cairo/1.12.16/gnu/include -I/share/apps/jpeg/9a/intel/include -I/share/apps/openssl/1.0.1g/gnu/include -I/share/apps/tiff/4.0.6/intel/include -I/share/apps/mpfr/3.1.2/gnu/include -I/share/apps/curl/7.49.1/intel/include -I/share/apps/xz/5.2.2/gnu/include -I/share/apps/gmp/5.1.3/gnu/include -I/share/apps/expat/2.1.0/intel/include -I/share/apps/gcc/4.8.2/include -I/share/apps/pcre/8.39/intel/include -I/share/apps/intel/14.0.2/composer_xe_2013_sp1.2.144/mkl/include -I/share/apps/bzip2/1.0.6/intel/include -I/share/apps/icu/52.1/gnu/include -I/share/apps/zlib/1.2.8/intel/include -I/share/apps/libssh2/1.7.0/intel/include -I/share/apps/mpc/1.0.2/gnu/include   -I./ -D_FASTMAP -DMAQ_LONGREADS   -I/share/apps/boost/1.58.0/gnu/include -fpic  -g -O2  -c bed2vector.cpp -o bed2vector.o

In file included from /share/apps/gcc/4.8.2/include/c++/4.8.2/ext/hash_map(60),

                 from pc.h(4),

                 from bed2vector.cpp(1):

/share/apps/gcc/4.8.2/include/c++/4.8.2/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 \

   ^

icc -I/share/apps/r/3.3.1/intel/lib64/R/include -DNDEBUG  -I/share/apps/cairo/1.12.16/gnu/include -I/share/apps/jpeg/9a/intel/include -I/share/apps/openssl/1.0.1g/gnu/include -I/share/apps/tiff/4.0.6/intel/include -I/share/apps/mpfr/3.1.2/gnu/include -I/share/apps/curl/7.49.1/intel/include -I/share/apps/xz/5.2.2/gnu/include -I/share/apps/gmp/5.1.3/gnu/include -I/share/apps/expat/2.1.0/intel/include -I/share/apps/gcc/4.8.2/include -I/share/apps/pcre/8.39/intel/include -I/share/apps/intel/14.0.2/composer_xe_2013_sp1.2.144/mkl/include -I/share/apps/bzip2/1.0.6/intel/include -I/share/apps/icu/52.1/gnu/include -I/share/apps/zlib/1.2.8/intel/include -I/share/apps/libssh2/1.7.0/intel/include -I/share/apps/mpc/1.0.2/gnu/include   -I./ -D_FASTMAP -DMAQ_LONGREADS    -fpic  -O2 -std=c99  -c cdensum.c -o cdensum.o

icc -I/share/apps/r/3.3.1/intel/lib64/R/include -DNDEBUG  -I/share/apps/cairo/1.12.16/gnu/include -I/share/apps/jpeg/9a/intel/include -I/share/apps/openssl/1.0.1g/gnu/include -I/share/apps/tiff/4.0.6/intel/include -I/share/apps/mpfr/3.1.2/gnu/include -I/share/apps/curl/7.49.1/intel/include -I/share/apps/xz/5.2.2/gnu/include -I/share/apps/gmp/5.1.3/gnu/include -I/share/apps/expat/2.1.0/intel/include -I/share/apps/gcc/4.8.2/include -I/share/apps/pcre/8.39/intel/include -I/share/apps/intel/14.0.2/composer_xe_2013_sp1.2.144/mkl/include -I/share/apps/bzip2/1.0.6/intel/include -I/share/apps/icu/52.1/gnu/include -I/share/apps/zlib/1.2.8/intel/include -I/share/apps/libssh2/1.7.0/intel/include -I/share/apps/mpc/1.0.2/gnu/include   -I./ -D_FASTMAP -DMAQ_LONGREADS    -fpic  -O2 -std=c99  -c maqmap.c -o maqmap.o

maqmap.c(137): warning #266: function "getopt" declared implicitly

  while ((c = getopt(argc, argv, "bN")) >= 0) {

              ^

maqmap.c(143): error: identifier "optind" is undefined

  if (argc == optind) {

              ^

maqmap.c(147): error: identifier "optind" is undefined

  gzFile fp = (strcmp(argv[optind], "-") == 0)? gzdopen(STDIN_FILENO, "r") : gzopen(argv[optind], "r");

                           ^

maqmap.c(160): error: identifier "optind" is undefined

  fp = (strcmp(argv[optind], "-") == 0)? gzdopen(STDIN_FILENO, "r") : gzopen(argv[1], "r");

                    ^

compilation aborted for maqmap.c (code 2)

make: *** [maqmap.o] Error 2

ERROR: compilation failed for package 'spp'

* removing '/home/rt/R/x86_64-centos-linux-gnu-library/3.3/spp'

Warning message:

In install.packages("spp-1.14.tar.gz") :

  installation of package 'spp-1.14.tar.gz' had non-zero exit status

[Venkat Malladi]

I have the same problem. Any solutions?

[Anshul Kundaje]

Jin - can you look into this. 

Anshul 

--
You received this message because you are subscribed to the Google Groups "idr-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to idr-discuss+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[lee...@gmail.com]

I am sorry about late reply. It looks like your R is compiled with Intel compilers with -std=c99. Can you try the following?

# unpack spp-1.14

$ tar zxvf spp-1.14.tar.gz

# modify spp-1.14/src/Makevars.in (add -std=gnu99)

PKG_LIBS=@LIBS@ -lz

PKG_CFLAGS=-I./ -std=gnu99 -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@

PKG_CXXFLAGS=-I./ -std=gnu99 -D_FASTMAP -DMAQ_LONGREADS   @HAVE_LIBBZ2@  @BOOST_CPPFLAGS@

# make tar ball

$ tar zcvf test.tar.gz spp-1.14

# install modified spp-1.14

$ R

> install.packages("test.tar.gz")

[Edahí Gonzalez Avalos]

Sorry to inform you about this, but I am still having the same issue after the correction you suggested. Attached the error it pops out.

Thank you for your help.

Edahi GA.

[Jin]

This looks a complicated dependency problem and it's very hard to debug.

I recommend to use our pipeline's conda environment.

Please install Conda and dependencies using the following instructions:

1) Download pipeline:

https://github.com/kundajelab/chipseq_pipeline#aquas-pipeline

2) Install Conda:

https://github.com/kundajelab/chipseq_pipeline#conda

3) Install dependencies (including R and SPP):

https://github.com/kundajelab/chipseq_pipeline#conda

4) Activate Conda environment to use R and SPP:

$ source activate aquas_chipseq

Thanks,

Jin

--