JunHuang023
commented
8 years ago sorry, typo. I meant I am not a sophisticated bioinformatician...
Closed JunHuang023 closed 8 years ago
JunHuang023
commented
8 years ago sorry, typo. I meant I am not a sophisticated bioinformatician...
sebastian-luna-valero
commented
8 years ago Hello,
There seems to be a problem with your R/rpy2 installation.
Could you please have a look at our alternative installation instructions? https://www.cgat.org/downloads/public/cgat/documentation/CGATInstallation.html#cgat-code-clean-installation
Best regards, Sebastian.
JunHuang023
commented
8 years ago Dear Sebastian,
Thank you for your kind help.
I think that I resolved the issue by reinstall R with the configuration " --enable-R-shlib".
but now I have another issue of usage:
$ cgat bed2gff.py < H3K27ac_MBDCKOprec_peaks.bed > H3K27ac_MBDCKOprec_peaks.gff
Traceback (most recent call last):
File "~/anaconda2/bin/cgat", line 11, in
Despite that I got complain from python as shown above, I did have a new gff file created: -rw-r--r-- 1 myusername groupname 0 May 1 00:21 2016 H3K27ac_MBDCKOprec_peaks.gff but without any content.
I guess the installation was successful, because I could get the help information of cgat $ cgat --help
:Author: Andreas Heger, CGAT :Release: $Id$ :Date: |today| :Tags: Genomics
To use a specific tool, type::
cgat <tool> [tool options] [tool arguments]Tools are grouped by keywords. For this message and a list of available keywords type::
cgat --helpFor a list of tools matching a certain keyword, type::
cgat --help
or::
cgat --help all
for a list of all available tools.
To get help for a specific tool, type::
cgat <tool> --helpCGAT tools are grouped by keywords. The following keywords are defined:
Genomics Python Genesets
Conversion FASTQ GenomeAlignment
MultipleAlignments Protein Variants
BIGWIG Manipulation PSL
BED FASTA Intervals
WIGGLE Annotation Sequences
NGS BEDGRAPH Fasta
BAM Comparison Counting
Transformation GTF GFF
CHAIN Summary
Could you kindly let me know what might go wrong? Thank you very much. Best, Jun
sebastian-luna-valero
commented
8 years ago Not sure what's the root cause of the problem. Please double check that your PYTHONPATH is pointing to the correct site-packages folder.
On the other hand, I see that you are using anaconda. If that is the case, you could also try: https://anaconda.org/cgat/cgat-scripts
I was trying install cgat,but ran into problem like this:
$ pip install cgat Collecting cgat Downloading CGAT-0.2.5.tar.gz (557kB) 100% |████████████████████████████████| 563kB 213kB/s Requirement already satisfied (use --upgrade to upgrade): setuptools>=1.1 in ~/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg (from cgat) Requirement already satisfied (use --upgrade to upgrade): pyparsing>=1.5.7 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): cython>=0.19 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): numpy>=1.7 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Collecting MySQL-python>1.2.3 (from cgat) Downloading MySQL-python-1.2.5.zip (108kB) 100% |████████████████████████████████| 112kB 3.4MB/s Requirement already satisfied (use --upgrade to upgrade): PyYAML>=3.1.0 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Collecting alignlib-lite>=0.2.3 (from cgat) Downloading alignlib-lite-0.2.3.tar.gz (226kB) 100% |████████████████████████████████| 235kB 515kB/s Collecting biopython>=1.61 (from cgat) Downloading biopython-1.66.tar.gz (13.7MB) 100% |████████████████████████████████| 13.7MB 18kB/s ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): networkx>=1.8.1 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): pandas>=0.12.0 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): pysam>=0.8.4 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Collecting rdflib>=0.4.1 (from cgat) Downloading rdflib-4.2.1.tar.gz (889kB) 100% |████████████████████████████████| 890kB 824kB/s Collecting psycopg2>=2.5 (from cgat) Downloading psycopg2-2.6.1.tar.gz (371kB) 100% |████████████████████████████████| 378kB 1.8MB/s Collecting rpy2>=2.6 (from cgat) Downloading rpy2-2.7.8.tar.gz (178kB) 100% |████████████████████████████████| 184kB 3.4MB/s Collecting ruffus>=2.4 (from cgat) Downloading ruffus-2.6.3.tar.gz (36.9MB) 100% |████████████████████████████████| 36.9MB 20kB/s Requirement already satisfied (use --upgrade to upgrade): scipy>=0.11 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Requirement already satisfied (use --upgrade to upgrade): sphinx>=1.0.5 in /user/ifrec/junhuang/anaconda2/lib/python2.7/site-packages/Sphinx-1.3.5-py2.7.egg (from cgat) Collecting weblogo>=3.0 (from cgat) Downloading weblogo-3.4.tar.gz (921kB) 100% |████████████████████████████████| 931kB 820kB/s Collecting ggplot>=0.6.5 (from cgat) Downloading ggplot-0.6.8.tar.gz (8.5MB) 100% |████████████████████████████████| 8.6MB 83kB/s Collecting pybedtools>=0.6.5 (from cgat) Downloading pybedtools-0.7.7.tar.gz (12.6MB) 100% |████████████████████████████████| 12.6MB 58kB/s Requirement already satisfied (use --upgrade to upgrade): pep8>=1.4.0 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Collecting web.py>=0.37 (from cgat) Downloading web.py-0.37.tar.gz (90kB) 100% |████████████████████████████████| 92kB 4.5MB/s Requirement already satisfied (use --upgrade to upgrade): xlwt>=0.7.4 in ~/anaconda2/lib/python2.7/site-packages (from cgat) Collecting matplotlib-venn>=0.5 (from cgat) Downloading matplotlib-venn-0.11.3.zip Requirement already satisfied (use --upgrade to upgrade): python-dateutil in ~/anaconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->cgat) Requirement already satisfied (use --upgrade to upgrade): pytz in ~/anaconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->cgat) Requirement already satisfied (use --upgrade to upgrade): cycler in ~/anaconda2/lib/python2.7/site-packages (from matplotlib>=1.3.0->cgat) Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in ~/anaconda2/lib/python2.7/site-packages (from networkx>=1.8.1->cgat) Collecting isodate (from rdflib>=0.4.1->cgat) Downloading isodate-0.5.4.tar.gz Collecting SPARQLWrapper (from rdflib>=0.4.1->cgat) Downloading SPARQLWrapper-1.7.6.zip Collecting html5lib (from rdflib>=0.4.1->cgat) Downloading html5lib-0.9999999.tar.gz (889kB) 100% |████████████████████████████████| 890kB 840kB/s Requirement already satisfied (use --upgrade to upgrade): six in ~/anaconda2/lib/python2.7/site-packages (from rpy2>=2.6->cgat) Requirement already satisfied (use --upgrade to upgrade): singledispatch in ~/anaconda2/lib/python2.7/site-packages (from rpy2>=2.6->cgat) Requirement already satisfied (use --upgrade to upgrade): Jinja2>=2.3 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): Pygments>=2.0 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): docutils>=0.11 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): snowballstemmer>=1.1 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): babel!=2.0,>=1.3 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): alabaster<0.8,>=0.7 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): sphinx-rtd-theme<2.0,>=0.1 in ~/anaconda2/lib/python2.7/site-packages (from sphinx>=1.0.5->cgat) Requirement already satisfied (use --upgrade to upgrade): statsmodels in ~/anaconda2/lib/python2.7/site-packages (from ggplot>=0.6.5->cgat) Collecting brewer2mpl (from ggplot>=0.6.5->cgat) Downloading brewer2mpl-1.4.1-py2.py3-none-any.whl Requirement already satisfied (use --upgrade to upgrade): patsy in ~/anaconda2/lib/python2.7/site-packages (from ggplot>=0.6.5->cgat) Collecting keepalive>=0.5 (from SPARQLWrapper->rdflib>=0.4.1->cgat) Downloading keepalive-0.5.zip Requirement already satisfied (use --upgrade to upgrade): MarkupSafe in ~/anaconda2/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx>=1.0.5->cgat) Building wheels for collected packages: cgat, MySQL-python, alignlib-lite, biopython, rdflib, psycopg2, rpy2, ruffus, weblogo, ggplot, pybedtools, web.py, matplotlib-venn, isodate, SPARQLWrapper, html5lib, keepalive Running setup.py bdist_wheel for cgat ... done Stored in directory: /user/~/.cache/pip/wheels/20/bb/38/57a5c87a318f069e88ad22097cfb1f73c21b9f8dac0743a4a7 Running setup.py bdist_wheel for MySQL-python ... done Stored in directory: /user/~/.cache/pip/wheels/38/a3/89/ec87e092cfb38450fc91a62562055231deb0049a029054dc62 Running setup.py bdist_wheel for alignlib-lite ... done Stored in directory: /user/~/.cache/pip/wheels/fa/e0/89/95871c3ef80cc65c7484edb82258a6cdf382144fd5a9745c57 Running setup.py bdist_wheel for biopython ... done Stored in directory: /user/~/.cache/pip/wheels/1a/d6/62/e401d463e89b7534625f89fa21dbdaec5d18ad2c71d72aa714 Running setup.py bdist_wheel for rdflib ... done Stored in directory: /user/~/.cache/pip/wheels/fb/93/10/4f8a3e95937d8db410a490fa235bd95e0e0d41b5f6274b20e5 Running setup.py bdist_wheel for psycopg2 ... done Stored in directory: /user/~/.cache/pip/wheels/21/21/80/89c21755b92a5874b6a8930d015bf1c4fc1b253f24e8d880cb Running setup.py bdist_wheel for rpy2 ... error Complete output from command /user/ifrec/junhuang/anaconda2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-_F8tjf/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" bdist_wheel -d /tmp/tmpdmHbg4pip-wheel- --python-tag cp27: R version 3.2.2 (2015-08-14) -- "Fire Safety" /user/~/Programme/lib64/R/bin/R CMD config --ldflags R was not built as a library /user/~/Programme/lib64/R/bin/R CMD config --cppflags R was not built as a library /tmp/pip-build-_F8tjf/rpy2/setup.py:211: UserWarning: No include specified warnings.warn('No include specified') /tmp/pip-build-_F8tjf/rpy2/setup.py:222: UserWarning: No libraries as -l arguments to the compiler. warnings.warn('No libraries as -l arguments to the compiler.')
running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/init.py -> build/lib.linux-x86_64-2.7/rpy2 creating build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/init.py -> build/lib.linux-x86_64-2.7/rpy2/rlike creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests creating build/lib.linux-x86_64-2.7/rpy2/rinterface copying ./rpy/rinterface/init.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests creating build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/vectors.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/methods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/language.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/packages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/packages_utils.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/robject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/environments.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/constants.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/init.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/conversion.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/functions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects creating build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/init.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/grid.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests creating build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/packages.py -> build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/process_revents.py -> build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/init.py -> build/lib.linux-x86_64-2.7/rpy2/interactive creating build/lib.linux-x86_64-2.7/rpy2/interactive/tests copying ./rpy/interactive/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/interactive/tests creating build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/init.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-2.7/rpy2/ipython creating build/lib.linux-x86_64-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/init.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests running build_clib building 'r_utils' library creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/rpy creating build/temp.linux-x86_64-2.7/rpy/rinterface gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface -c ./rpy/rinterface/r_utils.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o ./rpy/rinterface/r_utils.c:31:22: error: Rdefines.h: そのようなファイルやディレクトリはありません ./rpy/rinterface/r_utils.c:32:31: error: R_ext/Rallocators.h: そのようなファイルやディレクトリはありません ./rpy/rinterface/r_utils.c:33 から include されたファイル中: ./rpy/rinterface/r_utils.h:5:22: error: Rversion.h: そのようなファイルやディレクトリはありません In file included from ./rpy/rinterface/r_utils.c:33: ./rpy/rinterface/r_utils.h:7: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_serialize’ ./rpy/rinterface/r_utils.h:8: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_unserialize’ ./rpy/rinterface/r_utils.h:9: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_remove’ ./rpy/rinterface/r_utils.h:11: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_list_attr’ ./rpy/rinterface/r_utils.h:13: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_lang2str’ ./rpy/rinterface/r_utils.h:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘externallymanaged_vector’ ./rpy/rinterface/r_utils.h:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_newenv’ ./rpy/rinterface/r_utils.h:27: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_findfun’ ./rpy/rinterface/r_utils.c:59: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_findfun’ ./rpy/rinterface/r_utils.c:86: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_serialize’ ./rpy/rinterface/r_utils.c:110: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_unserialize’ ./rpy/rinterface/r_utils.c:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_list_attr’ ./rpy/rinterface/r_utils.c:153: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_remove’ ./rpy/rinterface/r_utils.c:169: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_newenv’ ./rpy/rinterface/r_utils.c:186: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘rpy2_lang2str’ ./rpy/rinterface/rutils.c:219: error: expected ‘)’ before ‘’ token ./rpy/rinterface/rutils.c:225: error: expected ‘)’ before ‘’ token ./rpy/rinterface/r_utils.c:231: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘attribute’ before ‘externallymanaged_vector’ error: command 'gcc' failed with exit status 1
Failed building wheel for rpy2 Running setup.py clean for rpy2 Running setup.py bdist_wheel for ruffus ... done Stored in directory: /user~/.cache/pip/wheels/c5/1e/39/ed1694a501078a2c4e8cfdbc3d5e68d9e0febbdb39487b8819 Running setup.py bdist_wheel for weblogo ... done Stored in directory: /user/~/.cache/pip/wheels/33/57/8a/792970ecaeab597e0f0d6d194ebaa4baeba667b766f8764de0 Running setup.py bdist_wheel for ggplot ... done Stored in directory: /user/~/.cache/pip/wheels/e9/67/80/a2ce27ba095d1041f3d412f201587d32181ffe97b78359debf Running setup.py bdist_wheel for pybedtools ... done Stored in directory: /user/~/.cache/pip/wheels/77/a0/35/2254abad3268d1a8176665ac46d0647c78c6bba92faec586b8 Running setup.py bdist_wheel for web.py ... done Stored in directory: /user/~/.cache/pip/wheels/53/55/50/a3c9f9cd6f4d55de2eb651ee79392478785f5c4b29727db3f5 Running setup.py bdist_wheel for matplotlib-venn ... done Stored in directory: /user/~/.cache/pip/wheels/09/a6/fe/6c1f803eb98bbf718c8033ae259b89b6d69140bb84ab75de3d Running setup.py bdist_wheel for isodate ... done Stored in directory: /user/~/.cache/pip/wheels/61/c0/d2/6b4a10c222ba9261ab9872a8f05d471652962284e8c677e5e7 Running setup.py bdist_wheel for SPARQLWrapper ... done Stored in directory: /user/~/.cache/pip/wheels/50/fe/25/be6e98daa4f576494df2a18d5e86a182e3d7e0735d062cc984 Running setup.py bdist_wheel for html5lib ... done Stored in directory: /user/~/.cache/pip/wheels/6f/85/6c/56b8e1292c6214c4eb73b9dda50f53e8e977bf65989373c962 Running setup.py bdist_wheel for keepalive ... done Stored in directory: /user/~/.cache/pip/wheels/16/4f/c1/121ddff67b131a371b66d682feefac055fbdbb9569bfde5c51 Successfully built cgat MySQL-python alignlib-lite biopython rdflib psycopg2 ruffus weblogo ggplot pybedtools web.py matplotlib-venn isodate SPARQLWrapper html5lib keepalive Failed to build rpy2 Installing collected packages: MySQL-python, alignlib-lite, biopython, isodate, keepalive, SPARQLWrapper, html5lib, rdflib, psycopg2, rpy2, ruffus, weblogo, brewer2mpl, ggplot, pybedtools, web.py, matplotlib-venn, cgat Running setup.py install for rpy2 ... error Complete output from command /user/ifrec/junhuang/anaconda2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-_F8tjf/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-lnJdKI-record/install-record.txt --single-version-externally-managed --compile: R version 3.2.2 (2015-08-14) -- "Fire Safety" /user/~/Programme/lib64/R/bin/R CMD config --ldflags R was not built as a library /user/~/Programme/lib64/R/bin/R CMD config --cppflags R was not built as a library /tmp/pip-build-_F8tjf/rpy2/setup.py:211: UserWarning: No include specified warnings.warn('No include specified') /tmp/pip-build-_F8tjf/rpy2/setup.py:222: UserWarning: No libraries as -l arguments to the compiler. warnings.warn('No libraries as -l arguments to the compiler.')
Command "/user/~/anaconda2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-_F8tjf/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-lnJdKI-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-_F8tjf/rpy2/
Could anyone suggest how to resolve this issue? I am a sophisticated bioinformatician,so this might be a dumb question.