Notebook

In [1]:

pwd

Out[1]:

u'/root/jupyter_nbs'

In [2]:

cd /root

/root

In [3]:

ls

data/  jupyter_nbs/  miniconda2/  owl_home/  owl_web/

In [1]:

pwd

Out[1]:

u'/gitrepos/LabDocs/jupyter_nbs/sam'

In [2]:

cd /gitrepos/LabDocs/

/gitrepos/LabDocs

In [3]:

ls

CONTRIBUTING.md             OlyO_Master.tsv          labinventory_qrcode.png
DMPseq.md                   OpenScienceResources.md  manuscripts/
DataSharePlan.md            PrimerDatabase.tab       nb/
GradeScale.txt              Proposal_database.md     pd-position-description.md
Lab_Inventory.csv           README.md                protocols/
Lab_Software.md             Roberts_SB_Tenure_2.pdf  slidedecks/
Next_Gen_Seq_Libraries.tsv  Roberts_cv-Chew.md       templates/
Nightingales-master.csv     code/                    web/
Nightingales.tsv            jupyter_nbs/

In [4]:

cd ..

/gitrepos

In [5]:

ls

2bRAD_GATK/  LabDocs/

In [6]:

cd 2bRAD_GATK/

/gitrepos/2bRAD_GATK

In [7]:

ls

2bRAD_GATK_scripts_manual.pdf      launcher_creator.py*
2bRAD_bowtie2_launch.pl*           mix_illumina_qpcr.R
2bRAD_gatk_README.txt              ngs_concat.pl*
2bRAD_protocol_mar31_2016.pdf      picogreen.R
2bRAD_trim_launch.pl*              recalibrateSNPs_gatk.pl*
2bRAD_trim_launch_dedup.pl*        recalibrate_SNP.tranches.pdf
2bRAD_trim_launch_dedup2.pl        removeBayescanOutliers.pl*
GetHighQualVcfs.py                 repMatchStats.pl*
README.md                          replicatesMatch.pl*
admixturePlotting.R                retabvcf.pl*
alleleCounts.pl*                   runRepsStructure.pl*
analyzeLD.R                        thinner.pl*
concatFasta.pl*                    trim2bRAD.pl*
dna.mixing.R                       trim2bRAD_2barcodes.pl*
fastStructurePlotting.R            trim2bRAD_2barcodes_dedup.pl*
fastStructurePlotting_functions.R  trim2bRAD_2barcodes_dedup2.pl
filterStats_gatk.pl*               vcf2dadi.pl*
genomeScanPlots.R                  vcf2dadi2.pl*
hetfilter.pl*                      vcf2fasta_ref.pl*
illumina_mix_data.csv              vcf2map.pl*

In [8]:

%%R
all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

ERROR:root:Cell magic `%%R` not found.

In [9]:

%load_ext rpy2.ipython

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-9-691c6d73b073> in <module>()
----> 1 get_ipython().magic(u'load_ext rpy2.ipython')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
   2156         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2157         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158         return self.run_line_magic(magic_name, magic_arg_s)
   2159 
   2160     #-------------------------------------------------------------------------

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
   2077                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2078             with self.builtin_trap:
-> 2079                 result = fn(*args,**kwargs)
   2080             return result
   2081 

<decorator-gen-62> in load_ext(self, module_str)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc in load_ext(self, module_str)
     35         if not module_str:
     36             raise UsageError('Missing module name.')
---> 37         res = self.shell.extension_manager.load_extension(module_str)
     38 
     39         if res == 'already loaded':

/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     81             if module_str not in sys.modules:
     82                 with prepended_to_syspath(self.ipython_extension_dir):
---> 83                     __import__(module_str)
     84             mod = sys.modules[module_str]
     85             if self._call_load_ipython_extension(mod):

ImportError: No module named rpy2.ipython

In [10]:

%load_ext rpy2

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-10-c317c5300f0c> in <module>()
----> 1 get_ipython().magic(u'load_ext rpy2')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
   2156         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2157         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158         return self.run_line_magic(magic_name, magic_arg_s)
   2159 
   2160     #-------------------------------------------------------------------------

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
   2077                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2078             with self.builtin_trap:
-> 2079                 result = fn(*args,**kwargs)
   2080             return result
   2081 

<decorator-gen-62> in load_ext(self, module_str)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc in load_ext(self, module_str)
     35         if not module_str:
     36             raise UsageError('Missing module name.')
---> 37         res = self.shell.extension_manager.load_extension(module_str)
     38 
     39         if res == 'already loaded':

/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     81             if module_str not in sys.modules:
     82                 with prepended_to_syspath(self.ipython_extension_dir):
---> 83                     __import__(module_str)
     84             mod = sys.modules[module_str]
     85             if self._call_load_ipython_extension(mod):

ImportError: No module named rpy2

In [11]:

%load_ext rpy2.interactive.ipython

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-11-d5ba4dbf60b7> in <module>()
----> 1 get_ipython().magic(u'load_ext rpy2.interactive.ipython')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
   2156         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2157         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158         return self.run_line_magic(magic_name, magic_arg_s)
   2159 
   2160     #-------------------------------------------------------------------------

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
   2077                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2078             with self.builtin_trap:
-> 2079                 result = fn(*args,**kwargs)
   2080             return result
   2081 

<decorator-gen-62> in load_ext(self, module_str)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc in load_ext(self, module_str)
     35         if not module_str:
     36             raise UsageError('Missing module name.')
---> 37         res = self.shell.extension_manager.load_extension(module_str)
     38 
     39         if res == 'already loaded':

/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     81             if module_str not in sys.modules:
     82                 with prepended_to_syspath(self.ipython_extension_dir):
---> 83                     __import__(module_str)
     84             mod = sys.modules[module_str]
     85             if self._call_load_ipython_extension(mod):

ImportError: No module named rpy2.interactive.ipython

In [12]:

%load_ext rmagic

/root/miniconda2/lib/python2.7/site-packages/IPython/extensions/rmagic.py:11: UserWarning: The rmagic extension in IPython has moved to `rpy2.ipython`, please see `rpy2` documentation.
  warnings.warn("The rmagic extension in IPython has moved to "

In [13]:

pip install rpy2

  File "<ipython-input-13-75b8616e5642>", line 1
    pip install rpy2
              ^
SyntaxError: invalid syntax

In [14]:

python pip install rpy2

  File "<ipython-input-14-2da0e9dd9008>", line 1
    python pip install rpy2
             ^
SyntaxError: invalid syntax

In [15]:

%%bash
which pip

/root/miniconda2/bin/pip

In [16]:

%%bash
pip install rpy2

Collecting rpy2
  Downloading rpy2-2.8.4.tar.gz (183kB)
Requirement already satisfied (use --upgrade to upgrade): six in /root/miniconda2/lib/python2.7/site-packages (from rpy2)
Requirement already satisfied (use --upgrade to upgrade): singledispatch in /root/miniconda2/lib/python2.7/site-packages (from rpy2)
Building wheels for collected packages: rpy2
  Running setup.py bdist_wheel for rpy2: started
  Running setup.py bdist_wheel for rpy2: finished with status 'done'
  Stored in directory: /root/.cache/pip/wheels/63/61/2e/3f71937be6d9efa37641143e18d76224f62a5128cb6fca926f
Successfully built rpy2
Installing collected packages: rpy2
Successfully installed rpy2-2.8.4

You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

In [17]:

%load_ext rpy2.ipython

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-17-691c6d73b073> in <module>()
----> 1 get_ipython().magic(u'load_ext rpy2.ipython')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
   2156         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2157         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158         return self.run_line_magic(magic_name, magic_arg_s)
   2159 
   2160     #-------------------------------------------------------------------------

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
   2077                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2078             with self.builtin_trap:
-> 2079                 result = fn(*args,**kwargs)
   2080             return result
   2081 

<decorator-gen-62> in load_ext(self, module_str)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc in load_ext(self, module_str)
     35         if not module_str:
     36             raise UsageError('Missing module name.')
---> 37         res = self.shell.extension_manager.load_extension(module_str)
     38 
     39         if res == 'already loaded':

/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     81             if module_str not in sys.modules:
     82                 with prepended_to_syspath(self.ipython_extension_dir):
---> 83                     __import__(module_str)
     84             mod = sys.modules[module_str]
     85             if self._call_load_ipython_extension(mod):

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/__init__.py in <module>()
----> 1 from .rmagic import load_ipython_extension

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.py in <module>()
     50 # numpy and rpy2 imports
     51 
---> 52 import rpy2.rinterface as ri
     53 import rpy2.robjects as ro
     54 import rpy2.robjects.packages as rpacks

/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py in <module>()
     90 del(os)
     91 
---> 92 from rpy2.rinterface._rinterface import (baseenv,
     93                                          emptyenv,
     94                                          endr,

ImportError: /root/miniconda2/lib/libreadline.so.6: undefined symbol: PC

In [18]:

%%bash
conda install rpy2

Fetching package metadata ...........
Solving package specifications: .


PackageNotFoundError: Package not found: '' Dependency missing in current linux-64 channels: 
  - rpy2 -> r 3.3.1*

You can search for packages on anaconda.org with

    anaconda search -t conda r

In [19]:

%%bash
Rscript all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

bash: line 1: syntax error near unexpected token `('
bash: line 1: `Rscript all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)'

In [20]:

%%bash
R /usr/local/bin/R

bash: line 1: syntax error near unexpected token `('
bash: line 1: `R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)'

In [21]:

%%bash
which R

/usr/local/bin/R

In [22]:

%%bash
/usr/local/bin/R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

bash: line 1: syntax error near unexpected token `('
bash: line 1: `/usr/local/bin/R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)'

In [23]:

R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

  File "<ipython-input-23-55bcf82a14a4>", line 1
    R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)
            ^
SyntaxError: invalid syntax

In [24]:

%%bash
apt-get install rpy2

Reading package lists...
Building dependency tree...
Reading state information...

E: Unable to locate package rpy2

In [25]:

conda install -c r rpy2=2.8.2

  File "<ipython-input-25-57d396b50b13>", line 1
    conda install -c r rpy2=2.8.2
                ^
SyntaxError: invalid syntax

In [26]:

%%bash
conda install -c r rpy2=2.8.2

Fetching package metadata .............
Solving package specifications: .


PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: 
  - rpy2 2.8.2*

You can search for packages on anaconda.org with

    anaconda search -t conda rpy2

In [27]:

%%bash
conda install -c bioconda rpy2=2.7.8

Fetching package metadata ...........
Solving package specifications: .


PackageNotFoundError: Package not found: '' Dependency missing in current linux-64 channels: 
  - rpy2 2.7.8* -> r 3.3.1*

You can search for packages on anaconda.org with

    anaconda search -t conda r

In [28]:

%R all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

ERROR:root:Line magic function `%R` not found.

In [29]:

%install_ext rmagic

ERROR:root:Line magic function `%install_ext` not found.

In [1]:

%%bash
anaconda search -t conda rpy2

Run 'anaconda show <USER/PACKAGE>' to get more details:
Packages:
     Name                      |  Version | Package Types   | Platforms      
     ------------------------- |   ------ | --------------- | ---------------
     Richarizardd/rpy2         |    2.5.6 | conda           | win-64         
                                          : Python interface to the R language (embedded R)
     andywocky/rpy2            |    2.5.6 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     asmeurer/rpy2             |    2.7.0 | conda           | linux-64, linux-32, osx-64
                                          : Python interface to the R language (embedded R)
     bce/rpy2                  |          | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     bioconda/rpy2             |    2.7.8 | conda           | linux-64, osx-64
                                          : Python interface to the R language (embedded R)
     cgat/rpy2                 |    2.6.1 | conda           | linux-64       
     cgat/rpy2-lite            |    2.6.1 | conda           | linux-64       
     desilinguist/rpy2         |    2.5.4 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     equipoise/rpy2            |    2.3.9 | conda           | win-64         
     hisanor/rpy2              |    2.7.9 | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     ijstokes/rpy2             |    2.8.3 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     joshadel/rpy2             |    2.3.9 | conda           | win-64         
     jrderuiter/rpy2           |    2.5.3 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     kundajelab/rpy2           |    2.7.0 | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     leriomaggio/rpy2          |    2.4.4 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     omgarcia/rpy2             |    2.8.3 | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     pmlandwehr/rpy2           |    2.8.0 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     r-old/rpy2                |    2.4.2 | conda           | linux-64       
     r/rpy2                    |    2.8.2 | conda           | linux-64, win-32, win-64, linux-32, osx-64
     ralexx/rpy2               |    2.7.6 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
     rdonnelly/rpy2            |          | conda           | linux-64, win-64
     rmcgibbo/rpy2             |    2.4.2 | conda           | linux-64       
     rmkoesterer/rpy2          |    2.7.4 | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     ryan/rpy2                 |    2.5.6 | conda           | linux-64       
                                          : Python interface to the R language (embedded R)
     sebp/rpy2                 |    2.8.3 | conda           | linux-64, osx-64
                                          : Python interface to the R language (embedded R)
     trent/rpy2                |    2.3.8 | conda           | linux-64       
                                          : http://rpy.sourceforge.net/index.html
     xbsd/rpy2                 |    2.4.4 | conda           | osx-64         
                                          : Python interface to the R language (embedded R)
Found 27 packages

Using Anaconda API: https://api.anaconda.org

In [2]:

%%bash
conda install -c r rpy2

Fetching package metadata .............
Solving package specifications: ..........

Package plan for installation in environment /root/miniconda2:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.6                |                3          83 KB
    jbig-2.1                   |                0          29 KB
    ncurses-5.9                |               10         904 KB
    xz-5.2.2                   |                0         644 KB
    curl-7.45.0                |                2         684 KB  bioconda
    gsl-2.2.1                  |                0         7.7 MB
    libtiff-4.0.6              |                2         1.5 MB
    pcre-8.39                  |                0         553 KB
    conda-4.2.13               |           py27_0         391 KB
    harfbuzz-0.9.39            |                1         1.1 MB
    pango-1.39.0               |                1         668 KB
    r-base-3.3.1               |                5        21.7 MB  r
    r-boot-1.3_18              |         r3.3.1_0         578 KB  r
    r-cluster-2.0.4            |         r3.3.1_0         470 KB  r
    r-codetools-0.2_14         |         r3.3.1_0          45 KB  r
    r-foreign-0.8_66           |         r3.3.1_0         220 KB  r
    r-kernsmooth-2.23_15       |         r3.3.1_0          84 KB  r
    r-lattice-0.20_33          |         r3.3.1_0         699 KB  r
    r-mass-7.3_45              |         r3.3.1_0         1.0 MB  r
    r-nnet-7.3_12              |         r3.3.1_0          99 KB  r
    r-rpart-4.1_10             |         r3.3.1_0         863 KB  r
    r-spatial-7.3_11           |         r3.3.1_0         123 KB  r
    r-class-7.3_14             |         r3.3.1_0          82 KB  r
    r-matrix-1.2_6             |         r3.3.1_0         3.1 MB  r
    r-nlme-3.1_128             |         r3.3.1_0         2.0 MB  r
    r-mgcv-1.8_12              |         r3.3.1_0         1.9 MB  r
    r-survival-2.39_4          |         r3.3.1_0         4.5 MB  r
    r-3.3.1                    |         r3.3.1_0          584 B  r
    r-recommended-3.3.1        |         r3.3.1_0          758 B  r
    rpy2-2.8.1                 |     py27r3.3.1_1         365 KB  r
    ------------------------------------------------------------
                                           Total:        51.8 MB

The following NEW packages will be INSTALLED:

    bzip2:         1.0.6-3                    
    curl:          7.45.0-2           bioconda
    gsl:           2.2.1-0                    
    harfbuzz:      0.9.39-1                   
    jbig:          2.1-0                      
    libtiff:       4.0.6-2                    
    ncurses:       5.9-10                     
    pango:         1.39.0-1                   
    pcre:          8.39-0                     
    r:             3.3.1-r3.3.1_0     r       
    r-base:        3.3.1-5            r       
    r-boot:        1.3_18-r3.3.1_0    r       
    r-class:       7.3_14-r3.3.1_0    r       
    r-cluster:     2.0.4-r3.3.1_0     r       
    r-codetools:   0.2_14-r3.3.1_0    r       
    r-foreign:     0.8_66-r3.3.1_0    r       
    r-kernsmooth:  2.23_15-r3.3.1_0   r       
    r-lattice:     0.20_33-r3.3.1_0   r       
    r-mass:        7.3_45-r3.3.1_0    r       
    r-matrix:      1.2_6-r3.3.1_0     r       
    r-mgcv:        1.8_12-r3.3.1_0    r       
    r-nlme:        3.1_128-r3.3.1_0   r       
    r-nnet:        7.3_12-r3.3.1_0    r       
    r-recommended: 3.3.1-r3.3.1_0     r       
    r-rpart:       4.1_10-r3.3.1_0    r       
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    rpy2:          2.8.1-py27r3.3.1_1 r       
    xz:            5.2.2-0                    

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In [3]:

%%R
all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

ERROR:root:Cell magic `%%R` not found.

In [4]:

%load_ext rpy2.ipython

In [5]:

%%R
all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)

/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width,  : 
  unable to start device PNG

  warnings.warn(x, RRuntimeWarning)
/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: In addition: 
  warnings.warn(x, RRuntimeWarning)
/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Warning message:

  warnings.warn(x, RRuntimeWarning)
/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: In (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  warnings.warn(x, RRuntimeWarning)
/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: 
 
  warnings.warn(x, RRuntimeWarning)
/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning:  unable to open connection to X11 display ''

  warnings.warn(x, RRuntimeWarning)

---------------------------------------------------------------------------
RRuntimeError                             Traceback (most recent call last)
<ipython-input-5-8a32374b2bdd> in <module>()
----> 1 get_ipython().run_cell_magic(u'R', u'', u'all_fst <- read.table("/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst",header = TRUE)')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_cell_magic(self, magic_name, line, cell)
   2113             magic_arg_s = self.var_expand(line, stack_depth)
   2114             with self.builtin_trap:
-> 2115                 result = fn(magic_arg_s, cell)
   2116             return result
   2117 

<decorator-gen-126> in R(self, line, cell, local_ns)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc in R(self, line, cell, local_ns)
    663                     ro.r.assign(input, localconverter.py2ri(val))
    664 
--> 665         tmpd = self.setup_graphics(args)
    666 
    667         text_output = ''

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc in setup_graphics(self, args)
    413                 # Note: that %% is to pass into R for interpolation there
    414                 ro.r.png("%s/Rplots%%03d.png" % tmpd_fix_slashes,
--> 415                         **argdict)
    416             elif self.device == 'svg':
    417                 self.cairo.CairoSVG("%s/Rplot.svg" % tmpd_fix_slashes,

/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs)
    176                 v = kwargs.pop(k)
    177                 kwargs[r_k] = v
--> 178         return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
    179 
    180 pattern_link = re.compile(r'\\link\{(.+?)\}')

/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs)
    104         for k, v in kwargs.items():
    105             new_kwargs[k] = conversion.py2ri(v)
--> 106         res = super(Function, self).__call__(*new_args, **new_kwargs)
    107         res = conversion.ri2ro(res)
    108         return res

RRuntimeError: Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width,  : 
  unable to start device PNG

In [6]:

%%R Running capabilities();

UsageError: %%R is a cell magic, but the cell body is empty. Did you mean the line magic %R (single %)?

In [7]:

%%R
Running capabilities();

---------------------------------------------------------------------------
RRuntimeError                             Traceback (most recent call last)
<ipython-input-7-32328842bf65> in <module>()
----> 1 get_ipython().run_cell_magic(u'R', u'', u'Running capabilities();')

/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_cell_magic(self, magic_name, line, cell)
   2113             magic_arg_s = self.var_expand(line, stack_depth)
   2114             with self.builtin_trap:
-> 2115                 result = fn(magic_arg_s, cell)
   2116             return result
   2117 

<decorator-gen-126> in R(self, line, cell, local_ns)

/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc in R(self, line, cell, local_ns)
    663                     ro.r.assign(input, localconverter.py2ri(val))
    664 
--> 665         tmpd = self.setup_graphics(args)
    666 
    667         text_output = ''

/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc in setup_graphics(self, args)
    413                 # Note: that %% is to pass into R for interpolation there
    414                 ro.r.png("%s/Rplots%%03d.png" % tmpd_fix_slashes,
--> 415                         **argdict)
    416             elif self.device == 'svg':
    417                 self.cairo.CairoSVG("%s/Rplot.svg" % tmpd_fix_slashes,

/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs)
    176                 v = kwargs.pop(k)
    177                 kwargs[r_k] = v
--> 178         return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
    179 
    180 pattern_link = re.compile(r'\\link\{(.+?)\}')

/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs)
    104         for k, v in kwargs.items():
    105             new_kwargs[k] = conversion.py2ri(v)
--> 106         res = super(Function, self).__call__(*new_args, **new_kwargs)
    107         res = conversion.ri2ro(res)
    108         return res

RRuntimeError: Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width,  : 
  unable to start device PNG

In [ ]: