search

ContinuumIO / anaconda-issues

Anaconda issue tracking
647 stars 220 forks source link

Microsoft R Open produces jagged plots #10280

Closed raivivek closed 5 years ago

raivivek commented 5 years ago

For some reason, it appears that when using a MRO-3.5.1 Kernel with Jupyterlab (also otherwise) produces PNG plots that have jagged output (likely no anti-aliasing). When I switch to base R-3.3.3 version, everything looks great!

I have cairo functionality and everything else I could find on internet appears to be as expected, so I'm not sure what the problem is. I installed MRO through Anaconda.

>sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /home/vivekrai/.anaconda3/envs/mro_env/lib/R/lib/libRblas.so
LAPACK: /home/vivekrai/.anaconda3/envs/mro_env/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RevoUtils_11.0.1     RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
[1] compiler_3.5.1

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE        TRUE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE

For base R:

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Example outputs:

image image

Steps to Reproduce

  1. Install MRO-3.5.1 using Anaconda
  2. plot(iris)
Anaconda or Miniconda version:
↪ conda --version
conda 4.5.11
Operating System:
conda info
↪ conda info

     active environment : mro_env
    active env location : /home/vivekrai/.anaconda3/envs/mro_env
            shell level : 1
       user config file : /home/vivekrai/.condarc
 populated config files : /home/vivekrai/.condarc
          conda version : 4.5.11
    conda-build version : 3.10.9
         python version : 3.6.5.final.0
       base environment : /home/vivekrai/.anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/vivekrai/.anaconda3/pkgs
                          /home/vivekrai/.conda/pkgs
       envs directories : /home/vivekrai/.anaconda3/envs
                          /home/vivekrai/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.18.4 CPython/3.6.5 Linux/4.9.0-6-amd64 debian/9 glibc/2.24
                UID:GID : 99538288:2308692
             netrc file : None
           offline mode : False
conda list --show-channel-urls
↪ conda list --show-channel-urls
# packages in environment at /home/vivekrai/.anaconda3/envs/mro_env:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0                     mro_2    defaults
backcall                  0.1.0                      py_0    conda-forge
binutils_impl_linux-64    2.31.1               h6176602_1    defaults
binutils_linux-64         2.31.1               h6176602_3    defaults
bleach                    3.0.2                      py_0    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
cairo                     1.14.12              h8948797_3    defaults
certifi                   2018.10.15            py37_1000    conda-forge
curl                      7.61.1               h74213dd_2    conda-forge
decorator                 4.3.0                      py_0    conda-forge
entrypoints               0.2.3                 py37_1002    conda-forge
font-ttf-dejavu-sans-mono 2.37                 h6964260_0    anaconda
font-ttf-inconsolata      2.001                hcb22688_0    anaconda
font-ttf-source-code-pro  2.030                h7457263_0    anaconda
font-ttf-ubuntu           0.83                 h8b1ccd4_0    anaconda
fontconfig                2.13.0               h9420a91_0    defaults
fonts-anaconda            1                    h8fa9717_0    anaconda
fonts-continuum           1                             0    anaconda
freetype                  2.9.1                h6debe1e_4    conda-forge
fribidi                   1.0.5                h7b6447c_0    defaults
gcc_impl_linux-64         7.3.0                habb00fd_1    defaults
gcc_linux-64              7.3.0                h553295d_3    defaults
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1    defaults
gfortran_linux-64         7.3.0                h553295d_3    defaults
glib                      2.56.2               h464dc38_0    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
graphite2                 1.3.12               hfc679d8_1    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    defaults
gxx_linux-64              7.3.0                h553295d_3    defaults
harfbuzz                  1.9.0                h04dbb29_1    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
ipykernel                 5.1.0              pyh24bf2e0_0    conda-forge
ipython                   7.0.1           py37h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.13.1                py37_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
jsonschema                2.6.0                 py37_1002    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
krb5                      1.16.1               hbb41f41_0    conda-forge
lapack                    3.6.1                         1    conda-forge
libcurl                   7.61.1               hbdb9355_2    conda-forge
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc-ng                 8.2.0                hdf63c60_1    defaults
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0    defaults
libiconv                  1.15                 h470a237_3    conda-forge
libpng                    1.6.35               ha92aebf_2    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1    defaults
libtiff                   4.0.9                he6b73bb_2    conda-forge
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
make                      4.2.1             h470a237_1002    conda-forge
markupsafe                1.0              py37h470a237_1    conda-forge
mistune                   0.8.4            py37h470a237_0    conda-forge
mro-base                  3.5.1                         3    defaults
mro-base_impl             3.5.1                h9a62091_0    defaults
mro-basics                3.5.1                         0    defaults
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
notebook                  5.7.0                 py37_1000    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
pandoc                    2.3.1                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.42.4               h049681c_0    defaults
parso                     0.3.1                      py_0    conda-forge
pcre                      8.42                 h439df22_0    defaults
pexpect                   4.6.0                 py37_1000    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pip                       18.1                  py37_1000    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
prometheus_client         0.4.2                      py_0    conda-forge
prompt_toolkit            2.0.6                      py_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                 py37_1000    conda-forge
pygments                  2.2.0                      py_1    conda-forge
python                    3.7.0                h5001a0f_4    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pyzmq                     17.1.2           py37hae99301_1    conda-forge
r-abind                   1.4_5           mro351hf348343_0    defaults
r-assertthat              0.2.0           mro351hf348343_0    defaults
r-backports               1.1.2           mro351hd10c6a6_0    defaults
r-base64enc               0.1_3           mro351hd10c6a6_0    defaults
r-bh                      1.66.0_1        mro351hf348343_0    defaults
r-bindr                   0.1.1           mro351hf348343_0    defaults
r-bindrcpp                0.2.2           mro351hebc1506_0    defaults
r-boot                    1.3_20                 mro351_0    defaults
r-broom                   0.5.0           mro351hf348343_0    defaults
r-cairo                   1.5_9           mro351hd10c6a6_0    defaults
r-callr                   2.0.4           mro351hf348343_0    defaults
r-caret                   6.0_80          mro351hd10c6a6_0    defaults
r-cellranger              1.1.0           mro351hf348343_0    defaults
r-checkpoint              0.4.4                  mro351_0    defaults
r-class                   7.3_14          mro351hd10c6a6_0    defaults
r-cli                     1.0.0           mro351hf348343_0    defaults
r-clipr                   0.4.1           mro351hf348343_0    defaults
r-cluster                 2.0.7_1         mro351hac1494b_0    defaults
r-codetools               0.2_15          mro351hf348343_0    defaults
r-colorspace              1.3_2           mro351hd10c6a6_0    defaults
r-crayon                  1.3.4           mro351hf348343_0    defaults
r-curl                    3.2             mro351hd10c6a6_0    defaults
r-cvst                    0.2_2           mro351hf348343_0    defaults
r-data.table              1.11.4          mro351hd10c6a6_0    defaults
r-dbi                     1.0.0           mro351hf348343_0    defaults
r-dbplyr                  1.2.2           mro351hf348343_0    defaults
r-ddalpha                 1.3.4           mro351h2efac65_0    defaults
r-deoptimr                1.0_8           mro351hf348343_0    defaults
r-deployrrserve           9.0.0                  mro351_0    defaults
r-dichromat               2.0_0           mro351hf348343_0    defaults
r-digest                  0.6.15          mro351hd10c6a6_0    defaults
r-dimred                  0.1.0           mro351hf348343_0    defaults
r-doparallel              1.0.13                 mro351_0    defaults
r-dplyr                   0.7.6           mro351hebc1506_0    defaults
r-drr                     0.0.3           mro351hf348343_0    defaults
r-essentials              3.5.1                  mro351_0    defaults
r-evaluate                0.11            mro351hf348343_0    defaults
r-fansi                   0.2.3           mro351hd10c6a6_0    defaults
r-forcats                 0.3.0           mro351hf348343_0    defaults
r-foreach                 1.5.0                  mro351_0    defaults
r-foreign                 0.8_70                 mro351_0    defaults
r-formatr                 1.5             mro351hf348343_0    defaults
r-geometry                0.3_6           mro351hd10c6a6_0    defaults
r-ggplot2                 3.0.0           mro351hf348343_0    defaults
r-glmnet                  2.0_16          mro351hac1494b_0    defaults
r-glue                    1.3.0           mro351hd10c6a6_0    defaults
r-gower                   0.1.2           mro351hd10c6a6_0    defaults
r-gtable                  0.2.0           mro351hf348343_0    defaults
r-haven                   1.1.2           mro351hebc1506_0    defaults
r-hexbin                  1.27.2          mro351hac1494b_0    defaults
r-highr                   0.7             mro351hf348343_0    defaults
r-hms                     0.4.2           mro351hf348343_0    defaults
r-htmltools               0.3.6           mro351hebc1506_0    defaults
r-htmlwidgets             1.2             mro351hf348343_0    defaults
r-httpuv                  1.4.5           mro351hebc1506_0    defaults
r-httr                    1.3.1           mro351hf348343_0    defaults
r-ipred                   0.9_6           mro351hd10c6a6_0    defaults
r-irdisplay               0.5.0           mro351hf348343_0    defaults
r-irkernel                0.8.11                 mro351_0    defaults
r-iterators               1.0.10          mro351hf348343_0    defaults
r-jsonlite                1.5             mro351hd10c6a6_0    defaults
r-kernlab                 0.9_26          mro351h2efac65_0    defaults
r-kernsmooth              2.23_15         mro351hac1494b_0    defaults
r-knitr                   1.20            mro351hf348343_0    defaults
r-labeling                0.3             mro351hf348343_0    defaults
r-later                   0.7.3           mro351hebc1506_0    defaults
r-lattice                 0.20_35         mro351hd10c6a6_0    defaults
r-lava                    1.6.2           mro351hf348343_0    defaults
r-lazyeval                0.2.1           mro351hd10c6a6_0    defaults
r-lubridate               1.7.4           mro351hebc1506_0    defaults
r-magic                   1.5_8           mro351hf348343_0    defaults
r-magrittr                1.5             mro351hf348343_0    defaults
r-maps                    3.3.0           mro351hd10c6a6_0    defaults
r-markdown                0.8             mro351hd10c6a6_0    defaults
r-mass                    7.3_49                 mro351_0    defaults
r-matrix                  1.2_14          mro351hac1494b_0    defaults
r-mgcv                    1.8_23                 mro351_0    defaults
r-microsoftr              3.5.0.108              mro351_0    defaults
r-mime                    0.5             mro351hd10c6a6_0    defaults
r-modelmetrics            1.1.0           mro351hebc1506_0    defaults
r-modelr                  0.1.2           mro351hf348343_0    defaults
r-munsell                 0.5.0           mro351hf348343_0    defaults
r-nlme                    3.1_137         mro351hac1494b_0    defaults
r-nnet                    7.3_12          mro351hd10c6a6_0    defaults
r-numderiv                2016.8_1        mro351hf348343_0    defaults
r-openssl                 1.0.2           mro351hd10c6a6_0    defaults
r-pbdzmq                  0.3_3           mro351hebc1506_0    defaults
r-pillar                  1.3.0           mro351hf348343_0    defaults
r-pkgconfig               2.0.1           mro351hf348343_0    defaults
r-plogr                   0.2.0           mro351hf348343_0    defaults
r-pls                     2.6_0           mro351hf348343_0    defaults
r-plyr                    1.8.4           mro351hebc1506_0    defaults
r-png                     0.1_7           mro351hd10c6a6_0    defaults
r-praise                  1.0.0           mro351hf348343_0    defaults
r-processx                3.1.0           mro351hebc1506_0    defaults
r-prodlim                 2018.04.18      mro351hebc1506_0    defaults
r-promises                1.0.1           mro351hebc1506_0    defaults
r-purrr                   0.2.5           mro351hd10c6a6_0    defaults
r-quantmod                0.4_13          mro351hf348343_0    defaults
r-r6                      2.2.2           mro351hf348343_0    defaults
r-randomforest            4.6_14          mro351hac1494b_0    defaults
r-rbokeh                  0.6.3                  mro351_0    defaults
r-rcolorbrewer            1.1_2           mro351hf348343_0    defaults
r-rcpp                    0.12.18         mro351hebc1506_0    defaults
r-rcpproll                0.3.0           mro351hebc1506_0    defaults
r-readr                   1.1.1           mro351hebc1506_0    defaults
r-readxl                  1.1.0           mro351hebc1506_0    defaults
r-recipes                 0.1.3           mro351hf348343_0    defaults
r-recommended             3.5.1                  mro351_0    defaults
r-rematch                 1.0.1           mro351hf348343_0    defaults
r-repr                    0.15.0          mro351hf348343_0    defaults
r-reprex                  0.2.0           mro351hf348343_0    defaults
r-reshape2                1.4.3           mro351hebc1506_0    defaults
r-revoioq                 10.0.0                 mro351_0    defaults
r-revomods                11.0.0                 mro351_0    defaults
r-revoutils               11.0.0                 mro351_0    defaults
r-revoutilsmath           11.0.0                 mro351_0    defaults
r-rlang                   0.2.1           mro351hd10c6a6_0    defaults
r-rmarkdown               1.10            mro351hf348343_0    defaults
r-robustbase              0.93_2          mro351hac1494b_0    defaults
r-rpart                   4.1_13          mro351hd10c6a6_0    defaults
r-rprojroot               1.3_2           mro351hf348343_0    defaults
r-rstudioapi              0.7             mro351hf348343_0    defaults
r-runit                   0.4.26                 mro351_0    defaults
r-rvest                   0.3.2           mro351hf348343_0    defaults
r-scales                  0.5.0           mro351hebc1506_0    defaults
r-selectr                 0.4_1           mro351hf348343_0    defaults
r-sfsmisc                 1.1_2           mro351hf348343_0    defaults
r-shiny                   1.1.0           mro351hf348343_0    defaults
r-sourcetools             0.1.7           mro351hebc1506_0    defaults
r-spatial                 7.3_11                 mro351_0    defaults
r-squarem                 2017.10_1       mro351hf348343_0    defaults
r-stringi                 1.2.4           mro351hebc1506_0    defaults
r-stringr                 1.3.1           mro351hf348343_0    defaults
r-survival                2.41_3                 mro351_0    defaults
r-testthat                2.0.0           mro351hebc1506_0    defaults
r-tibble                  1.4.2           mro351hd10c6a6_0    defaults
r-tidyr                   0.8.1           mro351hebc1506_0    defaults
r-tidyselect              0.2.4           mro351hebc1506_0    defaults
r-tidyverse               1.2.1           mro351hf348343_0    defaults
r-timedate                3043.102        mro351hf348343_0    defaults
r-tinytex                 0.6             mro351hf348343_0    defaults
r-ttr                     0.23_3          mro351hac1494b_0    defaults
r-utf8                    1.1.4           mro351hd10c6a6_0    defaults
r-uuid                    0.1_2           mro351hd10c6a6_0    defaults
r-viridislite             0.3.0           mro351hf348343_0    defaults
r-whisker                 0.3_2           mro351hf348343_0    defaults
r-withr                   2.1.2           mro351hf348343_0    defaults
r-xfun                    0.3             mro351hf348343_0    defaults
r-xml2                    1.2.0           mro351hebc1506_0    defaults
r-xtable                  1.8_2           mro351hf348343_0    defaults
r-xts                     0.11_0          mro351hd10c6a6_0    defaults
r-yaml                    2.2.0           mro351hd10c6a6_0    defaults
r-zoo                     1.8_3           mro351hd10c6a6_0    defaults
readline                  7.0                  haf1bffa_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.4.3                   py37_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
six                       1.11.0                py37_1001    conda-forge
sqlite                    3.25.2               hb1c47c0_0    conda-forge
terminado                 0.8.1                 py37_1001    conda-forge
testpath                  0.4.2                 py37_1000    conda-forge
tk                        8.6.8                ha92aebf_0    conda-forge
tornado                   5.1.1            py37h470a237_0    conda-forge
traitlets                 4.3.2                 py37_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.32.1                   py37_0    conda-forge
xorg-font-util            1.3.1                h470a237_1    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.2                h470a237_5    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_6    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge
mingwandroid commented 5 years ago

Closed, this is either a bug in MRO itself (which MS build, not I), or a bug in some of the conda-forge packages you have installed. Please report this to Microsoft and/or conda-forge.

Also please avoid mixing conda-forge and defaults in the same environment. They are incompatible at present.

raivivek commented 5 years ago

@mingwandroid Thanks for the update. I tested another installation without conda-forge packages and the result is same. So it is probably a problem with MRO build itself.