Error: no package called ‘dada2’ in Qiime2.2017.2

I have installed the newer qiime2 2017.2 based on the manual. Howerver, when I run the qiime dada2 denoise-single command, an error was throwed:

Command: run_dada_single.R /tmp/qiime2-archive-2898ww0a/26bd94e3-c63e-4208-a60c-6a7e4b42dd7c/data /tmp/tmpdwnq7bkj/output.tsv.biom /tmp/tmpdwnq7bkj 100 0 2.0 2 1 1000000

R version 3.3.2 (2016-10-31)
Error in library(dada2) : there is no package called ‘dada2’
Execution halted

The dada2 library couldn’t be find in R 3.3.2, but I have installed the q2-dada2 module. And I also run the command qiime dev refresh-cache, it’s useless for me. Do I need open the R and install the dada2 library from biocLite?

Any help would be appreciated. Thank you!

My conda env list was as follows:

biom-format               2.1.5                    py35_3    qiime2
bokeh                     0.12.4                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bzip2                     1.0.6                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cachecontrol              0.11.7                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cairo                     1.14.8                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
click                     6.7                      py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
curl                      7.52.1                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cycler                    0.10.0                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dbus                      1.10.10                       0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
decorator                 4.0.11                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
emperor                   1.0.0beta5               py35_2    conda-forge
entrypoints               0.2.2                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
expat                     2.1.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
fasttree                  2.1.8                         0    biocore
fontconfig                2.12.1                        3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
freetype                  2.5.5                         2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
future                    0.16.0                   py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
glib                      2.50.2                        1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gsl                       2.2.1                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gst-plugins-base          1.8.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gstreamer                 1.8.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
h5py                      2.6.0               np111py35_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
harfbuzz                  0.9.39                        2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
hdf5                      1.8.17                        1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
icu                       54.1                          0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ijson                     2.3                      py35_0    qiime2
ipykernel                 4.5.2                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython                   5.1.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython_genutils          0.1.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipywidgets                5.2.2                    py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jbig                      2.1                           0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jinja2                    2.9.4                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jpeg                      9b                            0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jsonschema                2.5.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_client            4.4.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_core              4.2.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libffi                    3.2.1                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libgcc                    5.2.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libgfortran               3.0.0                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libiconv                  1.14                          0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libpng                    1.6.27                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libsodium                 1.0.10                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libtiff                   4.0.6                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxcb                    1.12                          1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxml2                   2.9.4                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
lockfile                  0.12.2                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mafft                     7.305                         0    bioconda
markupsafe                0.23                     py35_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
matplotlib                2.0.0               np111py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mistune                   0.7.3                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mkl                       2017.0.1                      0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
natsort                   5.0.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbconvert                 4.2.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbformat                  4.2.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ncurses                   5.9                          10    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nose                      1.3.7                    py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
notebook                  4.3.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
numpy                     1.11.3                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
openssl                   1.0.2k                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pandas                    0.19.2              np111py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pango                     1.40.3                        1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
path.py                   10.0                     py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
patsy                     0.4.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pcre                      8.39                          1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pexpect                   4.2.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pickleshare               0.7.4                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pip                       9.0.1                    py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pixman                    0.34.0                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
prompt_toolkit            1.0.9                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
psutil                    5.1.2                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ptyprocess                0.5.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pygments                  2.1.3                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyparsing                 2.1.4                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyqt                      5.6.0                    py35_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python                    3.5.2                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python-dateutil           2.6.0                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pytz                      2016.10                  py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyyaml                    3.12                     py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyzmq                     16.0.2                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
q2-alignment              2017.2.0                 py35_0    qiime2
q2-composition            2017.2.0                 py35_0    qiime2
q2-dada2                  2017.2.0           py35r3.3.2_0    qiime2
q2-demux                  2017.2.0                 py35_0    qiime2
q2-diversity              2017.2.0                 py35_0    qiime2
q2-emperor                2017.2.0                 py35_0    qiime2
q2-feature-classifier     2017.2.0                 py35_0    qiime2
q2-feature-table          2017.2.0                 py35_0    qiime2
q2-phylogeny              2017.2.0                 py35_0    qiime2
q2-taxa                   2017.2.0                 py35_0    qiime2
q2-types                  2017.2.0                 py35_0    qiime2
q2cli                     2017.2.0                 py35_0    qiime2
q2templates               2017.2.0                 py35_0    qiime2
qiime2                    2017.2.0                 py35_0    qiime2
qt                        5.6.2                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
r                         3.3.2                  r3.3.2_0    r
r-base                    3.3.2                         1    r
r-boot                    1.3_18                 r3.3.2_0    r
r-class                   7.3_14                 r3.3.2_0    r
r-cluster                 2.0.5                  r3.3.2_0    r
r-codetools               0.2_15                 r3.3.2_0    r
r-foreign                 0.8_67                 r3.3.2_0    r
r-kernsmooth              2.23_15                r3.3.2_0    r
r-lattice                 0.20_34                r3.3.2_0    r
r-mass                    7.3_45                 r3.3.2_0    r
r-matrix                  1.2_7.1                r3.3.2_0    r
r-mgcv                    1.8_16                 r3.3.2_0    r
r-nlme                    3.1_128                r3.3.2_0    r
r-nnet                    7.3_12                 r3.3.2_0    r
r-recommended             3.3.2                  r3.3.2_0    r
r-rpart                   4.1_10                 r3.3.2_0    r
r-spatial                 7.3_11                 r3.3.2_0    r
r-survival                2.40_1                 r3.3.2_0    r
readline                  6.2                           2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
requests                  2.12.4                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scikit-bio                0.5.1               np111py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scikit-learn              0.18.1              np111py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scipy                     0.18.1              np111py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
seaborn                   0.7.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
setuptools                27.2.0                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
simplegeneric             0.8.1                    py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sip                       4.18                     py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
six                       1.10.0                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sqlite                    3.13.0                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
statsmodels               0.6.1               np111py35_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
terminado                 0.6                      py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tk                        8.5.18                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tornado                   4.4.2                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
traitlets                 4.3.1                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tzlocal                   1.3                      py35_0    qiime2
wcwidth                   0.1.7                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wheel                     0.29.0                   py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
widgetsnbextension        1.2.6                    py35_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xz                        5.2.2                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
yaml                      0.1.6                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zeromq                    4.1.5                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zlib                      1.2.8                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free

Hi @Yujun,

Do I need open the R and install the dada2 library from biocLite?

Yes! Take a look at the last section in the installation document, there is a one-line command listed there to install dada2.

The dada2 library couldn’t be find in R 3.3.2, but I have installed the q2-dada2 module.

q2-dada2 is a thin wrapper around dada2, which is where the actual functionality is implemented. Right now we have to include the extra step of installing dada2 separately (what I linked to above) due to some upstream packaging and distribution problems. We have an issue open to fix this when the upstream problems are sorted out. Thanks!

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Thank you very much. I was to careless when reading the installation document. After I installed the dada2 library in R, the error has been fixed.

2 Likes