png.dylib version interferes with running dada2

Note:

Please note that this is a followup issue to @Heather_Maughan 's issue HERE.

I am opening a new issue because the above topic/issue has been locked due to inactivity. If the moderators would prefer to unlock the topic, I will gladly delete this one.


Problem

@lzgles and I are trying to run dada2 on a new computer and are running into incompatibility issues between the installed version (54.0.0) and the required/expected version (55.0.0) of r-png/png.dlyib.

Command resulting in error
qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table dada2_table_2 --o-representative-sequences representative_sequences_2 --p-trunc-len-f 220 --p-trunc-len-r 120 --p-trim-left-f 19 --p-trim-left-r 20 --p-n-threads 0 --p-n-reads-learn 1000000 --o-denoising-stats denoising-stats_2.qza --verbose &

stdout/stderr output

(qiime2-2022.8) [email protected] ~/Documents/Soils2 % qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table dada2_table_2 --o-representative-sequences representative_sequences_2 --p-trunc-len-f 220 --p-trunc-len-r 120 --p-trim-left-f 19 --p-trim-left-r 20 --p-n-threads 0 --p-n-reads-learn 1000000 --o-denoising-stats denoising-stats_2.qza --verbose &
[1] 9222
(qiime2-2022.8) [email protected] ~/Documents/Soils2 % Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/forward --input_directory_reverse /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/reverse --output_path /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/output.tsv.biom --output_track /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/track.tsv --filtered_directory /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_f --filtered_directory_reverse /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_r --truncation_length 220 --truncation_length_reverse 120 --trim_left 19 --trim_left_reverse 20 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 0 --learn_min_reads 1000000

R version 4.1.3 (2022-03-10) 
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib':
  dlopen(/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib, 6): Library not loaded: @rpath/libpng16.16.dylib
  Referenced from: /Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib
  Reason: Incompatible library version: png.dylib requires version 55.0.0 or later, but libpng16.16.dylib provides version 54.0.0
Execution halted
Traceback (most recent call last):
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 308, in denoise_paired
    run_commands([cmd])
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
    subprocess.run(cmd, check=True)
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/forward', '--input_directory_reverse', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/reverse', '--output_path', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/output.tsv.biom', '--output_track', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/track.tsv', '--filtered_directory', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_f', '--filtered_directory_reverse', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_r', '--truncation_length', '220', '--truncation_length_reverse', '120', '--trim_left', '19', '--trim_left_reverse', '20', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '0', '--learn_min_reads', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-292>", line 2, in denoise_paired
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 321, in denoise_paired
    raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Plugin error from dada2:

  An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

See above for debug info.

[1]  + exit 1     qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table

Computer and Environment/Session Info

Computer

  • iMac (Retina 5K, 27-inch, 2020)
  • macOS Catalina v 10.15.7
  • 3.6 GHz 10-Core Intel Core i9
  • 128 GB 2667 MHz DDR4

Conda and QIIME versions

Note:

  • miniconda was installed according to the "regular" instructions here.
  • QIIME2 was (natively) installed following the instructions here.
  • homebrew/brew is not used on this machine so there should be no conflicts due to conflicts with different installed versions (as @colinbrislawn suggested might be the case)
(qiime2-2022.8) [email protected] ~ % conda --version
conda 22.11.1
(qiime2-2022.8) [email protected] ~ % qiime --version
q2cli version 2022.8.0
Run `qiime info` for more version details.

conda info

(qiime2-2022.8) [email protected] ~ % conda info

     active environment : qiime2-2022.8
    active env location : /Users/micro/miniconda3/envs/qiime2-2022.8
            shell level : 1
       user config file : /Users/micro/.condarc
 populated config files : /Users/micro/.condarc
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __archspec=1=x86_64
                          __osx=10.15.7=0
                          __unix=0=0
       base environment : /Users/micro/miniconda3  (writable)
      conda av data dir : /Users/micro/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/micro/miniconda3/pkgs
                          /Users/micro/.conda/pkgs
       envs directories : /Users/micro/miniconda3/envs
                          /Users/micro/.conda/envs
               platform : osx-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.12 Darwin/19.6.0 OSX/10.15.7
                UID:GID : 501:20
             netrc file : None
           offline mode : False

qiime (environment) packages

(qiime2-2022.8) [email protected] ~ % conda list
# packages in environment at /Users/micro/miniconda3/envs/qiime2-2022.8:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
asttokens                 2.0.8              pyhd8ed1ab_0    conda-forge
atpublic                  3.0.1              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bibtexparser              1.3.0              pyhd8ed1ab_0    conda-forge
bioconductor-biobase      2.54.0            r41h3be46a4_2    bioconda
bioconductor-biocgenerics 0.40.0            r41hdfd78af_0    bioconda
bioconductor-biocparallel 1.28.3            r41hb890f52_1    bioconda
bioconductor-biostrings   2.62.0            r41h3be46a4_2    bioconda
bioconductor-dada2        1.22.0            r41hb890f52_2    bioconda
bioconductor-delayedarray 0.20.0            r41h3be46a4_2    bioconda
bioconductor-genomeinfodb 1.30.0            r41hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.7             r41hdfd78af_2    bioconda
bioconductor-genomicalignments 1.30.0            r41h3be46a4_2    bioconda
bioconductor-genomicranges 1.46.1            r41h3be46a4_1    bioconda
bioconductor-iranges      2.28.0            r41h3be46a4_2    bioconda
bioconductor-matrixgenerics 1.6.0             r41hdfd78af_0    bioconda
bioconductor-rhtslib      1.26.0            r41h3be46a4_2    bioconda
bioconductor-rsamtools    2.10.0            r41hb890f52_2    bioconda
bioconductor-s4vectors    0.32.3            r41haba8685_0    bioconda
bioconductor-shortread    1.52.0            r41hb890f52_2    bioconda
bioconductor-summarizedexperiment 1.24.0            r41hdfd78af_0    bioconda
bioconductor-xvector      0.34.0            r41h3be46a4_2    bioconda
bioconductor-zlibbioc     1.40.0            r41h3be46a4_2    bioconda
biom-format               2.1.12           py38hbd87e4b_2    conda-forge
blast                     2.12.0               h0370960_3    bioconda
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
bowtie2                   2.4.5            py38h85b03c0_3    bioconda
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py38hef030d1_1005    conda-forge
bwidget                   1.9.14               h694c41f_1    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.6.15.2          h033912b_0    conda-forge
cachecontrol              0.12.11            pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h904041c_1013    conda-forge
cctools_osx-64            973.0.1             h3eff9a4_10    conda-forge
certifi                   2022.6.15.2        pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38hb368cf1_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
clang                     14.0.4               h694c41f_0    conda-forge
clang-14                  14.0.4          default_h55ffa42_0    conda-forge
clang_osx-64              14.0.4               h3a95cd4_2    conda-forge
clangxx                   14.0.4          default_h55ffa42_0    conda-forge
clangxx_osx-64            14.0.4               he1dbc44_2    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
compiler-rt               14.0.4               h7fcd477_0    conda-forge
compiler-rt_osx-64        14.0.4               h6df654d_0    conda-forge
cryptography              37.0.4           py38h0f8513e_0    conda-forge
curl                      7.83.1               h372c54d_0    conda-forge
cutadapt                  4.1              py38h431a6f7_1    bioconda
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.32          py38h4cd09af_1    conda-forge
deblur                    1.1.1              pyhdfd78af_0    bioconda
debugpy                   1.6.3            py38h4cd09af_1    conda-forge
decorator                 4.4.2                      py_0    conda-forge
dendropy                  4.5.2              pyh3252c3a_0    bioconda
dill                      0.3.5.1            pyhd8ed1ab_0    conda-forge
dnaio                     0.9.1            py38h431a6f7_1    bioconda
emperor                   1.0.3            py38h50d1736_0    conda-forge
entrez-direct             16.2                 h193322a_1    bioconda
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.0.0              pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h96cf925_0    conda-forge
fastcluster               1.2.6            py38hec72209_2    conda-forge
fasttree                  2.1.11               hdcdfbac_1    bioconda
flufl.lock                7.1                pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h5bb23bf_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.37.1           py38hef030d1_0    conda-forge
freetype                  2.12.1               h3f81eb7_0    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
future                    0.18.2             pyhd8ed1ab_6    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gfortran_impl_osx-64      9.5.0               h2221f41_25    conda-forge
gfortran_osx-64           9.5.0                h18f7dce_0    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
gneiss                    0.4.6                      py_0    bioconda
graphite2                 1.3.13            h2e338ed_1001    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
h5py                      2.10.0          nompi_py38h9a16e60_106    conda-forge
harfbuzz                  5.1.0                h00bb2c2_0    conda-forge
hdf5                      1.10.6          nompi_hc5d9132_1114    conda-forge
hdmedians                 0.14.2           py38hbd87e4b_3    conda-forge
hmmer                     3.1b2                         3    bioconda
htslib                    1.15.1               hc057d7f_0    bioconda
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
ijson                     3.1.3              pyhd3deb0d_0    conda-forge
importlib-metadata        4.11.4           py38h50d1736_0    conda-forge
importlib_resources       5.9.0              pyhd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
iow                       1.0.5            py38hb139fc8_1    bioconda
ipykernel                 6.15.2             pyh736e0ef_0    conda-forge
ipython                   8.5.0              pyhd1c38e8_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
iqtree                    2.2.0.3              h135ad0d_1    bioconda
isa-l                     2.30.0               h0d85af4_4    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hac89ed1_2    conda-forge
jsonschema                4.15.0             pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.5              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1           py38h50d1736_1    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4            py38h98b9b1b_1    conda-forge
krb5                      1.19.3               hb49756b_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
ld64_osx-64               609                 h1e06c2b_10    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libclang-cpp14            14.0.4          default_h55ffa42_0    conda-forge
libcurl                   7.83.1               h372c54d_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdeflate                1.10                 h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_27    conda-forge
libgfortran-devel_osx-64  9.5.0               hc2d6858_27    conda-forge
libgfortran5              11.3.0              h082f757_27    conda-forge
libglib                   2.72.1               hfbcb929_0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
libidn2                   2.3.3                hac89ed1_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
liblapacke                3.9.0           16_osx64_openblas    conda-forge
libllvm10                 10.0.1               h009f743_3    conda-forge
libllvm13                 13.0.1               h64f94b2_2    conda-forge
libllvm14                 14.0.4               h41df66c_0    conda-forge
libnghttp2                1.47.0               h7cbc4dc_1    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.37               h5481273_4    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.39.3               ha978bb4_0    conda-forge
libssh2                   1.10.0               h7535e13_3    conda-forge
libtiff                   4.4.0                hfca7e8f_0    conda-forge
libunistring              0.9.10               h0d85af4_0    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.9.14               hea49891_4    conda-forge
libxslt                   1.1.35               heaa0ce8_0    conda-forge
libzlib                   1.2.12               hfd90126_4    conda-forge
llvm-openmp               14.0.4               ha654fa7_0    conda-forge
llvm-tools                14.0.4               h41df66c_0    conda-forge
llvmlite                  0.36.0           py38h872f124_0    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
lxml                      4.9.1            py38h0dd4459_0    conda-forge
lz4                       4.0.0            py38h10aaa5c_3    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
mafft                     7.505                ha5712d3_0    bioconda
make                      4.3                  h22f3db7_1    conda-forge
markupsafe                2.1.1            py38hef030d1_2    conda-forge
matplotlib                3.5.3            py38h50d1736_2    conda-forge
matplotlib-base           3.5.3            py38hae485fc_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
msgpack-python            1.0.4            py38h98b9b1b_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.2.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
networkx                  2.8.6              pyhd8ed1ab_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
numba                     0.53.1           py38h5b9a75a_1    conda-forge
numpy                     1.23.2           py38h84cd246_0    conda-forge
openjdk                   17.0.3               hbc0c0cd_2    conda-forge
openjpeg                  2.5.0                h5d0d7b0_1    conda-forge
openssl                   1.1.1q               hfd90126_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.4            py38h5e0dbaf_0    conda-forge
pango                     1.50.9               hc8ec20f_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pbzip2                    1.1.13               h9d27c22_1    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pcre2                     10.37                h3f55489_1    conda-forge
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-carp                 1.50            pl5321hd8ed1ab_0    conda-forge
perl-common-sense         3.75            pl5321hd8ed1ab_0    conda-forge
perl-compress-raw-bzip2   2.201           pl5321h775f41a_0    conda-forge
perl-compress-raw-zlib    2.202           pl5321h775f41a_0    conda-forge
perl-encode               3.19            pl5321hb7f2c08_0    conda-forge
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-exporter-tiny        1.002002        pl5321hd8ed1ab_0    conda-forge
perl-extutils-makemaker   7.64            pl5321hd8ed1ab_0    conda-forge
perl-io-compress          2.106           pl5321h9722bc1_1    bioconda
perl-io-zlib              1.11            pl5321hdfd78af_0    bioconda
perl-json                 4.09            pl5321hdfd78af_0    bioconda
perl-json-xs              2.34            pl5321hcd10b59_5    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321ha5712d3_1    bioconda
perl-parent               0.238           pl5321hd8ed1ab_0    conda-forge
perl-pathtools            3.75            pl5321h775f41a_0    conda-forge
perl-scalar-list-utils    1.63            pl5321h775f41a_0    conda-forge
perl-storable             3.15            pl5321h775f41a_0    conda-forge
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pigz                      2.6                  h5dbffcc_0    conda-forge
pillow                    9.2.0            py38h7bff4d5_2    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
psutil                    5.9.2            py38hef030d1_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.7              pyh6c4a22f_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.1           py38hef030d1_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.1.3            py38h50d1736_0    conda-forge
python                    3.8.13          h394c593_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.1             pyhd8ed1ab_0    conda-forge
python-isal               1.0.1            py38h35d34b1_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2022.2.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38hef030d1_5    conda-forge
pyzmq                     23.2.1           py38hde384ec_0    conda-forge
q2-alignment              2022.8.0                 py38_0    qiime2/label/r2022.8
q2-composition            2022.8.0                 py38_0    qiime2/label/r2022.8
q2-cutadapt               2022.8.0                 py38_0    qiime2/label/r2022.8
q2-dada2                  2022.8.0                 py38_0    qiime2/label/r2022.8
q2-deblur                 2022.8.0                 py38_0    qiime2/label/r2022.8
q2-demux                  2022.8.0                 py38_0    qiime2/label/r2022.8
q2-diversity              2022.8.0                 py38_0    qiime2/label/r2022.8
q2-diversity-lib          2022.8.0                 py38_0    qiime2/label/r2022.8
q2-emperor                2022.8.0                 py38_0    qiime2/label/r2022.8
q2-feature-classifier     2022.8.0                 py38_0    qiime2/label/r2022.8
q2-feature-table          2022.8.1                 py38_0    qiime2/label/r2022.8
q2-fragment-insertion     2022.8.0                 py38_0    qiime2/label/r2022.8
q2-gneiss                 2022.8.0                 py38_0    qiime2/label/r2022.8
q2-longitudinal           2022.8.0                 py38_0    qiime2/label/r2022.8
q2-metadata               2022.8.0                 py38_0    qiime2/label/r2022.8
q2-mystery-stew           2022.8.0                 py38_0    qiime2/label/r2022.8
q2-phylogeny              2022.8.0                 py38_0    qiime2/label/r2022.8
q2-quality-control        2022.8.0                 py38_0    qiime2/label/r2022.8
q2-quality-filter         2022.8.0                 py38_0    qiime2/label/r2022.8
q2-sample-classifier      2022.8.0                 py38_0    qiime2/label/r2022.8
q2-taxa                   2022.8.0                 py38_0    qiime2/label/r2022.8
q2-types                  2022.8.0                 py38_0    qiime2/label/r2022.8
q2-vsearch                2022.8.0                 py38_0    qiime2/label/r2022.8
q2cli                     2022.8.0                 py38_0    qiime2/label/r2022.8
q2galaxy                  2022.8.1                 py38_0    qiime2/label/r2022.8
q2templates               2022.8.0                 py38_0    qiime2/label/r2022.8
qiime2                    2022.8.3                 py38_0    qiime2/label/r2022.8
r-backports               1.4.1             r41h815d134_1    conda-forge
r-base                    4.1.3                h85fa70c_2    conda-forge
r-bh                      1.78.0_0          r41hc72bb7e_1    conda-forge
r-bitops                  1.0_7             r41h815d134_1    conda-forge
r-brio                    1.1.3             r41h815d134_1    conda-forge
r-callr                   3.7.2             r41hc72bb7e_1    conda-forge
r-cli                     3.4.0             r41h49197e3_0    conda-forge
r-cluster                 2.1.3             r41h1e4e481_1    conda-forge
r-colorspace              2.0_3             r41h815d134_1    conda-forge
r-crayon                  1.5.1             r41hc72bb7e_0    conda-forge
r-deldir                  1.0_6             r41h1e4e481_1    conda-forge
r-desc                    1.4.2             r41hc72bb7e_1    conda-forge
r-diffobj                 0.3.5             r41h815d134_1    conda-forge
r-digest                  0.6.29            r41h49197e3_1    conda-forge
r-ellipsis                0.3.2             r41h815d134_1    conda-forge
r-evaluate                0.16              r41hc72bb7e_0    conda-forge
r-fansi                   1.0.3             r41h815d134_1    conda-forge
r-farver                  2.1.1             r41h49197e3_1    conda-forge
r-formatr                 1.12              r41hc72bb7e_1    conda-forge
r-fs                      1.5.2             r41h49197e3_2    conda-forge
r-futile.logger           1.4.3           r41hc72bb7e_1004    conda-forge
r-futile.options          1.0.1           r41hc72bb7e_1003    conda-forge
r-getopt                  1.20.3            r41ha770c72_3    conda-forge
r-ggplot2                 3.3.6             r41hc72bb7e_1    conda-forge
r-glue                    1.6.2             r41h815d134_1    conda-forge
r-gtable                  0.3.1             r41hc72bb7e_1    conda-forge
r-hwriter                 1.3.2.1           r41hc72bb7e_1    conda-forge
r-interp                  1.1_3             r41h49197e3_1    conda-forge
r-isoband                 0.2.5             r41h9951f98_0    conda-forge
r-jpeg                    0.1_9             r41h815d134_1    conda-forge
r-jsonlite                1.8.0             r41h0f1d5c4_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_2    conda-forge
r-lambda.r                1.2.4             r41hc72bb7e_2    conda-forge
r-lattice                 0.20_45           r41h815d134_1    conda-forge
r-latticeextra            0.6_30            r41hc72bb7e_1    conda-forge
r-lifecycle               1.0.1             r41hc72bb7e_0    conda-forge
r-magrittr                2.0.3             r41h815d134_1    conda-forge
r-mass                    7.3_58.1          r41h815d134_1    conda-forge
r-matrix                  1.4_1             r41hce01bf1_1    conda-forge
r-matrixstats             0.62.0            r41h815d134_1    conda-forge
r-mgcv                    1.8_40            r41h40f944a_1    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1005    conda-forge
r-nlme                    3.1_159           r41h1e4e481_1    conda-forge
r-optparse                1.7.3             r41hc72bb7e_1    conda-forge
r-permute                 0.9_7             r41hc72bb7e_1    conda-forge
r-pillar                  1.8.1             r41hc72bb7e_1    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_2    conda-forge
r-pkgload                 1.3.0             r41hc72bb7e_1    conda-forge
r-plyr                    1.8.7             r41h49197e3_1    conda-forge
r-png                     0.1_7           r41h815d134_1005    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1006    conda-forge
r-processx                3.7.0             r41h815d134_1    conda-forge
r-ps                      1.7.1             r41h815d134_1    conda-forge
r-r6                      2.5.1             r41hc72bb7e_1    conda-forge
r-rcolorbrewer            1.1_3             r41h785f33e_1    conda-forge
r-rcpp                    1.0.9             r41h49197e3_2    conda-forge
r-rcppeigen               0.3.3.9.2         r41h4f1a15b_1    conda-forge
r-rcppparallel            5.1.5             r41h49197e3_1    conda-forge
r-rcurl                   1.98_1.8          r41h67d6963_0    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_2    conda-forge
r-reshape2                1.4.4             r41h49197e3_2    conda-forge
r-rlang                   1.0.5             r41h49197e3_0    conda-forge
r-rprojroot               2.0.3             r41hc72bb7e_1    conda-forge
r-scales                  1.2.1             r41hc72bb7e_1    conda-forge
r-snow                    0.4_4             r41hc72bb7e_1    conda-forge
r-stringi                 1.7.8             r41h7183e51_1    conda-forge
r-stringr                 1.4.1             r41hc72bb7e_1    conda-forge
r-testthat                3.1.4             r41h8619c4b_0    conda-forge
r-tibble                  3.1.8             r41h815d134_1    conda-forge
r-utf8                    1.2.2             r41h815d134_1    conda-forge
r-vctrs                   0.4.1             r41hc4bb905_0    conda-forge
r-vegan                   2.6_2             r41h63324e3_1    conda-forge
r-viridislite             0.4.1             r41hc72bb7e_1    conda-forge
r-waldo                   0.4.0             r41hc72bb7e_1    conda-forge
r-withr                   2.5.0             r41hc72bb7e_1    conda-forge
raxml                     8.2.12               ha5712d3_4    bioconda
readline                  8.1.2                h3899abd_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
samtools                  1.15.1               h9f30945_0    bioconda
scikit-bio                0.5.7            py38hbe852b5_0    conda-forge
scikit-learn              0.24.1           py38hfd19401_0    conda-forge
scipy                     1.8.1            py38hfb8b963_3    conda-forge
seaborn                   0.12.0               hd8ed1ab_0    conda-forge
seaborn-base              0.12.0             pyhd8ed1ab_0    conda-forge
sepp                      4.3.10           py38h3252c3a_2    bioconda
setuptools                65.3.0             pyhd8ed1ab_1    conda-forge
sigtool                   0.1.3                h57ddcff_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sortmerna                 2.0                  h5c9b4e4_4    bioconda
sqlite                    3.39.3               h9ae0607_0    conda-forge
stack_data                0.5.0              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.2           py38hc1426ef_0    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tbb                       2020.2               h940c156_4    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tktable                   2.10                 h49f0cf7_3    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.2              py38hef030d1_1    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.3.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
umap-learn                0.5.3            py38h50d1736_0    conda-forge
unicodedata2              14.0.0           py38hef030d1_2    conda-forge
unifrac                   1.1.1            py38h6da613f_0    bioconda
unifrac-binaries          1.1.1                h8c74715_4    bioconda
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
vsearch                   2.21.1               h1a264f4_1    bioconda
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wget                      1.20.3               h52ee1ee_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
xopen                     1.6.0            py38h50d1736_1    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               hfd90126_4    conda-forge
zstd                      1.5.2                hfa58983_4    conda-forge

Attempts to correct the issues

I've tried a number of things to try to get this fixed.

Attempt 1: Could R be corrected? Reinstall png r package.

R executable outside of the conda environment is located here:

[email protected] ~ % which R
/usr/local/bin/R

While the R executable within the QIIME environment is at:

(qiime2-2022.8) [email protected] ~ % which R
/Users/micro/miniconda3/envs/qiime2-2022.8/bin/R

So there should be no issues due to different R installations, conda is doing its job at keeping track of the paths to be used.

Asking (QIIME envt) R to load the png package results in an error:

(qiime2-2022.8) [email protected] ~ % R                                            

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("png")
Error: package or namespace load failed for ‘png’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib':
  dlopen(/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib, 6): Library not loaded: @rpath/libpng16.16.dylib
  Referenced from: /Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib
  Reason: Incompatible library version: png.dylib requires version 55.0.0 or later, but libpng16.16.dylib provides version 54.0.0

Re-installing png and opening a new terminal instance (and R) allows me to load png, but attempting to execute the problematic qiime command (under "Problem") still results in an error.

Conclusion: this approach does not solve the issue.

Attempt 2: delete and remake the qiime environment

Following @Oddant1 's suggestion, I deleted the qiime2-2022.8 conda environment, and recreated it following the native install instructions on the QIIME website. This did not solve the issue.

Attempt 3: clean install of miniconda and qiime

@ebolyen indicated that this behavior might be related to the version of png on cran. They later commented/replied (on here) QIIME forum comment that the issue may have been fixed with an update to a new build on conda-forge; a link to the issue @ebolyen opened on conda-forge's github is here. Following all of this, I deleted miniconda completely (including the qiime environment) and did a clean install of both miniconda and qiime.
the problem still persists:

(qiime2-2022.8) [email protected] ~ % conda list r-png
# packages in environment at /Users/micro/miniconda3/envs/qiime2-2022.8:
#
# Name                    Version                   Build  Channel
r-png                     0.1_7           r41h815d134_1005    conda-forge

? Potential Solution ? As yet untested: specifically updating r-png

There are many versions of r-png available thorugh the terminal search feature:

[email protected] ~ % conda search r-png
Loading channels: done
# Name                       Version           Build  Channel             
r-png                          0.1_7        mro350_0  pkgs/r              
r-png                          0.1_7        r3.1.3_0  pkgs/r              
r-png                          0.1_7       r3.1.3_0a  pkgs/r              
r-png                          0.1_7        r3.2.0_1  pkgs/r              
r-png                          0.1_7       r3.2.0_1a  pkgs/r              
r-png                          0.1_7        r3.2.1_1  pkgs/r              
r-png                          0.1_7       r3.2.1_1a  pkgs/r              
r-png                          0.1_7        r3.2.2_1  pkgs/r              
r-png                          0.1_7       r3.2.2_1a  pkgs/r              
r-png                          0.1_7        r3.3.1_2  pkgs/r              
r-png                          0.1_7        r3.3.2_2  pkgs/r              
r-png                          0.1_7        r3.3.2_3  pkgs/r              
r-png                          0.1_7        r3.4.1_3  pkgs/r              
r-png                          0.1_7  r342hfd481a1_0  pkgs/r              
r-png                          0.1_7  r343h157672f_0  pkgs/r              
r-png                          0.1_7  r350h459e2dc_0  pkgs/r              
r-png                          0.1_7  r351h6402f54_0  pkgs/r              
r-png                          0.1_7   r36h46e59ec_0  pkgs/r 

And version 0.1_8 is available. I am going to try to figure out a way to manually update or specify this in the qiime environment, but I'm not sure how successfull I'll be.

Conclusion

We ran into the same problem that @Heather_Maughan experienced when trying to run dada2 on our data, which resulted from a version conflict of png. I unsuccessfully tried to remedy the situation as outlined above. We would like to use QIIME (specifically with dada2) to perform our analysis to have consistent bioinformatics pipelines between successive datasets. Unfortunately I'm not familliar enough with python and this level of computer science to problem solve this particular issue. Any input you'd be able to provide would be greatly appreciated.

Jake Price

1 Like

Following up on my own post here...

Looking further into the last point above (updating r-png manually), I noticed that the .yml document used to carry out qiime installation specifies version 0.1_7 explicitly. The relevant chunk in "qiime2-2022.8-py38-osx-conda.yml" is:

...
dependencies: 
...
- r-png=0.1_7
...

In case it is useful for you, I ran a little experiment...
I've removed my previous qiime environment, cleaned up conda, and then started the reinstallation process with an altered version of the .yml file which specifies

- r-png=0.1_8

Long story short, it failed spectacularly...
The full output was too long to paste in a code box (>10,000 lines), but it looks like that alteration causes conflicts that cascade though most of the R packages that need to be installed for the qiime environment. The final line of the output reads Your installed version is: not available, which I believe refers to version 0.1_8 of r-png; a failure to install that, would have a cascade effect through to other r dependencies through Rcpp.

A follow up or expansion question for the developers:
Could this line be what's causing the issues we are experiencing?

1 Like

@JacobRPrice,
Could you try with the most recent version of QIIME2? We just built/tested yesterday. You may want to run conda clean --all to clear your conda cache before installing the new version, just to make sure you are really starting clean.

If this still does not work, me know!

@Keegan-Evans & @lizgehret , It hasn't completed yet but it looks like it is running just fine! Thank you so much for your help.

For my own edification, would you mind sharing (or directing me to where I can find) what changes were made to fix the issue? 99% of my work is in R, and I'm not a python guru by any means, so this is an opportunity for me to learn.

@lzgles , for your records, the run was started at 18:55 on 2022/12/22.

2 Likes

@JacobRPrice,

Unfortunately I am not aware what specific changes were made to let this work, but I think @ebolyen was right when he said there were probably issues with the version Conda was getting from CRAN. We experienced several issues like this during our most recent release, and unfortunately it is simply of the build system actually having access to the required versions.

Your approach to rebuild your environments at different levels when encountering a dependency issue is generally the correct one, R in particular seems sensitive to path/dependency install locations/weirdness. Glad the conda-forge update took care of it for you!