package or namespace load failed for ‘dada2’ `CXXABI_1.3.11' not found

Hello! I use qiime2-2020.2 and run it by command
conda activate qiime2-2020.2

My command was:
qiime dada2 denoise-paired
–i-demultiplexed-seqs UMtutorial-demux-paired-end.qza
–o-table 111UMtable-dada2O
–o-representative-sequences UMrep-seqs-dada2O
–p-trim-left-f 27
–p-trim-left-r 28
–p-trunc-len-f 0
–p-trunc-len-r 0
–p-n-threads 4
–verbose
–o-denoising-stats UMdenoising-stats.qza

The message is:
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.

I tried to fix it, but nothing had happend…

–verbose show this:

qiime dada2 denoise-paired --i-demultiplexed-seqs UMtutorial-demux-paired-end.qza --o-table 111UMtable-dada2O --o-representative-sequences 111UMrep-seqs-dada2O --p-trim-left-f 27 --p-trim-left-r 28 --p-trunc-len-f 0 --p-trunc-len-r 0 --p-n-threads 4 --verbose --o-denoising-stats 111UMdenoising-stats.qza
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_paired.R /tmp/tmpdjxu6dyq/forward /tmp/tmpdjxu6dyq/reverse /tmp/tmpdjxu6dyq/output.tsv.biom /tmp/tmpdjxu6dyq/track.tsv /tmp/tmpdjxu6dyq/filt_f /tmp/tmpdjxu6dyq/filt_r 0 0 27 28 2.0 2.0 2 consensus 1.0 4 1000000

R version 3.6.1 (2019-07-05)
Загрузка требуемого пакета: Rcpp
Ошибка: package or namespace load failed for ‘dada2’:
.onLoad не удалось в loadNamespace() для ‘RcppParallel’, подробности:
вызов: dyn.load(tbb, local = FALSE, now = TRUE)
ошибка: не могу загрузить разделяемый объект ‘/home/irinab/miniconda3/envs/qiime2-2020.2/lib/R/library/RcppParallel/lib/libtbb.so.2’:
/home/linuxbrew/.linuxbrew/lib/libstdc++.so.6: version `CXXABI_1.3.11’ not found (required by /home/irinab/miniconda3/envs/qiime2-2020.2/lib/R/library/RcppParallel/lib/libtbb.so.2)
Выполнение остановлено
Traceback (most recent call last):
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 257, in denoise_paired
run_commands([cmd])
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpdjxu6dyq/forward’, ‘/tmp/tmpdjxu6dyq/reverse’, ‘/tmp/tmpdjxu6dyq/output.tsv.biom’, ‘/tmp/tmpdjxu6dyq/track.tsv’, ‘/tmp/tmpdjxu6dyq/filt_f’, ‘/tmp/tmpdjxu6dyq/filt_r’, ‘0’, ‘0’, ‘27’, ‘28’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘4’, ‘1000000’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-455>”, line 2, in denoise_paired
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 272, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Hi @Butterfly!

Somehow you have a different version of R leaking into your QIIME 2 conda environment. Can you run env and share the results here? Thanks!

Yes, there is it:

AS=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-as
LC_PAPER=ru_RU.UTF-8
RSTUDIO_WHICH_R=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/R
LDFLAGS=-Wl,-O2 -Wl,–sort-common -Wl,–as-needed -Wl,-z,relro -Wl,-z,now -Wl,–disable-new-dtags -Wl,–gc-sections -Wl,-rpath,/home/irinab/miniconda3/envs/qiime2-2020.2/lib -Wl,-rpath-link,/home/irinab/miniconda3/envs/qiime2-2020.2/lib -L/home/irinab/miniconda3/envs/qiime2-2020.2/lib
AR=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-ar
MANPATH=/home/linuxbrew/.linuxbrew/share/man:
RSTUDIO_PANDOC=/home/linuxbrew/.linuxbrew/lib/R/3.6/site-library/pandoc-1.17.0.3/
XDG_SESSION_ID=1
LC_ADDRESS=ru_RU.UTF-8
JAVA_LD_LIBRARY_PATH=/home/irinab/miniconda3/envs/qiime2-2020.2/lib/server
GCC_NM=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
LC_MONETARY=ru_RU.UTF-8
HOST=x86_64-conda_cos6-linux-gnu
TERM=xterm-256color
SHELL=/bin/bash
NM=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-nm
PYTHONNOUSERSITE=/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python*/site-packages/
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
HOMEBREW_REPOSITORY=/home/linuxbrew/.linuxbrew/Homebrew
SSH_CLIENT=91.76.105.64 33944 22
CONDA_SHLVL=2
PERL5LIB=/home/irinab/perl5/lib/perl5
CONDA_PROMPT_MODIFIER=(qiime2-2020.2)
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
SIZE=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-size
LC_NUMERIC=ru_RU.UTF-8
OLDPWD=/home/irinab/16s
PERL_MB_OPT=–install_base “/home/irinab/perl5”
SSH_TTY=/dev/pts/0
GFORTRAN=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gfortran
ARBHOME=/home/irinab/miniconda3/envs/qiime2-2020.2/lib/arb
USER=irinab
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:
LC_TELEPHONE=ru_RU.UTF-8
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
CONDA_EXE=/home/irinab/miniconda3/bin/conda
DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
LD_GOLD=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-ld.gold
CONDA_BUILD_SYSROOT=/home/irinab/miniconda3/envs/qiime2-2020.2/x86_64-conda_cos6-linux-gnu/sysroot
STRINGS=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-strings
CPP=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-cpp
_CE_CONDA=
CXXFILT=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-c++filt
CONDA_PREFIX_1=/home/irinab/miniconda3
ARBHOME_BACKUP=
MAIL=/var/mail/irinab
PATH=/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/irinab/bin:/home/irinab/.local/bin:/home/irinab/miniconda3/envs/qiime2-2020.2/bin:/home/irinab/miniconda3/condabin:/home/irinab/perl5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/irinab/gatk-4.1.4.0
GSETTINGS_SCHEMA_DIR=/home/irinab/miniconda3/envs/qiime2-2020.2/share/glib-2.0/schemas
DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
LD=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-ld
CONDA_PREFIX=/home/irinab/miniconda3/envs/qiime2-2020.2
LC_IDENTIFICATION=ru_RU.UTF-8
F90=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gfortran
PWD=/home/irinab/16s/run28_L04_128b
JAVA_HOME=/home/irinab/miniconda3/envs/qiime2-2020.2
STRIP=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-strip
ELFEDIT=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-elfedit
MPLBACKEND=Agg
F95=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-f95
GCC_RANLIB=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
LANG=ru_RU.UTF-8
LC_MEASUREMENT=ru_RU.UTF-8
DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
F77=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gfortran
CXX=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-c++
_CE_M=
OBJCOPY=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-objcopy
SHLVL=1
HOME=/home/irinab
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
HOMEBREW_PREFIX=/home/linuxbrew/.linuxbrew
FC=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gfortran
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
GCC=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gcc
PERL_LOCAL_LIB_ROOT=/home/irinab/perl5
ADDR2LINE=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/irinab/miniconda3/bin/python
LOGNAME=irinab
SSH_CONNECTION=91.76.105.64 33944 10.129.0.17 22
JAVA_HOME_CONDA_BACKUP=
CONDA_DEFAULT_ENV=qiime2-2020.2
LESSOPEN=| /usr/bin/lesspipe %s
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
RANLIB=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-ranlib
INFOPATH=/home/linuxbrew/.linuxbrew/share/info:
HOMEBREW_CELLAR=/home/linuxbrew/.linuxbrew/Cellar
CMAKE_PREFIX_PATH=/home/irinab/miniconda3/envs/qiime2-2020.2:/home/irinab/miniconda3/envs/qiime2-2020.2/x86_64-conda_cos6-linux-gnu/sysroot/usr
CC=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-cc
XDG_RUNTIME_DIR=/run/user/1000
READELF=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-readelf
JAVA_LD_LIBRARY_PATH_BACKUP=
GCC_AR=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
OBJDUMP=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-objdump
R_LIBS_USER=/home/irinab/miniconda3/envs/qiime2-2020.2/lib/R/library/
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-gprof
PERL_MM_OPT=INSTALL_BASE=/home/irinab/perl5
GXX=/home/irinab/miniconda3/envs/qiime2-2020.2/bin/x86_64-conda_cos6-linux-gnu-g++
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/irinab/miniconda3/envs/qiime2-2020.2/include
LC_NAME=ru_RU.UTF-8
_=/usr/bin/env