Rcpp not initiating with new qiime2 installation

Hi I am having trouble running dada2, here is the code I input as part of the moving pictures tutorial:
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 120 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza --verbose

And here is part of the error message:

R version 3.5.1 (2018-07-02)

Loading required package: Rcpp

Error: package or namespace load failed for ‘dada2’ in rbind(info, getNamespaceInfo(env, "S3methods")):

number of columns of matrices must match (see arg 2)

Execution halted
Traceback (most recent call last):
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 177, in _denoise_single
run_commands([cmd])
File "/Users/curanga/opt/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 "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/qiime2-archive-tnenva9b/ee0ddd31-47d3-435f-a143-68d7dc23daef/data', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0/output.tsv.biom', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0/track.tsv', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0', '120', '0', '2.0', '2', 'Inf', 'consensus', '1.0', '1', '1000000', 'NULL', '16']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-453>", line 2, in denoise_single
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/curanga/opt/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 "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 212, in denoise_single
band_size='16')
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 188, in _denoise_single
" 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.

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.

Hi @Carla_Uranga!

Rcpp is included with QIIME 2 (reference) — I suspect there is something larger at play here. Can you run the following command, and paste the results here:

env

Hi thank you kindly for your help, here are the results for running “env”:

(qiime2-2020.2) bash-3.2$ env

AS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-as

LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib -L/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib

AR=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ar

RSTUDIO_WHICH_R=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/R

CODESIGN_ALLOCATE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-codesign_allocate

JAVA_LD_LIBRARY_PATH=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/server

TERM_PROGRAM=Apple_Terminal

HOST=x86_64-apple-darwin13.4.0

SHELL=/bin/bash

TERM=xterm-256color

NM=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-nm

PYTHONNOUSERSITE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python*/site-packages/

CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

TMPDIR=/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/

PAGESTUFF=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-pagestuff

CONDA_SHLVL=6

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.bG4zYSajLt/Render

LIPO=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-lipo

CONDA_PROMPT_MODIFIER=(qiime2-2020.2) 

TERM_PROGRAM_VERSION=404.1

SIZE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-size

NMEDIT=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-nmedit

RSTUDIO_WHICH_R_PREV=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/R

OLDPWD=/Users/curanga/desktop

TERM_SESSION_ID=826DE3B5-4688-40ED-98FC-AA7FC38AF116

INSTALL_NAME_TOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-install_name_tool

SEGEDIT=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-segedit

GFORTRAN=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

ARBHOME=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/arb

SEG_HACK=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-seg_hack

USER=curanga

CLANGXX=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-clang++

LIBTOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-libtool

CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0

CONDA_EXE=/Users/curanga/opt/miniconda3/bin/conda

OTOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-otool

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.qXQYeI0XZF/Listeners

DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

CONDA_PREFIX_5=/Users/curanga/opt/miniconda3

CONDA_PREFIX_4=/Users/curanga/opt/anaconda3

CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

STRINGS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-strings

_CE_CONDA=

CHECKSYMS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-checksyms

CONDA_PREFIX_1=/Users/curanga/anaconda3

ARBHOME_BACKUP=

PATH=/opt/local/bin:/opt/local/sbin:/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

CONDA_PREFIX_3=/anaconda3

CONDA_PREFIX_2=/miniconda3

DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

LD=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ld

CONDA_PREFIX=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

F90=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

PWD=/Users/curanga/desktop/qiime2-metadata-tutorial

JAVA_HOME=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

STRIP=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-strip

MPLBACKEND=Agg

F95=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

LANG=en_US.UTF-8

DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

XPC_FLAGS=0x0

F77=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

REDO_PREBINDING=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-redo_prebinding

CXX=x86_64-apple-darwin13.4.0-clang++

CLANG=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-clang

_CE_M=

XPC_SERVICE_NAME=0

SHLVL=3

HOME=/Users/curanga

FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe

CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0

FC=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

INDR=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-indr

CONDA_PYTHON_EXE=/Users/curanga/opt/miniconda3/bin/python

LOGNAME=curanga

JAVA_HOME_CONDA_BACKUP=

CONDA_DEFAULT_ENV=qiime2-2020.2

DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

RANLIB=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ranlib

CMAKE_PREFIX_PATH=:/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

CC=x86_64-apple-darwin13.4.0-clang

SEG_ADDR_TABLE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-seg_addr_table

DISPLAY=/private/tmp/com.apple.launchd.jSsLHjInGE/org.macosforge.xquartz:0

JAVA_LD_LIBRARY_PATH_BACKUP=

LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib -L/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib

R_LIBS_USER=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/R/library/

SECURITYSESSIONID=186a9

FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe

_=/usr/bin/env

(qiime2-2020.2) bash-3.2$ env

AS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-as

LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib -L/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib

AR=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ar

RSTUDIO_WHICH_R=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/R

CODESIGN_ALLOCATE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-codesign_allocate

JAVA_LD_LIBRARY_PATH=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/server

TERM_PROGRAM=Apple_Terminal

HOST=x86_64-apple-darwin13.4.0

SHELL=/bin/bash

TERM=xterm-256color

NM=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-nm

PYTHONNOUSERSITE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python*/site-packages/

CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

TMPDIR=/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/

PAGESTUFF=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-pagestuff

CONDA_SHLVL=6

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.bG4zYSajLt/Render

LIPO=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-lipo

CONDA_PROMPT_MODIFIER=(qiime2-2020.2) 

TERM_PROGRAM_VERSION=404.1

SIZE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-size

NMEDIT=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-nmedit

RSTUDIO_WHICH_R_PREV=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/R

OLDPWD=/Users/curanga/desktop

TERM_SESSION_ID=826DE3B5-4688-40ED-98FC-AA7FC38AF116

INSTALL_NAME_TOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-install_name_tool

SEGEDIT=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-segedit

GFORTRAN=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

ARBHOME=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/arb

SEG_HACK=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-seg_hack

USER=curanga

CLANGXX=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-clang++

LIBTOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-libtool

CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0

CONDA_EXE=/Users/curanga/opt/miniconda3/bin/conda

OTOOL=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-otool

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.qXQYeI0XZF/Listeners

DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

CONDA_PREFIX_5=/Users/curanga/opt/miniconda3

CONDA_PREFIX_4=/Users/curanga/opt/anaconda3

CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

STRINGS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-strings

_CE_CONDA=

CHECKSYMS=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-checksyms

CONDA_PREFIX_1=/Users/curanga/anaconda3

ARBHOME_BACKUP=

PATH=/opt/local/bin:/opt/local/sbin:/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

CONDA_PREFIX_3=/anaconda3

CONDA_PREFIX_2=/miniconda3

DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

LD=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ld

CONDA_PREFIX=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

F90=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

PWD=/Users/curanga/desktop/qiime2-metadata-tutorial

JAVA_HOME=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

STRIP=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-strip

MPLBACKEND=Agg

F95=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

LANG=en_US.UTF-8

DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

XPC_FLAGS=0x0

F77=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

REDO_PREBINDING=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-redo_prebinding

CXX=x86_64-apple-darwin13.4.0-clang++

CLANG=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-clang

_CE_M=

XPC_SERVICE_NAME=0

SHLVL=3

HOME=/Users/curanga

FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe

CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0

FC=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-gfortran

INDR=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-indr

CONDA_PYTHON_EXE=/Users/curanga/opt/miniconda3/bin/python

LOGNAME=curanga

JAVA_HOME_CONDA_BACKUP=

CONDA_DEFAULT_ENV=qiime2-2020.2

DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/include

RANLIB=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-ranlib

CMAKE_PREFIX_PATH=:/Users/curanga/opt/miniconda3/envs/qiime2-2020.2

CC=x86_64-apple-darwin13.4.0-clang

SEG_ADDR_TABLE=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/bin/x86_64-apple-darwin13.4.0-seg_addr_table

DISPLAY=/private/tmp/com.apple.launchd.jSsLHjInGE/org.macosforge.xquartz:0

JAVA_LD_LIBRARY_PATH_BACKUP=

LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib -L/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib

R_LIBS_USER=/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/R/library/

SECURITYSESSIONID=186a9

FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe

_=/usr/bin/env

Thanks @Carla_Uranga!

One thing jumped out at me in here:

We have seen situations in the past where RStudio hijacked conda environments, causing these kinds of problems.

First off, in your QIIME 2 conda environment, please run the following:

R -e ".libPaths()"

Please paste the results here.

Do you have an .Rprofile? If so, run this so that we can learn more:

cat ~/.Rprofile

Thanks! :qiime2:

Hi! Thank you for your awesomeness :sunglasses:. I don’t have a .Rprofile, (should I have one and how do I get one?), but here is the output from
R -e “.libPaths()”

R version 3.5.1 (2018-07-02) – “Feather Spray”
Copyright © 2018 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.

.libPaths()
[1] “/Users/curanga/R/library”
[2] “/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/R/library”

(qiime2-2020.2) bash-3.2$

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Hello @Carla_Uranga!

Good news, you found the culprit!

This entry in your .libPaths() is telling R to search for R libraries and packages outside of your QIIME 2 environment, before searching inside, which is basically causing wires to become crossed. Yikes!

Okay, so why do you have that entry? I'm not really sure, it seems strange that you would have a custom value set there, but without an .Rprofile file, I'm a little lost. Are you working on an institutional compute cluster? If so, any chance you can ask your sysadmin about how the machine is configured?

One other thing jumped out at me - you appear to have anaconda and miniconda both active within your shell environment, which might also be causing some problems, but I'm not too sure.

Keep us posted :qiime2:

Hi and thanks again for all of your help! :nerd_face: I am probably working on an institutional cluster. I work at the J. Craig Venter Institute. I will consult with our IT team and see if they can help me change the settings.

I have both miniconda3 and anaconda3 installed because I was reading in the qiime2 installation guide that miniconda is the preferred environment for qiime2, so if you could let me know which is best I will remove the other one. I will for sure keep you posted if I am able to resolve the issue and use dada2. The good thing is that deblur is available and I was able to use it during the tutorial. Which quality filtering algorithm is better or preferred?

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Great, keep us posted!

This is a great question to ask in the “General Discussion” section of the forum, please post that as a new topic!

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Hi, so it is an institutional computing cluster issue! This is the email I got from our IT people. I was really looking forward to running it off my own computer from home, but alas, this shall not be :expressionless:, unless it turns out that deblur is the preferred quality filtering method.

Carla,

If you want to run this suite of applications (qiime2, python, R), you have to run the versions installed on the cluster. This means you need to run this on either an lserver host or a grid host. We can’t support user installed applications on user workstations. . . there are simply too many variables. That’s said, let me install qiime2 on our grid and see if you can try to run it from an lserver.

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An off-topic reply has been split into a new topic: Need help with Rpath

Please keep replies on-topic in the future.