Hello!
I don't mean to hijack Carla's forum thread but I am running into a similar issue and would greatly appreciate some advice! When I try to run dada2 (from a shellscript in VS Code) to Terminal, I get the same error that Rcpp fails to load. However if I run the identical dada2 command in the native Terminal window (not in VS Code) it appears to work.
Initial dada2 error code:
R version 4.1.1 (2021-08-10)
Loading required package: Rcpp
Error: package or namespace load failed for ‘Rcpp’ in library.dynam(lib, package, package.lib):
shared object ‘Rcpp.so’ not found
Error: package ‘Rcpp’ could not be loaded
When I run env:
USER=joshborin
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin:/Users/joshborin/opt/miniconda3/condabin
LOGNAME=joshborin
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.MxJSAaeJrt/Listeners
HOME=/Users/joshborin
SHELL=/bin/zsh
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0
TMPDIR=/var/folders/_4/1hz0xf69119dp52hpb0vjky80000gp/T/
XPC_SERVICE_NAME=0
XPC_FLAGS=0x0
ORIGINAL_XDG_CURRENT_DESKTOP=undefined
SHLVL=1
PWD=/Users/joshborin/Dropbox/UCSD/PrideLab/FecalViromeTransplant/16S_seq_analysis/toy-analysis
OLDPWD=/Users/joshborin/Dropbox/UCSD/PrideLab/FecalViromeTransplant/16S_seq_analysis
CONDA_EXE=/Users/joshborin/opt/miniconda3/bin/conda
CONDA_PYTHON_EXE=/Users/joshborin/opt/miniconda3/bin/python
CONDA_SHLVL=2
CONDA_PREFIX=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4
CONDA_DEFAULT_ENV=qiime2-2021.4
CONDA_PROMPT_MODIFIER=(qiime2-2021.4)
TERM_PROGRAM=vscode
TERM_PROGRAM_VERSION=1.60.0
LANG=en_US.UTF-8
COLORTERM=truecolor
VSCODE_GIT_IPC_HANDLE=/var/folders/_4/1hz0xf69119dp52hpb0vjky80000gp/T/vscode-git-caa3273eb8.sock
GIT_ASKPASS=/Applications/Visual Studio Code.app/Contents/Resources/app/extensions/git/dist/askpass.sh
VSCODE_GIT_ASKPASS_NODE=/Applications/Visual Studio Code.app/Contents/Frameworks/Code Helper (Renderer).app/Contents/MacOS/Code Helper (Renderer)
VSCODE_GIT_ASKPASS_MAIN=/Applications/Visual Studio Code.app/Contents/Resources/app/extensions/git/dist/askpass-main.js
TERM=xterm-256color
_CE_M=
_CE_CONDA=
CONDA_PREFIX_1=/Users/joshborin/opt/miniconda3
MPLBACKEND=Agg
R_LIBS_USER=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib/R/library/
PYTHONNOUSERSITE=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib/python*/site-packages/
GFORTRAN=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-gfortran
FC_FOR_BUILD=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/-gfortran
FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
FC=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-gfortran
F77=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-gfortran
F90=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-gfortran
F95=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-gfortran
RSTUDIO_WHICH_R=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/R
CONDA_BACKUP_HOST=meyer-144-74.ucsd.edu
HOST=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
AR=x86_64-apple-darwin13.4.0-ar
AS=x86_64-apple-darwin13.4.0-as
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
LIBTOOL=x86_64-apple-darwin13.4.0-libtool
LIPO=x86_64-apple-darwin13.4.0-lipo
NM=x86_64-apple-darwin13.4.0-nm
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
OTOOL=x86_64-apple-darwin13.4.0-otool
PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
RANLIB=x86_64-apple-darwin13.4.0-ranlib
REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
SEGEDIT=x86_64-apple-darwin13.4.0-segedit
SIZE=x86_64-apple-darwin13.4.0-size
STRINGS=x86_64-apple-darwin13.4.0-strings
STRIP=x86_64-apple-darwin13.4.0-strip
CLANG=x86_64-apple-darwin13.4.0-clang
LD=x86_64-apple-darwin13.4.0-ld
CC=x86_64-apple-darwin13.4.0-clang
OBJC=x86_64-apple-darwin13.4.0-clang
CC_FOR_BUILD=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-clang
OBJC_FOR_BUILD=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-clang
CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib -L/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib
LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib -L/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
CMAKE_PREFIX_PATH=:/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4
SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
CMAKE_ARGS=-DCMAKE_AR=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET= -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
MESON_ARGS=--buildtype release
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_realloc_0_nonnull=yes
host_alias=x86_64-apple-darwin13.4.0
build_alias=x86_64-apple-darwin13.4.0
BUILD=x86_64-apple-darwin13.4.0
CLANGXX=x86_64-apple-darwin13.4.0-clang++
CXX=x86_64-apple-darwin13.4.0-clang++
CXX_FOR_BUILD=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/bin/x86_64-apple-darwin13.4.0-clang++
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/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
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/joshborin/opt/miniconda3/envs/qiime2-2021.4/include
JAVA_HOME_CONDA_BACKUP=
JAVA_HOME=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4
JAVA_LD_LIBRARY_PATH_BACKUP=
JAVA_LD_LIBRARY_PATH=/Users/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib/server
_=/usr/bin/env
And when I run R -e ".libPaths()" I get:
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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/joshborin/opt/miniconda3/envs/qiime2-2021.4/lib/R/library"
[2] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"
It looks like I have 2 R libraries but the qiime2 library is first. I don't have an .Rprofile.
Do you see a solution for why the dada2 command works in native Terminal but not when run from shellscript to Terminal in VS Code? Any advice you have would be greatly appreciated!! 
Thanks!