Hi,
I'm running into an error, which I think is related to the fact that the castor package was built with R 4.0.5, but the R version in the picrust2 conda environment is 4.0.3. But I don't know how I would then go about fixing this.
This is running with the chemerin_16S tutorial data as per
the tutorial.
place_seqs.py -s ../seqs.fna -o out.tre -p 8 \
--intermediate intermediate/place_seqs
Place_seqs appears to works fine, and I get an out.tre file in the output. But when I run hsp.py, get an error:
hsp.py -i 16S -t out.tre -o marker_predicted_and_nsti.tsv.gz -p 8 -n
Error running this command:
Rscript /homevol/matt/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/Rscripts/castor_nsti.R out.tre /tmp/tmpziqeqga_/known_tips.txt /tmp/tmpziqeqga_/nsti_out.txt
Standard output of the above failed command:
WARNING: ignoring environment value of R_HOME
Standard error of the above failed command:
Warning message:
package ‘castor’ was built under R version 4.0.5
Error in read_Newick_string_CPP(input = string, underscores_as_blanks = underscores_as_blanks, :
function 'Rcpp_precious_preserve' not provided by package 'Rcpp'
Calls: read_tree -> read_Newick_string_CPP
Execution halted
I am aware that the R version in the conda environment and out (base) of it are different...and I wonder if that might be contributing? I'm also unsure about how to fix it if that is the case.
(picrust2) matt@m:~/analyses/picrust2/chemerin_16S/temp$ R --version
WARNING: ignoring environment value of R_HOME
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
(base) matt@m:~/analyses//picrust2$ R --version
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
And here are the details of the conda environment:
$ conda list
# packages in environment at /homevol/matt/anaconda3/envs/picrust2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_10 conda-forge
biom-format 2.1.12 py38h71d37f0_1 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
click 8.1.3 py38h578d9bd_0 conda-forge
coverage 6.4.2 py38h0a891b7_0 conda-forge
curl 7.71.1 he644dc0_3 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
epa-ng 0.3.8 hd03093a_2 bioconda
expat 2.4.8 h27087fc_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py38h578d9bd_5 conda-forge
gappa 0.8.0 hd03093a_1 bioconda
gcc_impl_linux-64 9.4.0 h03d3576_16 conda-forge
gcc_linux-64 9.4.0 h391b98a_10 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_16 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_10 conda-forge
glpk 4.65 h9202a9a_1004 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_16 conda-forge
gxx_linux-64 9.4.0 h0316aca_10 conda-forge
h5py 3.3.0 nompi_py38h9915d05_100 conda-forge
harfbuzz 2.9.1 h83ec7ef_1 conda-forge
hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge
hmmer 3.1b2 3 bioconda
icu 68.2 h9c3ff4c_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libcurl 7.71.1 hcdd3856_3 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_16 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.3 h166bdaf_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h753d276_3 conda-forge
libsanitizer 9.4.0 h79bfe98_16 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_16 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nlopt 2.7.1 py38h4ff0c24_1 conda-forge
numpy 1.23.1 py38h3a7f9d9_0 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.3 py38h47df419_0 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.36 h032f7d1_1 conda-forge
picrust2 2.5.0 pyhdfd78af_0 bioconda
pip 22.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pluggy 1.0.0 py38h578d9bd_3 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pytest 7.1.2 py38h578d9bd_0 conda-forge
pytest-cov 3.0.0 pyhd8ed1ab_0 conda-forge
python 3.8.13 h582c2e5_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
r-base 4.0.3 hd23ff56_6 conda-forge
r-castor 1.7.2 r40h03ef668_0 conda-forge
r-lattice 0.20_45 r40hcfec24a_0 conda-forge
r-matrix 1.4_1 r40h0154571_0 conda-forge
r-naturalsort 0.1.3 r40hc72bb7e_1003 conda-forge
r-nloptr 2.0.3 r40hb13c81a_0 conda-forge
r-rcpp 1.0.9 r40h7525677_0 conda-forge
r-rcppeigen 0.3.3.9.2 r40h43535f1_0 conda-forge
r-rspectra 0.16_1 r40h9f5de39_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
scipy 1.8.1 py38h1ee437e_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
sepp 4.3.10 py38h3252c3a_2 bioconda
setuptools 63.1.0 py38h578d9bd_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.39.0 h4ff8645_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge
Thanks in advance for any help ;)