fastspar install is weird in mac arm64 with qiime2 2026.1

[madiapgar]

installing fastspar into your qiime2 conda environment on mac osx-arm64

Caution

the following instructions currently DO NOT WORK with qiime2 2026.4 and will uninstall ALL of your qiime2 plugins (yes, I mean literally all of them)!! for further information, see the issue comments below.

Warning

if you're attempting to install fastspar into a newer qiime2 conda environment (2026 and above) on mac osx-arm64 (apple silicon, M chips), conda install -c bioconda -c conda-forge fastspar==1.0.0 (and any of its variations) WILL NOT WORK!!

this is because of the way that the conda-libmamba-solver deals with cross-platform virtual system packages during rosetta emulation (osx-64).

if you find a way to install fastspar with conda under these conditions, please let me know by creating an issue on this repo!

Note

if you're installing fastspar with conda install in mac osx-arm64, you NEED to use the rosetta emulator (conda config --set subdir osx-64) regardless of whether you're installing in a qiime environment or not!

THE ISSUE:mamba install repeatedly cannot find fastspar in the given channels, even when -c bioconda is called (see below)

• this is because even with the conda subdir set to osx-64, mamba does not respect it and pulls the actual system architecture (osx-arm64) - this can be seen in the screenshot above
• since fastspar does not support mac (and probs linux) osx-arm64, it will not be found in the bioconda/osx-arm64 channel and neither will the required dependencies through conda-forge/osx-arm64
  • this will cause your fastspar install to fail!!!

what you need to do to get fastspar to install with qiime2 in mac osx-arm64 (apple silicon/M chips):

1. install a mambaforge distribution (now called miniforge): instructions
2. create the qiime2 conda environment for the version you want (qiime2 2026.1 is recommended since q2-SCNIC will be compatible with it): instructions
3. activate your new qiime2 2026.1 conda environment

conda activate rachis-qiime2-2026.1

4. set the default system CONDA_SUBDIR environmental variable to osx-64

Important

you STILL need to run this command even though you already ran conda config --env --set subdir osx-64 when you installed the qiime2 environment since mamba ignores environment-level conda configurations (i.e. anything in the environment-level .condarc). DO NOT set your system-wide miniforge to the rosetta emulator (running the conda config command above without --env) since it can break your entire conda install by getting your system architecture confused (trust me, I've done this many times)

this command forces conda to set the global shell CONDA_SUBDIR environmental variable to the rosetta emulator (osx-64) every time your qiime2 environment is activated. this is important because mamba WILL respect this global shell variable (but not your .condarc/.mambarc).

conda env config vars set CONDA_SUBDIR=osx-64

5. deactivate and reactivate your qiime2 conda environment - this allows the changes you just made to take affect

conda deactivate rachis-qiime2-2026.1

conda activate rachis-qiime2-2026.1

6. verify that mamba now uses the rosetta emulator in this environment

mamba info

the output should look like this with platform: osx-64 listed at the bottom:

7. now you can finally install fastspar with mamba

mamba install -c bioconda -c conda-forge fastspar==1.0.0

8. verify your fastspar install

fastspar --help

Originally posted by @madiapgar in #22

[acolorado1]

I have managed to follow these an instructions and successfully installed fastspar in a the QIIME2-2026.4 version (I am on a Mac OS with M1). HOWEVER:

Warning

Because fastspar requires R4.4.0 and QIIME installs R4.5.0 all of R needs to be rebuilt with downgraded packages in the evironment

This leads to several QIIME1 plugins being removed. Here is the summary of changes happening

 Summary:

  Install: 21 packages
  Remove: 32 packages
  Change: 177 packages
  Upgrade: 23 packages
  Downgrade: 55 packages

  Total download: 372MB

fastspar 1.0.0 Install Transaction Summary

Install (21 packages)

Package	Version	Channel
argcomplete	3.6.3	conda-forge
armadillo	14.6.3	conda-forge
arpack	3.9.1	conda-forge
bioconductor-data-packages	20260207	bioconda
bioconductor-genomeinfodb	1.42.0	bioconda
bioconductor-genomeinfodbdata	1.2.13	bioconda
bioconductor-ucsc.utils	1.2.0	bioconda
bioconductor-zlibbioc	1.52.0	bioconda
fastspar	1.0.0	bioconda
gettext	0.25.1	conda-forge
gettext-tools	0.25.1	conda-forge
gnu-getopt	1.1.6	bioconda
jq	1.5	bioconda
libasprintf-devel	0.25.1	conda-forge
libgettextpo-devel	0.25.1	conda-forge
libintl-devel	0.25.1	conda-forge
libuv	1.52.1	conda-forge
openblas	0.3.30	conda-forge
superlu	5.2.2	conda-forge
toml	0.10.2	conda-forge
yq	3.4.3	conda-forge

---

⚠️ Remove (32 packages)

Warning: All QIIME 2 plugins and several key bioconductor packages are removed as part of this transaction.

Package	Version	Channel
bioconductor-cigarillo	1.0.0	bioconda
bioconductor-microbiome	1.32.0	bioconda
bioconductor-phyloseq	1.54.0	bioconda
bioconductor-seqinfo	1.0.0	bioconda
q2-alignment	2026.4.0	qiime2
q2-boots	2026.4.0	qiime2
q2-composition	2026.4.0	qiime2
q2-cutadapt	2026.4.0	qiime2
q2-dada2	2026.4.0	qiime2
q2-deblur	2026.4.0	qiime2
q2-demux	2026.4.0	qiime2
q2-diversity	2026.4.0	qiime2
q2-diversity-lib	2026.4.0	qiime2
q2-emperor	2026.4.0	qiime2
q2-feature-classifier	2026.4.0	qiime2
q2-feature-table	2026.4.0	qiime2
q2-fondue	2026.4.0	qiime2
q2-fragment-insertion	2026.4.0	qiime2
q2-kmerizer	2026.4.0	qiime2
q2-longitudinal	2026.4.0	qiime2
q2-metadata	2026.4.0	qiime2
q2-phylogeny	2026.4.0	qiime2
q2-quality-control	2026.4.0	qiime2
q2-quality-filter	2026.4.0	qiime2
q2-sample-classifier	2026.4.0	qiime2
q2-stats	2026.4.0	qiime2
q2-taxa	2026.4.0	qiime2
q2-types	2026.4.0	qiime2
q2-vizard	2026.4.0	qiime2
q2-vsearch	2026.4.0	qiime2
r-igraph	2.1.4	conda-forge
rescript	2026.4.0	qiime2

---

Upgrade (23 packages)

Package	Old Version	New Version
libsqlite	3.53.0	3.53.1
r-bit64	4.6.0_1	4.8.2
r-broom	1.0.12	1.0.13
r-bslib	0.10.0	0.11.0
r-clipr	0.8.0	0.8.1
r-cpp11	0.5.4	0.5.5
r-curl	7.0.0	7.1.0
r-ecosolver	0.5.5	0.6.1
r-fs	1.6.7	2.1.0
r-getopt	1.20.4	1.21.1
r-ggplot2	4.0.2	4.0.3
r-htmltable	2.4.3	2.5.0
r-lme4	1.1_38	2.0_1
r-matrix	1.7_4	1.7_5
r-openssl	2.4.0	2.4.1
r-optparse	1.7.5	1.8.2
r-processx	3.8.7	3.9.0
r-ps	1.9.2	1.9.3
r-rcpparmadillo	15.2.4_1	15.2.7_1
r-readxl	1.4.5	1.5.0
r-reticulate	1.45.0	1.46.0
r-s7	0.2.1	0.2.2
rpy2	3.6.4	3.6.6

---

⬇️ Downgrade (55 packages)

Root cause: fastspar 1.0.0 requires libgfortran5 >=12.2.0 but the env had 15.2.0, forcing r-base from 4.5.2 → 4.4.3 and cascading across all R/Bioconductor packages (r45 → r44 builds).

Package	Old Version	New Version
bioconductor-ancombc	2.12.0	2.8.0
bioconductor-biobase	2.70.0	2.66.0
bioconductor-biocgenerics	0.56.0	0.52.0
bioconductor-biocparallel	1.44.0	1.40.0
bioconductor-biomformat	1.38.0	1.34.0
bioconductor-biostrings	2.78.0	2.74.0
bioconductor-dada2	1.38.0	1.34.0
bioconductor-decontam	1.30.0	1.26.0
bioconductor-delayedarray	0.36.0	0.32.0
bioconductor-genomicalignments	1.46.0	1.42.0
bioconductor-genomicranges	1.62.1	1.58.0
bioconductor-iranges	2.44.0	2.40.0
bioconductor-matrixgenerics	1.22.0	1.18.0
bioconductor-multtest	2.66.0	2.62.0
bioconductor-pwalign	1.6.0	1.2.0
bioconductor-rhdf5	2.54.1	2.50.0
bioconductor-rhdf5filters	1.22.0	1.18.0
bioconductor-rhdf5lib	1.32.0	1.28.0
bioconductor-rhtslib	3.6.0	3.2.0
bioconductor-rsamtools	2.26.0	2.22.0
bioconductor-s4arrays	1.10.1	1.6.0
bioconductor-s4vectors	0.48.0	0.44.0
bioconductor-shortread	1.68.0	1.64.0
bioconductor-sparsearray	1.10.8	1.6.0
bioconductor-summarizedexperiment	1.40.0	1.36.0
bioconductor-xvector	0.50.0	0.46.0
gfortran_impl_osx-64	14.3.0	13.4.0
gfortran_osx-64	14.3.0	13.4.0
harfbuzz	14.1.0	11.1.0
icu	78.3	75.1
libgfortran	15.2.0	5.0.0
libgfortran-devel_osx-64	14.3.0	13.4.0
libgfortran5	15.2.0	14.2.0
libglib	2.86.4	2.84.0
libopenblas	0.3.32	0.3.30
libxml2	2.15.3	2.15.1
libxml2-16	2.15.3	2.15.1
nlopt	2.10.1	2.9.0
pango	1.56.4	1.56.3
pcre2	10.47	10.44
r-base	4.5.2	4.4.3
r-bayesm	3.1_7	3.1_6
r-bh	1.90.0_1	1.87.0_1
r-cluster	2.1.8.2	2.1.8.1
r-desctools	0.99.60	0.99.59
r-gsl	2.1_9	2.1_8
r-hmisc	5.2_5	5.2_3
r-lmom	3.3	3.2
r-mvtnorm	1.3_6	1.3_3
r-nlme	3.1_169	3.1_168
r-robustbase	0.99_7	0.99_4_1
r-textshaping	1.0.5	1.0.1
r-vegan	2.7_3	2.7_1
scipy	1.17.1	1.16.0
wget	1.25.0	1.21.4

---

Change (177 packages)

These are same-version rebuilds switching from r45 to r44 build strings due to the r-base downgrade. No version changes — only the build tag changes.

Package	Version	Old Build	New Build
cairo	1.18.4	h7656bdc_1	h950ec3b_0
hdf5	1.14.6	nompi_h13accda_108	nompi_hc8237f9_102
libblas	3.11.0	6_he492b99_openblas	5_he492b99_openblas
libcblas	3.11.0	6_h9b27e0a_openblas	5_h9b27e0a_openblas
liblapack	3.11.0	6_h859234e_openblas	5_h859234e_openblas
liblapacke	3.11.0	6_h94b3770_openblas	5_h94b3770_openblas
r-abind	1.4_8	r45 → r44	—
r-ade4	1.7_24	r45 → r44	—
r-ape	5.8_1	r45 → r44	—
r-askpass	1.2.1	r45 → r44	—
r-assertthat	0.2.1	r45 → r44	—
r-backports	1.5.1	r45 → r44	—
r-base64enc	0.1_6	r45 → r44	—
r-bibtex	0.5.2	r45 → r44	—
r-bit	4.6.0	r45 → r44	—
r-bitops	1.0_9	r45 → r44	—
r-blob	1.3.0	r45 → r44	—
r-boot	1.3_32	r45 → r44	—
r-cachem	1.1.0	r45 → r44	—
r-callr	3.7.6	r45 → r44	—
r-cellranger	1.1.0	r45 → r44	—
r-checkmate	2.3.3	r45 → r44	—
r-class	7.3_23	r45 → r44	—
r-cli	3.6.6	r45 → r44	—
r-codetools	0.2_20	r45 → r44	—
r-colorspace	2.1_2	r45 → r44	—
r-compositions	2.0_9	r45 → r44	—
r-conflicted	1.2.0	r45 → r44	—
r-crayon	1.5.3	r45 → r44	—
r-cvxr	1.0_15	r45 → r44	—
r-data.table	1.17.8	r45 → r44	—
r-dbi	1.3.0	r45 → r44	—
r-dbplyr	2.5.2	r45 → r44	—
r-deldir	2.0_4	r45 → r44	—
r-deoptimr	1.1_4	r45 → r44	—
r-digest	0.6.39	r45 → r44	—
r-doparallel	1.0.17	r45 → r44	—
r-dorng	1.8.6.3	r45 → r44	—
r-dplyr	1.2.1	r45 → r44	—
r-dtplyr	1.3.3	r45 → r44	—
r-e1071	1.7_17	r45 → r44	—
r-ellipsis	0.3.3	r45 → r44	—
r-energy	1.7_12	r45 → r44	—
r-evaluate	1.0.5	r45 → r44	—
r-exact	3.3	r45 → r44	—
r-expm	1.0_0	r45 → r44	—
r-fansi	1.0.7	r45 → r44	—
r-farver	2.1.2	r45 → r44	—
r-fastmap	1.2.0	r45 → r44	—
r-fontawesome	0.5.3	r45 → r44	—
r-forcats	1.0.1	r45 → r44	—
r-foreach	1.5.2	r45 → r44	—
r-foreign	0.8_91	r45 → r44	—
r-formatr	1.14	r45 → r44	—
r-formula	1.2_5	r45 → r44	—
r-frictionless	1.2.1	r45 → r44	—
r-futile.logger	1.4.9	r45 → r44	—
r-futile.options	1.0.1	r45 → r44	—
r-gargle	1.6.1	r45 → r44	—
r-gbrd	0.4.12	r45 → r44	—
r-generics	0.1.4	r45 → r44	—
r-gld	2.6.8	r45 → r44	—
r-glue	1.8.1	r45 → r44	—
r-gmp	0.7_5.1	r45 → r44	—
r-googledrive	2.1.2	r45 → r44	—
r-googlesheets4	1.1.2	r45 → r44	—
r-gridextra	2.3	r45 → r44	—
r-gtable	0.3.6	r45 → r44	—
r-gtools	3.9.5	r45 → r44	—
r-haven	2.5.5	r45 → r44	—
r-here	1.0.2	r45 → r44	—
r-highr	0.12	r45 → r44	—
r-hms	1.1.4	r45 → r44	—
r-htmltools	0.5.9	r45 → r44	—
r-htmlwidgets	1.6.4	r45 → r44	—
r-httr	1.4.8	r45 → r44	—
r-hwriter	1.3.2.1	r45 → r44	—
r-ids	1.0.1	r45 → r44	—
r-interp	1.1_6	r45 → r44	—
r-isoband	0.3.0	r45 → r44	—
r-iterators	1.0.14	r45 → r44	—
r-jpeg	0.1_11	r45 → r44	—
r-jquerylib	0.1.4	r45 → r44	—
r-jsonlite	2.0.0	r45 → r44	—
r-knitr	1.51	r45 → r44	—
r-labeling	0.4.3	r45 → r44	—
r-lambda.r	1.2.4	r45 → r44	—
r-lattice	0.22_9	r45 → r44	—
r-latticeextra	0.6_31	r45 → r44	—
r-lifecycle	1.0.5	r45 → r44	—
r-lmertest	3.2_1	r45 → r44	—
r-lubridate	1.9.5	r45 → r44	—
r-magrittr	2.0.5	r45 → r44	—
r-mass	7.3_65	r45 → r44	—
r-matrixstats	1.5.0	r45 → r44	—
r-memoise	2.0.1	r45 → r44	—
r-mgcv	1.9_4	r45 → r44	—
r-mime	0.13	r45 → r44	—
r-minqa	1.2.8	r45 → r44	—
r-modelr	0.1.11	r45 → r44	—
r-multcomp	1.4_30	r45 → r44	—
r-munsell	0.5.1	r45 → r44	—
r-nloptr	2.2.1	r45 → r44	—
r-nnet	7.3_20	r45 → r44	—
r-numderiv	2016.8_1.1	r45 → r44	—
r-osqp	1.0.0	r45 → r44	—
r-permute	0.9_10	r45 → r44	—
r-pillar	1.11.1	r45 → r44	—
r-pixmap	0.4_14	r45 → r44	—
r-pkgconfig	2.0.3	r45 → r44	—
r-pkgmaker	0.32.10	r45 → r44	—
r-plyr	1.8.9	r45 → r44	—
r-png	0.1_9	r45 → r44	—
r-prettyunits	1.2.0	r45 → r44	—
r-progress	1.2.3	r45 → r44	—
r-proxy	0.4_29	r45 → r44	—
r-purrr	1.2.2	r45 → r44	—
r-r6	2.6.1	r45 → r44	—
r-ragg	1.5.2	r45 → r44	—
r-rappdirs	0.3.4	r45 → r44	—
r-rbibutils	2.4.1	r45 → r44	—
r-rcolorbrewer	1.1_3	r45 → r44	—
r-rcpp	1.1.1_1.1	r45 → r44	—
r-rcppeigen	0.3.4.0.2	r45 → r44	—
r-rcppparallel	5.1.11_2	r45 → r44	—
r-rcpptoml	0.2.3	r45 → r44	—
r-rdpack	2.6.6	r45 → r44	—
r-readr	2.2.0	r45 → r44	—
r-reformulas	0.4.4	r45 → r44	—
r-registry	0.5_1	r45 → r44	—
r-rematch	2.0.0	r45 → r44	—
r-rematch2	2.1.2	r45 → r44	—
r-reprex	2.1.1	r45 → r44	—
r-reshape2	1.4.5	r45 → r44	—
r-rlang	1.2.0	r45 → r44	—
r-rmarkdown	2.31	r45 → r44	—
r-rmpfr	1.1_1	r45 → r44	—
r-rngtools	1.5.2	r45 → r44	—
r-rootsolve	1.8.2.4	r45 → r44	—
r-rpart	4.1.27	r45 → r44	—
r-rprojroot	2.1.1	r45 → r44	—
r-rstudioapi	0.18.0	r45 → r44	—
r-rtsne	0.17	r45 → r44	—
r-rvest	1.0.5	r45 → r44	—
r-sandwich	3.1_1	r45 → r44	—
r-sass	0.4.10	r45 → r44	—
r-scales	1.4.0	r45 → r44	—
r-scs	3.2.7	r45 → r44	—
r-selectr	0.5_1	r45 → r44	—
r-snow	0.4_4	r45 → r44	—
r-sp	2.2_1	r45 → r44	—
r-stringi	1.8.7	r45 → r44	—
r-stringr	1.6.0	r45 → r44	—
r-survival	3.8_6	r45 → r44	—
r-sys	3.4.3	r45 → r44	—
r-systemfonts	1.3.2	r45 → r44	—
r-tensora	0.36.2.1	r45 → r44	—
r-th.data	1.1_5	r45 → r44	—
r-tibble	3.3.1	r45 → r44	—
r-tidyr	1.3.2	r45 → r44	—
r-tidyselect	1.2.1	r45 → r44	—
r-tidyverse	2.0.0	r45 → r44	—
r-timechange	0.4.0	r45 → r44	—
r-tinytex	0.59	r45 → r44	—
r-tzdb	0.5.0	r45 → r44	—
r-utf8	1.2.6	r45 → r44	—
r-uuid	1.2_2	r45 → r44	—
r-vctrs	0.7.3	r45 → r44	—
r-viridis	0.6.5	r45 → r44	—
r-viridislite	0.4.3	r45 → r44	—
r-vroom	1.7.1	r45 → r44	—
r-withr	3.0.2	r45 → r44	—
r-xfun	0.57	r45 → r44	—
r-xml2	1.5.2	r45 → r44	—
r-xtable	1.8_8	r45 → r44	—
r-yaml	2.3.12	r45 → r44	—
r-zoo	1.8_15	r45 → r44	—

---

Generated from mamba transaction log for fastspar==1.0.0 install into rachis-qiime2-2026.4

Environment Info

mamba info

       libmamba version : 2.7.0
          mamba version : 2.7.0
           curl version : libcurl/8.20.0 OpenSSL/3.6.2 zlib/1.3.2 brotli/1.2.0 zstd/1.5.7 libidn2/2.3.8 libssh2/1.11.1 nghttp2/1.69.0 mit-krb5/1.22.1
     libarchive version : libarchive 3.8.7 zlib/1.3.2 liblzma/5.8.3 bz2lib/1.0.8 liblz4/1.10.0 libzstd/1.5.7 liblzo2/2.10 CommonCrypto/system libb2/bundled
       envs directories : /opt/homebrew/Caskroom/miniforge/base/envs
          package cache : /opt/homebrew/Caskroom/miniforge/base/pkgs
                          /Users/burkhang/.mamba/pkgs
            environment : /opt/miniconda3/envs/rachis-qiime2-2026.4 (active)
           env location : /opt/miniconda3/envs/rachis-qiime2-2026.4
      user config files : /Users/burkhang/.mambarc
 populated config files : /Users/burkhang/.condarc
                          /opt/homebrew/Caskroom/miniforge/base/.condarc
       virtual packages : __unix=0=0
                          __osx=15.0.1=0
                          __archspec=1=x86_64
               channels : https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
       base environment : /opt/homebrew/Caskroom/miniforge/base
               platform : osx-64

conda info

     active environment : rachis-qiime2-2026.4
    active env location : /opt/miniconda3/envs/rachis-qiime2-2026.4
            shell level : 2
       user config file : /Users/burkhang/.condarc
 populated config files : /Users/burkhang/.condarc
          conda version : 24.11.3
    conda-build version : not installed
         python version : 3.12.2.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=x86_64
                          __conda=24.11.3=0
                          __osx=15.0.1=0
                          __unix=0=0
       base environment : /opt/miniconda3  (writable)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          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 : /opt/miniconda3/pkgs
                          /Users/burkhang/.conda/pkgs
       envs directories : /opt/miniconda3/envs
                          /Users/burkhang/.conda/envs
               platform : osx-64
             user-agent : conda/24.11.3 requests/2.32.3 CPython/3.12.2 Darwin/24.0.0 OSX/15.0.1 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.8 aau/0.4.4 c/HHdv-xSkM_iYg_Eam4JuWw s/GCqbD1XSoNtok4J6OJEY3w e/Uhzwz9sgXqUKomD7uxh2Ag
                UID:GID : 502:20
             netrc file : None
           offline mode : False

[madiapgar]

@acolorado1 #32 (comment) has been replicated in mac M2 with rachis-qiime2-2026.4!

Note

this DOES NOT happen when installing fastspar in rachis-qiime2-2026.4 with ubuntu 22.04!!

environment info

mamba:

conda:

qiime environment config changes after fastspar install

qiime info command output BEFORE fastspar install according to the directions above:

qiime info command output AFTER fastspar install according to the directions above: