error code 1 from Lapack routine 'dsyevr'

[nick-youngblut]

I recently updated my conda env (see below), which broke the R function cmdscale() for for larger distance matrices. If I provide a distance matrix larger than the lower triangle of a 200 x 200 matrix, I get the error:

Error in eigen(-x/2, symmetric = TRUE): error code 1 from Lapack routine 'dsyevr'
Traceback:

1. cmdscale(df)
2. eigen(-x/2, symmetric = TRUE)

The function works with any "small" distance matrix.

My conda env:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
binutils_impl_linux-64    2.35.1               h193b22a_1    conda-forge
binutils_linux-64         2.35                hc3fd857_29    conda-forge
bioconductor-ancombc      1.2.0             r41hdfd78af_0    bioconda
bioconductor-annotate     1.70.0            r41hdfd78af_0    bioconda
bioconductor-annotationdbi 1.54.0            r41hdfd78af_0    bioconda
bioconductor-biobase      2.52.0            r41hd029910_0    bioconda
bioconductor-biocgenerics 0.38.0            r41hdfd78af_0    bioconda
bioconductor-biocparallel 1.26.0            r41h399db7b_0    bioconda
bioconductor-biomformat   1.20.0            r41hdfd78af_0    bioconda
bioconductor-biostrings   2.60.0            r41hd029910_0    bioconda
bioconductor-delayedarray 0.18.0            r41hd029910_0    bioconda
bioconductor-deseq2       1.32.0            r41h399db7b_0    bioconda
bioconductor-fgsea        1.18.0            r41h399db7b_0    bioconda
bioconductor-genefilter   1.74.0            r41hba52eb8_0    bioconda
bioconductor-geneplotter  1.70.0            r41hdfd78af_0    bioconda
bioconductor-genomeinfodb 1.28.0            r41hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.6             r41hdfd78af_0    bioconda
bioconductor-genomicranges 1.44.0            r41hd029910_0    bioconda
bioconductor-ggtree       3.0.1             r41hdfd78af_0    bioconda
bioconductor-iranges      2.26.0            r41hd029910_0    bioconda
bioconductor-keggrest     1.32.0            r41hdfd78af_0    bioconda
bioconductor-matrixgenerics 1.4.0             r41hdfd78af_0    bioconda
bioconductor-microbiome   1.14.0            r41hdfd78af_0    bioconda
bioconductor-multtest     2.48.0            r41hd029910_0    bioconda
bioconductor-phyloseq     1.36.0            r41hdfd78af_0    bioconda
bioconductor-rhdf5        2.36.0            r41h399db7b_0    bioconda
bioconductor-rhdf5filters 1.4.0             r41h399db7b_0    bioconda
bioconductor-rhdf5lib     1.14.0            r41hd029910_0    bioconda
bioconductor-s4vectors    0.30.0            r41hd029910_0    bioconda
bioconductor-summarizedexperiment 1.22.0            r41hdfd78af_0    bioconda
bioconductor-treeio       1.16.1            r41hdfd78af_0    bioconda
bioconductor-xvector      0.32.0            r41hd029910_0    bioconda
bioconductor-zlibbioc     1.38.0            r41hd029910_0    bioconda
boost-cpp                 1.74.0               h312852a_4    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2021.7.5             h06a4308_1
cairo                     1.16.0            h7979940_1007    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
cfitsio                   3.470                hce51eda_7    conda-forge
curl                      7.77.0               hea6ffbf_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1004    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
freexl                    1.0.6                h27cfd23_0
fribidi                   1.0.10               h516909a_0    conda-forge
gcc_impl_linux-64         9.3.0               h70c0ae5_18    conda-forge
gcc_linux-64              9.3.0               h7247604_29    conda-forge
geos                      3.9.1                h9c3ff4c_2    conda-forge
geotiff                   1.6.0                hcf90da6_5    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
gfortran_impl_linux-64    9.3.0               hc4a2995_18    conda-forge
gfortran_linux-64         9.3.0               ha1c937c_29    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
graphite2                 1.3.14               h23475e2_0
gsl                       2.6                  he838d99_2    conda-forge
gxx_impl_linux-64         9.3.0               hd87eabc_18    conda-forge
gxx_linux-64              9.3.0               h0d07fa4_29    conda-forge
harfbuzz                  2.8.2                h83ec7ef_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
intel-openmp              2021.3.0          h06a4308_3350
ipykernel                 5.4.3            py39hef51801_0    conda-forge
ipython                   7.19.0           py39hef51801_2    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.17.2           py39hf3d152e_1    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
json-c                    0.15                 h98cffda_0    conda-forge
jupyter_client            6.1.11             pyhd8ed1ab_1    conda-forge
jupyter_core              4.7.0            py39hf3d152e_1    conda-forge
kealib                    1.4.14               hcc255d8_2    conda-forge
kernel-headers_linux-64   2.6.32              h77966d4_13    conda-forge
krb5                      1.19.1               hcc1bbae_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_1    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0                     9_mkl    conda-forge
libcblas                  3.9.0                     9_mkl    conda-forge
libcurl                   7.77.0               h2574ce0_0    conda-forge
libdap4                   3.20.6               hd7c4107_1    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-devel_linux-64     9.3.0               h7864c58_18    conda-forge
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgdal                   3.3.0                h3215d8d_1    conda-forge
libgfortran-ng            7.5.0               h14aa051_18    conda-forge
libgfortran4              7.5.0               h14aa051_18    conda-forge
libgfortran5              9.3.0               hff62375_18    conda-forge
libglib                   2.68.3               h3e27bee_0    conda-forge
libgomp                   9.3.0               h2828fa1_18    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libkml                    1.3.0             h238a007_1014    conda-forge
liblapack                 3.9.0                     9_mkl    conda-forge
libnetcdf                 4.8.0           nompi_hcd642e3_103    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
librttopo                 1.1.0                h1185371_6    conda-forge
libsodium                 1.0.18               h516909a_1    conda-forge
libspatialite             5.0.1                h20cb978_4    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-devel_linux-64  9.3.0               hb016644_18    conda-forge
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.2.0                h7f98852_0    conda-forge
libxcb                    1.14                 h7b6447c_0
libxml2                   2.9.12               h72842e0_0    conda-forge
libzip                    1.8.0                h4de3113_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
mkl                       2021.3.0           h06a4308_520
nb_conda_kernels          2.3.1            py39hf3d152e_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openjpeg                  2.4.0                hf7af979_0    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
pango                     1.48.7               hb8ff022_0    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pcre2                     10.36                h032f7d1_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pip                       21.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
poppler                   21.03.0              h93df280_0    conda-forge
poppler-data              0.4.10                        0    conda-forge
postgresql                13.3                 h2510834_0    conda-forge
proj                      8.0.0                h277dcde_0    conda-forge
prompt-toolkit            3.0.14             pyha770c72_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pygments                  2.7.4              pyhd8ed1ab_0    conda-forge
python                    3.9.1           hffdb5ce_5_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.9                      1_cp39    conda-forge
pyzmq                     20.0.0           py39hea8fd45_1    conda-forge
r-abind                   1.4_5           r41hc72bb7e_1003    conda-forge
r-ade4                    1.7_17            r41he454529_0    conda-forge
r-adegenet                2.1.4             r41hcfec24a_0    conda-forge
r-adephylo                1.1_11            r41hcfec24a_3    conda-forge
r-ape                     5.5               r41h306847c_0    conda-forge
r-aplot                   0.0.6             r41hc72bb7e_0    conda-forge
r-askpass                 1.1               r41hcfec24a_2    conda-forge
r-assertive               0.3_6             r41hc72bb7e_0    conda-forge
r-assertive.base          0.0_9             r41hc72bb7e_0    conda-forge
r-assertive.code          0.0_3             r41hc72bb7e_2    conda-forge
r-assertive.data          0.0_3             r41hc72bb7e_2    conda-forge
r-assertive.data.uk       0.0_2             r41hc72bb7e_2    conda-forge
r-assertive.data.us       0.0_2             r41hc72bb7e_2    conda-forge
r-assertive.datetimes     0.0_3             r41hc72bb7e_0    conda-forge
r-assertive.files         0.0_2           r41hc72bb7e_1003    conda-forge
r-assertive.matrices      0.0_2             r41hc72bb7e_2    conda-forge
r-assertive.models        0.0_2             r41hc72bb7e_2    conda-forge
r-assertive.numbers       0.0_2           r41hc72bb7e_1003    conda-forge
r-assertive.properties    0.0_4           r41hc72bb7e_1003    conda-forge
r-assertive.reflection    0.0_5             r41hc72bb7e_0    conda-forge
r-assertive.sets          0.0_3           r41hc72bb7e_1003    conda-forge
r-assertive.strings       0.0_3           r41hc72bb7e_1003    conda-forge
r-assertive.types         0.0_3           r41hc72bb7e_1004    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_2    conda-forge
r-backports               1.2.1             r41hcfec24a_0    conda-forge
r-base                    4.1.0                h9e01966_1    conda-forge
r-base64enc               0.1_3           r41hcfec24a_1004    conda-forge
r-bh                      1.75.0_0          r41hc72bb7e_0    conda-forge
r-biocmanager             1.30.16           r41hc72bb7e_0    conda-forge
r-bit                     4.0.4             r41hcfec24a_0    conda-forge
r-bit64                   4.0.5             r41hcfec24a_0    conda-forge
r-bitops                  1.0_7             r41hcfec24a_0    conda-forge
r-blob                    1.2.2             r41hc72bb7e_0    conda-forge
r-boot                    1.3_28            r41hc72bb7e_0    conda-forge
r-brio                    1.1.2             r41hcfec24a_0    conda-forge
r-broom                   0.7.8             r41hc72bb7e_0    conda-forge
r-bslib                   0.2.5.1           r41hc72bb7e_0    conda-forge
r-cachem                  1.0.5             r41hcfec24a_0    conda-forge
r-callr                   3.7.0             r41hc72bb7e_0    conda-forge
r-car                     3.0_11            r41hc72bb7e_0    conda-forge
r-cardata                 3.0_4             r41hc72bb7e_0    conda-forge
r-cellranger              1.1.0           r41hc72bb7e_1003    conda-forge
r-class                   7.3_19            r41hcfec24a_0    conda-forge
r-classint                0.4_3             r41h859d828_2    conda-forge
r-cli                     3.0.1             r41hc72bb7e_0    conda-forge
r-clipr                   0.7.1             r41hc72bb7e_0    conda-forge
r-cluster                 2.1.2             r41h859d828_0    conda-forge
r-clustermq               0.8.95.1          r41h42bf92c_2    conda-forge
r-coda                    0.19_4            r41hc72bb7e_0    conda-forge
r-codetools               0.2_18            r41hc72bb7e_0    conda-forge
r-colorspace              2.0_2             r41hcfec24a_0    conda-forge
r-commonmark              1.7             r41hcfec24a_1002    conda-forge
r-conquer                 1.0.2             r41h6dc32e9_1    conda-forge
r-cpp11                   0.3.1             r41hc72bb7e_0    conda-forge
r-crayon                  1.4.1             r41hc72bb7e_0    conda-forge
r-curl                    4.3.2             r41hcfec24a_0    conda-forge
r-data.table              1.14.0            r41hcfec24a_0    conda-forge
r-dbi                     1.1.1             r41hc72bb7e_0    conda-forge
r-deldir                  0.2_10            r41h859d828_0    conda-forge
r-desc                    1.3.0             r41hc72bb7e_0    conda-forge
r-diffobj                 0.3.4             r41hcfec24a_0    conda-forge
r-digest                  0.6.27            r41h03ef668_0    conda-forge
r-doparallel              1.0.16            r41hc72bb7e_0    conda-forge
r-dplyr                   1.0.7             r41h03ef668_0    conda-forge
r-e1071                   1.7_7             r41h03ef668_0    conda-forge
r-ellipsis                0.3.2             r41hcfec24a_0    conda-forge
r-evaluate                0.14              r41hc72bb7e_2    conda-forge
r-expm                    0.999_6           r41h52d45c5_0    conda-forge
r-fansi                   0.4.2             r41hcfec24a_0    conda-forge
r-farver                  2.1.0             r41h03ef668_0    conda-forge
r-fastmap                 1.1.0             r41h03ef668_0    conda-forge
r-fastmatch               1.1_3             r41hcfec24a_0    conda-forge
r-forcats                 0.5.1             r41hc72bb7e_0    conda-forge
r-foreach                 1.5.1             r41hc72bb7e_0    conda-forge
r-foreign                 0.8_81            r41hcfec24a_0    conda-forge
r-formatr                 1.11              r41hc72bb7e_0    conda-forge
r-fs                      1.5.0             r41h03ef668_0    conda-forge
r-futile.logger           1.4.3           r41hc72bb7e_1003    conda-forge
r-futile.options          1.0.1           r41hc72bb7e_1002    conda-forge
r-future                  1.21.0            r41hc72bb7e_0    conda-forge
r-future.apply            1.7.0             r41hc72bb7e_0    conda-forge
r-gbrd                    0.4_11          r41hc72bb7e_1002    conda-forge
r-gdata                   2.18.0          r41hc72bb7e_1003    conda-forge
r-generics                0.1.0             r41hc72bb7e_0    conda-forge
r-ggforce                 0.3.3             r41h03ef668_0    conda-forge
r-ggplot2                 3.3.5             r41hc72bb7e_0    conda-forge
r-ggraph                  2.0.5             r41h03ef668_0    conda-forge
r-ggrepel                 0.9.1             r41h03ef668_0    conda-forge
r-glmnet                  4.1_2             r41h859d828_0    conda-forge
r-globals                 0.14.0            r41hc72bb7e_0    conda-forge
r-glue                    1.4.2             r41hcfec24a_0    conda-forge
r-gmodels                 2.18.1          r41ha770c72_1003    conda-forge
r-graphlayouts            0.7.1             r41h03ef668_0    conda-forge
r-gridextra               2.3             r41hc72bb7e_1003    conda-forge
r-gtable                  0.3.0             r41hc72bb7e_3    conda-forge
r-gtools                  3.9.2             r41hcfec24a_0    conda-forge
r-haven                   2.4.1             r41h2713e49_0    conda-forge
r-highr                   0.9               r41hc72bb7e_0    conda-forge
r-hms                     1.1.0             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.1.1           r41h03ef668_0    conda-forge
r-httpuv                  1.6.1             r41h03ef668_0    conda-forge
r-httr                    1.4.2             r41hc72bb7e_0    conda-forge
r-huge                    1.3.5             r41h03ef668_0    conda-forge
r-igraph                  1.2.6             r41he0372cf_1    conda-forge
r-irdisplay               1.0               r41hd8ed1ab_0    conda-forge
r-irkernel                1.2               r41hc72bb7e_0    conda-forge
r-isoband                 0.2.5             r41h03ef668_0    conda-forge
r-iterators               1.0.13            r41hc72bb7e_0    conda-forge
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r-jsonlite                1.7.2             r41hcfec24a_0    conda-forge
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r-lambda.r                1.2.4             r41hc72bb7e_1    conda-forge
r-later                   1.2.0             r41h03ef668_0    conda-forge
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r-lme4                    1.1_27.1          r41h03ef668_0    conda-forge
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r-magrittr                2.0.1             r41hcfec24a_1    conda-forge
r-maptools                1.1_1             r41hcfec24a_0    conda-forge
r-markdown                1.1               r41hcfec24a_1    conda-forge
r-mass                    7.3_54            r41hcfec24a_0    conda-forge
r-matrix                  1.3_4             r41he454529_0    conda-forge
r-matrixmodels            0.5_0             r41hc72bb7e_0    conda-forge
r-matrixstats             0.59.0            r41hcfec24a_0    conda-forge
r-memoise                 2.0.0             r41hc72bb7e_0    conda-forge
r-mgcv                    1.8_36            r41he454529_0    conda-forge
r-mime                    0.11              r41hcfec24a_0    conda-forge
r-minqa                   1.2.4           r41h5ee154c_1006    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1003    conda-forge
r-narray                  0.4.1.1           r41hc72bb7e_0    conda-forge
r-nlme                    3.1_152           r41h859d828_0    conda-forge
r-nloptr                  1.2.2.2           r41h03ef668_0    conda-forge
r-nnet                    7.3_16            r41hcfec24a_0    conda-forge
r-numderiv                2016.8_1.1        r41hc72bb7e_3    conda-forge
r-openssl                 1.4.4             r41he36bf35_0    conda-forge
r-openxlsx                4.2.4             r41h03ef668_0    conda-forge
r-parallelly              1.27.0            r41hc72bb7e_0    conda-forge
r-patchwork               1.1.1             r41hc72bb7e_0    conda-forge
r-pbdzmq                  0.3_5             r41h42bf92c_1    conda-forge
r-pbkrtest                0.5.1             r41hc72bb7e_0    conda-forge
r-permute                 0.9_5             r41h785f33e_3    conda-forge
r-phylobase               0.8.10            r41h03ef668_2    conda-forge
r-phylosignal             1.3               r41h03ef668_3    conda-forge
r-pillar                  1.6.1             r41hc72bb7e_0    conda-forge
r-pixmap                  0.4_12            r41hc72bb7e_0    conda-forge
r-pkgbuild                1.2.0             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_1    conda-forge
r-pkgload                 1.2.1             r41h03ef668_0    conda-forge
r-plogr                   0.2.0           r41hc72bb7e_1003    conda-forge
r-plyr                    1.8.6             r41h03ef668_1    conda-forge
r-png                     0.1_7           r41hcfec24a_1004    conda-forge
r-polyclip                1.10_0            r41h03ef668_2    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1004    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_1    conda-forge
r-processx                3.5.2             r41hcfec24a_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_2    conda-forge
r-promises                1.2.0.1           r41h03ef668_0    conda-forge
r-proxy                   0.4_26            r41hcfec24a_0    conda-forge
r-ps                      1.6.0             r41hcfec24a_0    conda-forge
r-pulsar                  0.3.7             r41hc72bb7e_0    conda-forge
r-purrr                   0.3.4             r41hcfec24a_1    conda-forge
r-quantreg                5.86              r41h52d45c5_0    conda-forge
r-r.methodss3             1.8.1             r41hc72bb7e_0    conda-forge
r-r.oo                    1.24.0            r41hc72bb7e_0    conda-forge
r-r.utils                 2.10.1            r41hc72bb7e_0    conda-forge
r-r6                      2.5.0             r41hc72bb7e_0    conda-forge
r-rappdirs                0.3.3             r41hcfec24a_0    conda-forge
r-raster                  3.4_13            r41h03ef668_0    conda-forge
r-rbibutils               2.2.1             r41hcfec24a_0    conda-forge
r-rcolorbrewer            1.1_2           r41h785f33e_1003    conda-forge
r-rcpp                    1.0.7             r41h03ef668_0    conda-forge
r-rcpparmadillo           0.10.6.0.0        r41h306847c_0    conda-forge
r-rcppeigen               0.3.3.9.1         r41h306847c_0    conda-forge
r-rcurl                   1.98_1.3          r41hcfec24a_0    conda-forge
r-rdpack                  2.1.2             r41hc72bb7e_0    conda-forge
r-rdrop2                  0.8.2.1           r41hc72bb7e_0    conda-forge
r-readr                   1.4.0             r41h03ef668_0    conda-forge
r-readxl                  1.3.1             r41h2713e49_4    conda-forge
r-rematch                 1.0.1           r41hc72bb7e_1003    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_1    conda-forge
r-renv                    0.14.0            r41hc72bb7e_0    conda-forge
r-repr                    1.1.3             r41h785f33e_0    conda-forge
r-reshape2                1.4.4             r41h03ef668_1    conda-forge
r-rio                     0.5.27            r41hc72bb7e_0    conda-forge
r-rlang                   0.4.11            r41hcfec24a_0    conda-forge
r-rncl                    0.8.4             r41h03ef668_1    conda-forge
r-rnexml                  2.4.5             r41hc72bb7e_0    conda-forge
r-rprojroot               2.0.2             r41hc72bb7e_0    conda-forge
r-rsqlite                 2.2.5             r41h03ef668_0    conda-forge
r-rstudioapi              0.13              r41hc72bb7e_0    conda-forge
r-rtsne                   0.15              r41h6dc32e9_3    conda-forge
r-rvcheck                 0.1.8             r41hc72bb7e_1    conda-forge
r-sass                    0.4.0             r41h03ef668_0    conda-forge
r-scales                  1.1.1             r41hc72bb7e_0    conda-forge
r-segmented               1.3_4             r41hc72bb7e_0    conda-forge
r-seqinr                  4.2_8             r41hcfec24a_0    conda-forge
r-sf                      0.9_8             r41h778666c_1    conda-forge
r-shape                   1.4.6             r41ha770c72_0    conda-forge
r-shiny                   1.6.0             r41hc72bb7e_0    conda-forge
r-snow                    0.4_3           r41hc72bb7e_1002    conda-forge
r-sourcetools             0.1.7           r41h9c3ff4c_1002    conda-forge
r-sp                      1.4_5             r41hcfec24a_0    conda-forge
r-sparsem                 1.81              r41h859d828_0    conda-forge
r-spdata                  0.3.10            r41hc72bb7e_0    conda-forge
r-spdep                   1.1_8             r41hbfbffee_0    conda-forge
r-spieceasi               1.1.0             r41h1b792b2_2    bioconda
r-statmod                 1.4.36            r41h92ddd45_0    conda-forge
r-stringi                 1.7.3             r41hcabe038_0    conda-forge
r-stringr                 1.4.0             r41hc72bb7e_2    conda-forge
r-survival                3.2_11            r41hcfec24a_0    conda-forge
r-sys                     3.4               r41hcfec24a_0    conda-forge
r-testthat                3.0.4             r41h03ef668_0    conda-forge
r-tibble                  3.1.3             r41hcfec24a_0    conda-forge
r-tidygraph               1.2.0             r41h03ef668_0    conda-forge
r-tidyr                   1.1.3             r41h03ef668_0    conda-forge
r-tidyselect              1.1.1             r41hc72bb7e_0    conda-forge
r-tidytable               0.6.3             r41hc72bb7e_0    conda-forge
r-tidytree                0.3.4             r41hc72bb7e_0    conda-forge
r-tweenr                  1.0.2             r41h03ef668_0    conda-forge
r-units                   0.7_2             r41h03ef668_0    conda-forge
r-utf8                    1.2.1             r41hcfec24a_0    conda-forge
r-uuid                    0.1_4             r41hcfec24a_1    conda-forge
r-vctrs                   0.3.8             r41hcfec24a_1    conda-forge
r-vegan                   2.5_7             r41h52d45c5_0    conda-forge
r-vgam                    1.1_5             r41h859d828_0    conda-forge
r-viridis                 0.6.1             r41hc72bb7e_1    conda-forge
r-viridislite             0.4.0             r41hc72bb7e_0    conda-forge
r-waldo                   0.2.5             r41hc72bb7e_0    conda-forge
r-withr                   2.4.2             r41hc72bb7e_0    conda-forge
r-xfun                    0.24              r41h03ef668_0    conda-forge
r-xml                     3.99_0.6          r41hcfec24a_0    conda-forge
r-xml2                    1.3.2             r41h03ef668_1    conda-forge
r-xtable                  1.8_4             r41hc72bb7e_3    conda-forge
r-yaml                    2.2.1             r41hcfec24a_1    conda-forge
r-zeallot                 0.1.0           r41hc72bb7e_1002    conda-forge
r-zip                     2.2.0             r41hcfec24a_0    conda-forge
readline                  8.1                  h27cfd23_0
sed                       4.8                  he412f7d_0    conda-forge
setuptools                52.0.0           py39h06a4308_0
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.36.0               h9cd32fc_0    conda-forge
sysroot_linux-64          2.12                h77966d4_13    conda-forge
tiledb                    2.2.9                he87e0bf_1    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
tzcode                    2021a                h7f98852_1    conda-forge
tzdata                    2021a                he74cb21_0    conda-forge
udunits2                  2.2.27.27            h975c496_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xerces-c                  3.2.3                h9d8b166_2    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.2.1                h7f98852_0    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

conda info:

     active environment : /ebio/abt3_projects/ATM/envs/tidyverse-ecoPhy2
    active env location : /ebio/abt3_projects/ATM/envs/tidyverse-ecoPhy2
            shell level : 2
       user config file : /ebio/abt3/nyoungblut/.condarc
 populated config files : /ebio/abt3_projects/software/miniconda3/.condarc
                          /ebio/abt3/nyoungblut/.condarc
          conda version : 4.10.1
    conda-build version : not installed
         python version : 3.8.3.final.0
       virtual packages : __linux=5.4.89=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /ebio/abt3_projects/software/miniconda3  (writable)
      conda av data dir : /ebio/abt3_projects/software/miniconda3/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/leylabmpi/linux-64
                          https://conda.anaconda.org/leylabmpi/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://conda.anaconda.org/qiime2/linux-64
                          https://conda.anaconda.org/qiime2/noarch
          package cache : /ebio/abt3_projects/temp_data/nyoungblut/conda_cache
                          /ebio/abt3/nyoungblut/.conda/pkgs
                          /ebio/abt3_projects/software/miniconda3/pkgs
       envs directories : /ebio/abt3_projects/software/miniconda3/envs
                          /ebio/abt3/nyoungblut/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.8.3 Linux/5.4.89 ubuntu/18.04.5 glibc/2.27
                UID:GID : 6354:350
             netrc file : None
           offline mode : False

[nick-youngblut]

I tried a conda env with liblapack 3.9.0 7_openblas conda-forge installed versus liblapack 3.9.0 9_mkl conda-forge. The openblas version works with larger distance matrices.

Installing liblapack>=3.9.0=7_openblas over the 9_mkl version in my other conda env required upgrading/changing basically ever package installed, but that fixed the issue

[nick-youngblut]

Installing liblapack>=3.9.0=7_openblas then breaks bioconductor-deseq2. Specifically, the dependency GenomeInfoDb then cannot be installed. If I uninstall bioconductor-deseq2 or bioconductor-genomeinfodbdata, conda tried to re-install liblapack 3.9.0 9_mkl conda-forge!!!

If I use conda install bioconductor-deseq2 "liblapack>=3.9.0=7_openblas", to re-install the bioconductor packages, I just get the same error as before:

Loading required package: GenomeInfoDb

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’

Error: package ‘GenomeInfoDb’ could not be loaded
Traceback:

1. library(DESeq2)
2. .getRequiredPackages2(pkgInfo, quietly = quietly)
3. library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
 .     quietly = quietly)
4. .getRequiredPackages2(pkgInfo, quietly = quietly)
5. stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
 .     call. = FALSE, domain = NA)

I'm stuck in dependency conflict hell. This seems to happen quite a bit with conda & R.

[h-vetinari]

@isuruf, could you transfer this to the intel_repack feedstock? It sounds like an MKL issue to me.

[Gian77]

I am having a similar issue when trrying to generate a binary matrix from a large dataset. I tried everything, do you have a solution? Thanks! G.

library(phyloseq)
> pcoa_ecm_jac <-  ordinate(physeq_ecm, method = "PCoA", distance = "jaccard", binary=TRUE)
Error in eigen(delta1) : error code 1 from Lapack routine 'dsyevr'

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so;  LAPACK version 3.8.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Toronto
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.2       forcats_1.0.0         stringr_1.5.0         dplyr_1.1.2           purrr_1.0.1           readr_2.1.4           tidyr_1.3.0          
 [8] tibble_3.2.1          ggplot2_3.4.2         tidyverse_2.0.0       phyloseq_1.44.0       vegan_2.6-4           lattice_0.21-8        permute_0.9-7        
[15] BiocManager_1.30.21.1

loaded via a namespace (and not attached):
 [1] gtable_0.3.3            rhdf5_2.44.0            Biobase_2.60.0          tzdb_0.4.0              generics_0.1.3          rhdf5filters_1.12.1    
 [7] vctrs_0.6.3             tools_4.3.1             bitops_1.0-7            biomformat_1.28.0       stats4_4.3.1            parallel_4.3.1         
[13] fansi_1.0.4             cluster_2.1.4           pkgconfig_2.0.3         Matrix_1.6-0            data.table_1.14.8       S4Vectors_0.38.1       
[19] lifecycle_1.0.3         GenomeInfoDbData_1.2.10 compiler_4.3.1          Biostrings_2.68.1       munsell_0.5.0           codetools_0.2-19       
[25] GenomeInfoDb_1.36.1     RCurl_1.98-1.12         pillar_1.9.0            crayon_1.5.2            MASS_7.3-60             iterators_1.0.14       
[31] foreach_1.5.2           nlme_3.1-162            tidyselect_1.2.0        digest_0.6.33           stringi_1.7.12          reshape2_1.4.4         
[37] splines_4.3.1           ade4_1.7-22             grid_4.3.1              colorspace_2.1-0        cli_3.6.1               magrittr_2.0.3         
[43] survival_3.5-5          utf8_1.2.3              ape_5.7-1               withr_2.5.0             scales_1.2.1            timechange_0.2.0       
[49] XVector_0.40.0          igraph_1.5.0.1          multtest_2.56.0         hms_1.1.3               IRanges_2.34.1          mgcv_1.9-0             
[55] rlang_1.1.1             Rcpp_1.0.11             glue_1.6.2              BiocGenerics_0.46.0     rstudioapi_0.15.0       jsonlite_1.8.7         
[61] R6_2.5.1                Rhdf5lib_1.22.0         plyr_1.8.8              zlibbioc_1.46.0 

[adrianuzkcc]

Does anyone here found a solution?