Galaxy test fails with significant differences with a conda env built on 2023/11/21

Summary

Significant differences in actual output vs expected output: ego.txt
I suspect a change in an unconstrained dependency in the conda env has caused this difference, the outputs are so different that it is not possible to say that the tool is working as intended or whether any outputs are correct
Overview of differences

Link to full actual output
Expected is 1272 lines, 325 KB, Actual is 1450 lines, 364 KB
Output lines are not at in the same order.
Where lines match ID column, the numbers are often very different, one line example below:
Expected "GO:0000050" "GO:0000050" "urea cycle" "5/743" "12/17381" 8.6791664317187e-05 0.000579544339150248 0.000347756074343907 "ASL/CAD/ARG2/ASS1/ARG1" 5
Actual "GO:0000050" "GO:0000050" "urea cycle" "5/742" "11/18493" 3.87411727902345e-05 0.000270479220748553 0.000155764302570437 "ASL/CAD/ARG2/ASS1/ARG1" 5
Environment

The Galaxy tool version is 0.1.0 and the conda create command was:
conda create -y --quiet --strict-channel-priority --override-channels --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-385567416f296dfcbcb44fadc18ea6c9f7c7f365c124e50cde63831f12d4fb6d bioconductor-clusterprofiler=3.10.1 r-ggplot2 bioconductor-org.hs.eg.db=3.7.0
This produced an env with the following packages and versions:
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
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                hf3e587d_33    conda-forge
bioconductor-annotationdbi 1.44.0                   r351_0    bioconda
bioconductor-biobase      2.42.0           r351h14c3975_1    bioconda
bioconductor-biocgenerics 0.28.0                   r351_1    bioconda
bioconductor-biocparallel 1.16.6           r351h1c2f66e_0    bioconda
bioconductor-clusterprofiler 3.10.1                   r351_0    bioconda
bioconductor-do.db        2.9                      r351_4    bioconda
bioconductor-dose         3.8.0                    r351_0    bioconda
bioconductor-enrichplot   1.2.0                    r351_0    bioconda
bioconductor-fgsea        1.8.0            r351hf484d3e_0    bioconda
bioconductor-go.db        3.7.0                    r351_0    bioconda
bioconductor-gosemsim     2.8.0            r351hf484d3e_0    bioconda
bioconductor-iranges      2.16.0           r351h14c3975_0    bioconda
bioconductor-org.hs.eg.db 3.7.0                    r351_0    bioconda
bioconductor-qvalue       2.14.1                   r351_0    bioconda
bioconductor-s4vectors    0.20.1           r351h14c3975_0    bioconda
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
cairo                     1.16.0            hcf35c78_1003    conda-forge
curl                      7.68.0               hf8cf82a_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         7.5.0               hda68d29_13    conda-forge
gcc_linux-64              7.5.0               h47867f9_33    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    7.5.0               h56cb351_20    conda-forge
gfortran_linux-64         7.5.0               h78c8a43_33    conda-forge
glib                      2.78.1               hfc55251_1    conda-forge
glib-tools                2.78.1               hfc55251_1    conda-forge
gmp                       6.3.0                h59595ed_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
gxx_impl_linux-64         7.5.0               h64c220c_13    conda-forge
gxx_linux-64              7.5.0               h555fc39_33    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_16    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0                8_openblas    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libcurl                   7.68.0               hda55be3_0    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgfortran-ng            7.5.0               h14aa051_20    conda-forge
libgfortran4              7.5.0               h14aa051_20    conda-forge
libglib                   2.78.1               h783c2da_1    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsqlite                 3.44.0               h2797004_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libtiff                   4.4.0                h82bc61c_5    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
openssl                   1.1.1w               hd590300_0    conda-forge
pango                     1.42.4               h7062337_4    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.42                hcad00b1_0    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
python                    3.11.0          h10a6764_1_cpython    conda-forge
r-askpass                 1.1               r35hcdcec82_1    conda-forge
r-assertthat              0.2.1             r35h6115d3f_1    conda-forge
r-backports               1.1.6             r35hcdcec82_1    conda-forge
r-base                    3.5.1             hc461eb7_1012    conda-forge
r-bh                      1.72.0_3          r35h6115d3f_0    conda-forge
r-biocmanager             1.30.10           r35h6115d3f_0    conda-forge
r-bit                     1.1_15.2          r35hcdcec82_0    conda-forge
r-bit64                   0.9_7           r35hcdcec82_1001    conda-forge
r-blob                    1.2.1             r35h6115d3f_0    conda-forge
r-callr                   3.4.3             r35h6115d3f_0    conda-forge
r-cli                     2.0.2             r35h6115d3f_0    conda-forge
r-colorspace              1.4_1             r35hcdcec82_1    conda-forge
r-cowplot                 1.0.0             r35h6115d3f_1    conda-forge
r-crayon                  1.3.4           r35h6115d3f_1002    conda-forge
r-curl                    4.3               r35hcdcec82_0    conda-forge
r-data.table              1.12.8            r35hcdcec82_0    conda-forge
r-dbi                     1.1.0             r35h6115d3f_0    conda-forge
r-desc                    1.2.0           r35h6115d3f_1002    conda-forge
r-digest                  0.6.25            r35h0357c0b_1    conda-forge
r-dplyr                   0.8.5             r35h0357c0b_0    conda-forge
r-ellipsis                0.3.0             r35hcdcec82_0    conda-forge
r-europepmc               0.3             r35h6115d3f_1001    conda-forge
r-evaluate                0.14              r35h6115d3f_1    conda-forge
r-fansi                   0.4.1             r35hcdcec82_0    conda-forge
r-farver                  2.0.3             r35h0357c0b_0    conda-forge
r-fastmatch               1.1_0           r35hcdcec82_1004    conda-forge
r-formatr                 1.7               r35h6115d3f_1    conda-forge
r-futile.logger           1.4.3           r35h6115d3f_1002    conda-forge
r-futile.options          1.0.1           r35h6115d3f_1001    conda-forge
r-ggforce                 0.3.1             r35h0357c0b_0    conda-forge
r-ggplot2                 3.3.0             r35h6115d3f_0    conda-forge
r-ggplotify               0.0.5             r35h6115d3f_0    conda-forge
r-ggraph                  2.0.2             r35h0357c0b_0    conda-forge
r-ggrepel                 0.8.2             r35h0357c0b_0    conda-forge
r-ggridges                0.5.2             r35h6115d3f_1    conda-forge
r-glue                    1.4.0             r35hcdcec82_0    conda-forge
r-graphlayouts            0.7.0             r35h0357c0b_0    conda-forge
r-gridextra               2.3             r35h6115d3f_1002    conda-forge
r-gridgraphics            0.5_0             r35h6115d3f_0    conda-forge
r-gtable                  0.3.0             r35h6115d3f_2    conda-forge
r-hms                     0.5.3             r35h6115d3f_0    conda-forge
r-httr                    1.4.1             r35h6115d3f_1    conda-forge
r-igraph                  1.2.5             r35hd626d4e_0    conda-forge
r-isoband                 0.2.1             r35h0357c0b_0    conda-forge
r-jsonlite                1.6.1             r35hcdcec82_0    conda-forge
r-labeling                0.3             r35h6115d3f_1002    conda-forge
r-lambda.r                1.2.4             r35h6115d3f_0    conda-forge
r-lattice                 0.20_41           r35hcdcec82_1    conda-forge
r-lifecycle               0.2.0             r35h6115d3f_0    conda-forge
r-magrittr                1.5             r35h6115d3f_1002    conda-forge
r-mass                    7.3_51.6          r35hcdcec82_1    conda-forge
r-matrix                  1.2_18            r35h7fa42b6_2    conda-forge
r-memoise                 1.1.0           r35h6115d3f_1003    conda-forge
r-mgcv                    1.8_31            r35h7fa42b6_0    conda-forge
r-mime                    0.9               r35hcdcec82_0    conda-forge
r-munsell                 0.5.0           r35h6115d3f_1002    conda-forge
r-nlme                    3.1_147           r35h9bbef5b_0    conda-forge
r-openssl                 1.4.1             r35he5c4762_0    conda-forge
r-pillar                  1.4.3             r35h6115d3f_0    conda-forge
r-pkgbuild                1.0.7             r35h6115d3f_0    conda-forge
r-pkgconfig               2.0.3             r35h6115d3f_0    conda-forge
r-pkgload                 1.0.2           r35h0357c0b_1001    conda-forge
r-plogr                   0.2.0           r35h6115d3f_1002    conda-forge
r-plyr                    1.8.6             r35h0357c0b_0    conda-forge
r-polyclip                1.10_0            r35h0357c0b_1    conda-forge
r-praise                  1.0.0           r35h6115d3f_1003    conda-forge
r-prettyunits             1.1.1             r35h6115d3f_0    conda-forge
r-processx                3.4.2             r35hcdcec82_0    conda-forge
r-progress                1.2.2             r35h6115d3f_1    conda-forge
r-ps                      1.3.2             r35hcdcec82_0    conda-forge
r-purrr                   0.3.4             r35hcdcec82_0    conda-forge
r-r6                      2.4.1             r35h6115d3f_0    conda-forge
r-rcolorbrewer            1.1_2           r35h6115d3f_1002    conda-forge
r-rcpp                    1.0.4.6           r35h0357c0b_0    conda-forge
r-rcpparmadillo           0.9.870.2.0       r35h51c796c_0    conda-forge
r-rcppeigen               0.3.3.7.0         r35h0357c0b_0    conda-forge
r-reshape2                1.4.4             r35h0357c0b_0    conda-forge
r-rlang                   0.4.5             r35hcdcec82_2    conda-forge
r-rprojroot               1.3_2           r35h6115d3f_1002    conda-forge
r-rsqlite                 2.2.0             r35h0357c0b_0    conda-forge
r-rstudioapi              0.11              r35h6115d3f_0    conda-forge
r-rvcheck                 0.1.8             r35h6115d3f_0    conda-forge
r-scales                  1.1.0             r35h6115d3f_0    conda-forge
r-snow                    0.4_3           r35h6115d3f_1001    conda-forge
r-stringi                 1.4.6             r35h0e574ca_1    conda-forge
r-stringr                 1.4.0             r35h6115d3f_1    conda-forge
r-sys                     3.3               r35hcdcec82_0    conda-forge
r-testthat                2.3.2             r35h0357c0b_0    conda-forge
r-tibble                  3.0.1             r35hcdcec82_0    conda-forge
r-tidygraph               1.1.2             r35h0357c0b_1    conda-forge
r-tidyr                   1.0.2             r35h0357c0b_0    conda-forge
r-tidyselect              1.0.0             r35h6115d3f_0    conda-forge
r-triebeard               0.3.0           r35he1b5a44_1002    conda-forge
r-tweenr                  1.0.1           r35h0357c0b_1001    conda-forge
r-upsetr                  1.4.0             r35h6115d3f_1    conda-forge
r-urltools                1.7.3             r35h0357c0b_1    conda-forge
r-utf8                    1.1.4           r35hcdcec82_1002    conda-forge
r-vctrs                   0.2.4             r35hcdcec82_0    conda-forge
r-viridis                 0.5.1           r35h6115d3f_1003    conda-forge
r-viridislite             0.3.0           r35h6115d3f_1002    conda-forge
r-withr                   2.2.0             r35h6115d3f_0    conda-forge
r-xml2                    1.3.2             r35h0357c0b_0    conda-forge
r-zeallot                 0.1.0           r35h6115d3f_1001    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
sysroot_linux-64          2.12                he073ed8_16    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tktable                   2.10                 h0c5db8f_5    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.7                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge
kpbioteam / clusterProfiler_go
