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clusterprofiler_go's Issues
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
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
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