Package evaluation of BiobakeryUtils on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T11:19:49.170 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.16s ################################################################################ # Installation # Installing BiobakeryUtils... Resolving package versions... Installed Conda ─ v1.10.2 Updating `~/.julia/environments/v1.10/Project.toml` [fa5322f5] + BiobakeryUtils v0.7.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [fa5322f5] + BiobakeryUtils v0.7.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.16.0 [8f4d0f93] + Conda v1.10.2 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 ⌅ [85a47980] + Dictionaries v0.3.29 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [a58aae7d] + EcoBase v0.1.7 [48062228] + FilePathsBase v0.9.23 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.27 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.3 [bd334432] + InlineTest v0.2.0 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3bd8f0ae] + Microbiome v0.10.1 [e1d29d7a] + Missings v1.2.0 [6f286f6a] + MultivariateStats v0.10.3 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [e0db7c4e] + ReTest v0.3.4 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [68821587] + Arpack_jll v3.5.1+1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Installation completed after 9.69s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 43.28s ################################################################################ # Testing # Testing BiobakeryUtils Status `/tmp/jl_5AAVvU/Project.toml` [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [8bb1440f] DelimitedFiles v1.9.1 [3bd8f0ae] Microbiome v0.10.1 [e0db7c4e] ReTest v0.3.4 [9a3f8284] Random [2f01184e] SparseArrays v1.10.0 [8dfed614] Test Status `/tmp/jl_5AAVvU/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.16.0 [8f4d0f93] Conda v1.10.2 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 ⌅ [85a47980] Dictionaries v0.3.29 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 [a58aae7d] EcoBase v0.1.7 [48062228] FilePathsBase v0.9.23 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.27 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.3 [bd334432] InlineTest v0.2.0 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [2ab3a3ac] LogExpFunctions v0.3.29 [3bd8f0ae] Microbiome v0.10.1 [e1d29d7a] Missings v1.2.0 [6f286f6a] MultivariateStats v0.10.3 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [e0db7c4e] ReTest v0.3.4 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.3.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [3bb67fe8] TranscodingStreams v0.11.3 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [68821587] Arpack_jll v3.5.1+1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.1+4 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Downloading miniconda installer ... [ Info: Installing miniconda ... PREFIX=/home/pkgeval/.julia/conda/3/x86_64 Unpacking payload ... Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2 Extracting ca-certificates-2024.12.14-hbcca054_0.conda Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2 Extracting python_abi-3.12-5_cp312.conda Extracting tzdata-2025a-h78e105d_0.conda Extracting libgomp-14.2.0-h77fa898_1.conda Extracting _openmp_mutex-4.5-2_gnu.tar.bz2 Extracting libgcc-14.2.0-h77fa898_1.conda Extracting c-ares-1.34.4-hb9d3cd8_0.conda Extracting libexpat-2.6.4-h5888daf_0.conda Extracting libgcc-ng-14.2.0-h69a702a_1.conda Extracting liblzma-5.6.3-hb9d3cd8_1.conda Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda Extracting libzlib-1.3.1-hb9d3cd8_2.conda Extracting ncurses-6.5-h2d0b736_2.conda Extracting openssl-3.4.0-h7b32b05_1.conda Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda Extracting bzip2-1.0.8-h4bc722e_7.conda Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2 Extracting libedit-3.1.20240808-pl5321h7949ede_0.conda Extracting libev-4.33-hd590300_2.conda Extracting libffi-3.4.2-h7f98852_5.tar.bz2 Extracting libiconv-1.17-hd590300_2.conda Extracting libnsl-2.0.1-hd590300_0.conda Extracting libsqlite-3.48.0-hee588c1_0.conda Extracting libssh2-1.11.1-hf672d98_0.conda Extracting libstdcxx-ng-14.2.0-h4852527_1.conda Extracting libuuid-2.38.1-h0b41bf4_0.conda Extracting libxcrypt-4.4.36-hd590300_1.conda Extracting lz4-c-1.10.0-h5888daf_1.conda Extracting lzo-2.10-hd590300_1001.conda Extracting readline-8.2-h8228510_1.conda Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda Extracting tk-8.6.13-noxft_h4845f30_101.conda Extracting fmt-11.0.2-h434a139_0.conda Extracting krb5-1.21.3-h659f571_0.conda Extracting libnghttp2-1.64.0-h161d5f1_0.conda Extracting libsolv-0.7.30-h3509ff9_0.conda Extracting libxml2-2.13.5-h0d44e9d_1.conda Extracting python-3.12.8-h9e4cc4f_1_cpython.conda Extracting yaml-cpp-0.8.0-h59595ed_0.conda Extracting zstd-1.5.6-ha6fb4c9_0.conda Extracting libarchive-3.7.7-h4585015_3.conda Extracting libcurl-8.11.1-h332b0f4_0.conda Extracting menuinst-2.2.0-py312h7900ff3_0.conda Extracting archspec-0.2.5-pyhd8ed1ab_0.conda Extracting boltons-24.0.0-pyhd8ed1ab_1.conda Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda Extracting colorama-0.4.6-pyhd8ed1ab_1.conda Extracting distro-1.9.0-pyhd8ed1ab_1.conda Extracting frozendict-2.4.6-py312h66e93f0_0.conda Extracting hpack-4.0.0-pyhd8ed1ab_1.conda Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda Extracting idna-3.10-pyhd8ed1ab_1.conda Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda Extracting libmamba-1.5.12-h49b8a8d_0.conda Extracting packaging-24.2-pyhd8ed1ab_2.conda Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda Extracting pycosat-0.6.6-py312h66e93f0_2.conda Extracting pycparser-2.22-pyh29332c3_1.conda Extracting pysocks-1.7.1-pyha55dd90_7.conda Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda Extracting setuptools-75.8.0-pyhff2d567_0.conda Extracting truststore-0.10.0-pyhd8ed1ab_0.conda Extracting wheel-0.45.1-pyhd8ed1ab_1.conda Extracting cffi-1.17.1-py312h06ac9bb_0.conda Extracting h2-4.1.0-pyhd8ed1ab_1.conda Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda Extracting libmambapy-1.5.12-py312hbaee817_0.conda Extracting pip-24.3.1-pyh8b19718_2.conda Extracting ruamel.yaml-0.18.10-py312h66e93f0_0.conda Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda Extracting zstandard-0.23.0-py312hef9b889_1.conda Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda Extracting requests-2.32.3-pyhd8ed1ab_1.conda Extracting conda-package-handling-2.4.0-pyh7900ff3_2.conda Extracting conda-24.11.3-py312h7900ff3_0.conda Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda Extracting mamba-1.5.12-py312h9460a1c_0.conda Installing base environment... Transaction Prefix: /home/pkgeval/.julia/conda/3/x86_64 Updating specs: - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81] - conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de] - conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672] - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be] - conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260] - conda-forge/noarch::tzdata==2025a=h78e105d_0[md5=dbcace4706afdfb7eb891f7b37d07c04] - conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702] - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d] - conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df] - conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3] - conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c] - conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b] - conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84] - conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328] - conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8] - conda-forge/linux-64::ncurses==6.5=h2d0b736_2[md5=04b34b9a40cdc48cfdab261ab176ff74] - conda-forge/linux-64::openssl==3.4.0=h7b32b05_1[md5=4ce6875f75469b2757a65e10a5d05e31] - conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822] - conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553] - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3] - conda-forge/linux-64::libedit==3.1.20240808=pl5321h7949ede_0[md5=8247f80f3dc464d9322e85007e307fe8] - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055] - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3] - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e] - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7] - conda-forge/linux-64::libsqlite==3.48.0=hee588c1_0[md5=84bd1c9a82b455e7a2f390375fb38f90] - conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7] - conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051] - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b] - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc] - conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393] - conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339] - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4] - conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323] - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc] - conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04] - conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368] - conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b] - conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3] - conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1] - conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844] - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7] - conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45] - conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386] - conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c] - conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375] - conda-forge/noarch::archspec==0.2.5=pyhd8ed1ab_0[md5=845b38297fca2f2d18a29748e2ece7fa] - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4] - conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf] - conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400] - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875] - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7] - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08] - conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18] - conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865] - conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a] - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7] - conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d] - conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0] - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa] - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe] - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6] - conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23] - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef] - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac] - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d] - conda-forge/noarch::setuptools==75.8.0=pyhff2d567_0[md5=8f28e299c11afdd79e0ec1e279dcdc52] - conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67] - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986] - conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840] - conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1] - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691] - conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a] - conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f] - conda-forge/linux-64::ruamel.yaml==0.18.10=py312h66e93f0_0[md5=5260b7fb19694ee5bc4ed0ee7a2a769f] - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861] - conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67] - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd] - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29] - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737] - conda-forge/noarch::conda-package-handling==2.4.0=pyh7900ff3_2[md5=32c158f481b4fd7630c565030f7bc482] - conda-forge/linux-64::conda==24.11.3=py312h7900ff3_0[md5=bdaca5d82db98d8b5639f058a818ff03] - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d] - conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc] Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge + ca-certificates 2024.12.14 hbcca054_0 conda-forge + ld_impl_linux-64 2.43 h712a8e2_2 conda-forge + pybind11-abi 4 hd8ed1ab_3 conda-forge + python_abi 3.12 5_cp312 conda-forge + tzdata 2025a h78e105d_0 conda-forge + libgomp 14.2.0 h77fa898_1 conda-forge + _openmp_mutex 4.5 2_gnu conda-forge + libgcc 14.2.0 h77fa898_1 conda-forge + c-ares 1.34.4 hb9d3cd8_0 conda-forge + libexpat 2.6.4 h5888daf_0 conda-forge + libgcc-ng 14.2.0 h69a702a_1 conda-forge + liblzma 5.6.3 hb9d3cd8_1 conda-forge + libstdcxx 14.2.0 hc0a3c3a_1 conda-forge + libzlib 1.3.1 hb9d3cd8_2 conda-forge + ncurses 6.5 h2d0b736_2 conda-forge + openssl 3.4.0 h7b32b05_1 conda-forge + reproc 14.2.5.post0 hb9d3cd8_0 conda-forge + bzip2 1.0.8 h4bc722e_7 conda-forge + keyutils 1.6.1 h166bdaf_0 conda-forge + libedit 3.1.20240808 pl5321h7949ede_0 conda-forge + libev 4.33 hd590300_2 conda-forge + libffi 3.4.2 h7f98852_5 conda-forge + libiconv 1.17 hd590300_2 conda-forge + libnsl 2.0.1 hd590300_0 conda-forge + libsqlite 3.48.0 hee588c1_0 conda-forge + libssh2 1.11.1 hf672d98_0 conda-forge + libstdcxx-ng 14.2.0 h4852527_1 conda-forge + libuuid 2.38.1 h0b41bf4_0 conda-forge + libxcrypt 4.4.36 hd590300_1 conda-forge + lz4-c 1.10.0 h5888daf_1 conda-forge + lzo 2.10 hd590300_1001 conda-forge + readline 8.2 h8228510_1 conda-forge + reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge + tk 8.6.13 noxft_h4845f30_101 conda-forge + fmt 11.0.2 h434a139_0 conda-forge + krb5 1.21.3 h659f571_0 conda-forge + libnghttp2 1.64.0 h161d5f1_0 conda-forge + libsolv 0.7.30 h3509ff9_0 conda-forge + libxml2 2.13.5 h0d44e9d_1 conda-forge + python 3.12.8 h9e4cc4f_1_cpython conda-forge + yaml-cpp 0.8.0 h59595ed_0 conda-forge + zstd 1.5.6 ha6fb4c9_0 conda-forge + libarchive 3.7.7 h4585015_3 conda-forge + libcurl 8.11.1 h332b0f4_0 conda-forge + menuinst 2.2.0 py312h7900ff3_0 conda-forge + archspec 0.2.5 pyhd8ed1ab_0 conda-forge + boltons 24.0.0 pyhd8ed1ab_1 conda-forge + brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge + certifi 2024.12.14 pyhd8ed1ab_0 conda-forge + charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_1 conda-forge + distro 1.9.0 pyhd8ed1ab_1 conda-forge + frozendict 2.4.6 py312h66e93f0_0 conda-forge + hpack 4.0.0 pyhd8ed1ab_1 conda-forge + hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge + idna 3.10 pyhd8ed1ab_1 conda-forge + jsonpointer 3.0.0 py312h7900ff3_1 conda-forge + libmamba 1.5.12 h49b8a8d_0 conda-forge + packaging 24.2 pyhd8ed1ab_2 conda-forge + platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge + pluggy 1.5.0 pyhd8ed1ab_1 conda-forge + pycosat 0.6.6 py312h66e93f0_2 conda-forge + pycparser 2.22 pyh29332c3_1 conda-forge + pysocks 1.7.1 pyha55dd90_7 conda-forge + ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge + setuptools 75.8.0 pyhff2d567_0 conda-forge + truststore 0.10.0 pyhd8ed1ab_0 conda-forge + wheel 0.45.1 pyhd8ed1ab_1 conda-forge + cffi 1.17.1 py312h06ac9bb_0 conda-forge + h2 4.1.0 pyhd8ed1ab_1 conda-forge + jsonpatch 1.33 pyhd8ed1ab_1 conda-forge + libmambapy 1.5.12 py312hbaee817_0 conda-forge + pip 24.3.1 pyh8b19718_2 conda-forge + ruamel.yaml 0.18.10 py312h66e93f0_0 conda-forge + tqdm 4.67.1 pyhd8ed1ab_1 conda-forge + zstandard 0.23.0 py312hef9b889_1 conda-forge + conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge + urllib3 2.3.0 pyhd8ed1ab_0 conda-forge + requests 2.32.3 pyhd8ed1ab_1 conda-forge + conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge + conda 24.11.3 py312h7900ff3_0 conda-forge + conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge + mamba 1.5.12 py312h9460a1c_0 conda-forge Summary: Install: 84 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────────────── Transaction starting Transaction finished To activate this environment, use: micromamba activate /home/pkgeval/.julia/conda/3/x86_64 Or to execute a single command in this environment, use: micromamba run -p /home/pkgeval/.julia/conda/3/x86_64 mycommand installation finished. [ Info: Running `conda create -q -y -p /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils` in root environment Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda config --add channels bioconda --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment [ Info: Running `conda config --add channels conda-forge --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment Warning: 'conda-forge' already in 'channels' list, moving to the top [ Info: Running `conda config --add channels biobakery --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment [ Info: Running `conda install -q -y humann` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - humann The following packages will be downloaded: package | build ---------------------------|----------------- backports-1.0 | pyhd8ed1ab_3 6 KB conda-forge backports.functools_lru_cache-1.6.1| py_0 8 KB conda-forge backports_abc-0.5 | py_1 5 KB conda-forge biom-format-2.1.7 |py27hc1659b7_1002 10.6 MB conda-forge biopython-1.76 | py27h516909a_0 2.6 MB conda-forge blast-2.16.0 | hc155240_3 141.1 MB bioconda bowtie2-2.5.4 | h7071971_4 14.3 MB bioconda brotlipy-0.7.0 |py27h516909a_1000 345 KB conda-forge ca-certificates-2025.1.31 | hbcca054_0 154 KB conda-forge certifi-2019.11.28 | py27h8c360ce_1 149 KB conda-forge cffi-1.14.0 | py27hd463f26_0 217 KB conda-forge chardet-3.0.4 |py27h8c360ce_1006 180 KB conda-forge click-7.1.2 | pyh9f0ad1d_0 64 KB conda-forge cryptography-2.8 | py27h2c19f6a_2 609 KB conda-forge curl-7.87.0 | h6312ad2_0 86 KB conda-forge cycler-0.10.0 | py_2 9 KB conda-forge dendropy-4.6.0 | pyh7cba7a3_0 315 KB bioconda diamond-2.1.10 | h43eeafb_2 3.5 MB bioconda entrez-direct-22.4 | he881be0_0 14.0 MB bioconda enum34-1.1.10 | py27h8c360ce_1 49 KB conda-forge freetype-2.12.1 | h267a509_2 620 KB conda-forge functools32-3.2.3.2 | py_3 15 KB conda-forge future-0.18.2 | py27h8c360ce_1 722 KB conda-forge futures-3.3.0 | py27h8c360ce_1 26 KB conda-forge gettext-0.23.1 | h5888daf_0 473 KB conda-forge gettext-tools-0.23.1 | h5888daf_0 2.8 MB conda-forge glpk-5.0 | h445213a_0 1023 KB conda-forge gmp-6.3.0 | hac33072_2 449 KB conda-forge humann-4.0.0a1 | py_0 79.4 MB biobakery icu-64.2 | he1b5a44_1 12.6 MB conda-forge idna-2.10 | pyh9f0ad1d_0 52 KB conda-forge ipaddress-1.0.23 | py_0 19 KB conda-forge kiwisolver-1.1.0 | py27h9e3301b_1 88 KB conda-forge krb5-1.20.1 | hf9c8cef_0 1.3 MB conda-forge ld_impl_linux-64-2.43 | h712a8e2_4 656 KB conda-forge libasprintf-0.23.1 | h8e693c7_0 42 KB conda-forge libasprintf-devel-0.23.1 | h8e693c7_0 33 KB conda-forge libblas-3.9.0 |20_linux64_openblas 14 KB conda-forge libcblas-3.9.0 |20_linux64_openblas 14 KB conda-forge libcurl-7.87.0 | h6312ad2_0 339 KB conda-forge libdeflate-1.23 | h4ddbbb0_0 71 KB conda-forge libedit-3.1.20250104 | pl5321h7949ede_0 132 KB conda-forge libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge libgcc-14.2.0 | h767d61c_2 828 KB conda-forge libgcc-ng-14.2.0 | h69a702a_2 52 KB conda-forge libgettextpo-0.23.1 | h5888daf_0 163 KB conda-forge libgettextpo-devel-0.23.1 | h5888daf_0 36 KB conda-forge libgfortran-ng-7.5.0 | h14aa051_20 23 KB conda-forge libgfortran4-7.5.0 | h14aa051_20 1.2 MB conda-forge libgfortran5-14.2.0 | hf1ad2bd_2 1.4 MB conda-forge libgomp-14.2.0 | h767d61c_2 449 KB conda-forge libidn2-2.3.7 | hd590300_0 124 KB conda-forge liblapack-3.9.0 |20_linux64_openblas 14 KB conda-forge libnghttp2-1.51.0 | hdcd2b5c_0 608 KB conda-forge libopenblas-0.3.25 |pthreads_h413a1c8_0 5.3 MB conda-forge libpng-1.6.43 | h2797004_0 281 KB conda-forge libsqlite-3.46.0 | hde9e2c9_0 845 KB conda-forge libssh2-1.10.0 | haa6b8db_3 234 KB conda-forge libstdcxx-14.2.0 | h8f9b012_2 3.7 MB conda-forge libstdcxx-ng-14.2.0 | h4852527_2 53 KB conda-forge libunistring-0.9.10 | h7f98852_0 1.4 MB conda-forge libzlib-1.2.13 | h4ab18f5_6 60 KB conda-forge matplotlib-base-2.2.5 | py27h250f245_1 6.6 MB conda-forge metaphlan-2.8.1 | py_1 50 KB bioconda msgpack-python-1.0.0 | py27h9e3301b_1 28 KB conda-forge muscle-5.3 | h4ac6f70_0 1.1 MB bioconda ncbi-vdb-3.2.0 | h9948957_0 10.6 MB bioconda ncurses-6.5 | h2d0b736_3 871 KB conda-forge numpy-1.16.5 | py27h95a1406_0 4.3 MB conda-forge openssl-1.1.1w | hd590300_0 1.9 MB conda-forge pandas-0.24.2 | py27hb3f55d8_0 10.9 MB conda-forge perl-5.32.1 | 7_hd590300_perl5 12.7 MB conda-forge perl-archive-tar-2.40 | pl5321hdfd78af_0 33 KB bioconda perl-carp-1.50 | pl5321hd8ed1ab_0 22 KB conda-forge perl-common-sense-3.75 | pl5321hd8ed1ab_0 20 KB conda-forge perl-compress-raw-bzip2-2.201| pl5321hbf60520_0 54 KB conda-forge perl-compress-raw-zlib-2.202| pl5321hadc24fc_0 78 KB conda-forge perl-encode-3.21 | pl5321hb9d3cd8_1 1.7 MB conda-forge perl-exporter-5.74 | pl5321hd8ed1ab_0 19 KB conda-forge perl-exporter-tiny-1.002002| pl5321hd8ed1ab_0 28 KB conda-forge perl-extutils-makemaker-7.70| pl5321hd8ed1ab_0 154 KB conda-forge perl-io-compress-2.201 | pl5321h503566f_4 85 KB bioconda perl-io-zlib-1.14 | pl5321hdfd78af_0 12 KB bioconda perl-json-4.10 | pl5321hdfd78af_1 56 KB bioconda perl-json-xs-4.03 | pl5321h9948957_4 73 KB bioconda perl-list-moreutils-0.430 | pl5321hdfd78af_0 32 KB bioconda perl-list-moreutils-xs-0.430| pl5321h7b50bb2_4 50 KB bioconda perl-parent-0.243 | pl5321hd8ed1ab_0 14 KB conda-forge perl-pathtools-3.75 | pl5321hb9d3cd8_1 49 KB conda-forge perl-scalar-list-utils-1.68| pl5321hb9d3cd8_0 50 KB conda-forge perl-storable-3.15 | pl5321hb9d3cd8_0 70 KB conda-forge perl-types-serialiser-1.01 | pl5321hdfd78af_0 13 KB bioconda pip-20.1.1 | pyh9f0ad1d_0 1.1 MB conda-forge pycparser-2.21 | pyhd8ed1ab_0 100 KB conda-forge pyopenssl-19.1.0 | py_1 47 KB conda-forge pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge pyqi-0.3.2 | py_0 36 KB conda-forge pysam-0.20.0 | py27h7835474_0 3.0 MB bioconda pysocks-1.7.1 | py27h8c360ce_1 26 KB conda-forge python-2.7.15 |h5a48372_1011_cpython 12.2 MB conda-forge python-dateutil-2.8.1 | py_0 220 KB conda-forge python_abi-2.7 | 1_cp27mu 4 KB conda-forge pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge raxml-8.2.13 | h7b50bb2_3 3.1 MB bioconda readline-8.2 | h8c095d6_2 276 KB conda-forge requests-2.25.1 | pyhd3deb0d_0 51 KB conda-forge rpsbproc-0.5.0 | h6a68c12_1 6.1 MB bioconda samtools-0.1.19 | h50ea8bc_11 3.4 MB bioconda scipy-1.2.1 | py27h921218d_2 18.4 MB conda-forge setuptools-44.0.0 | py27_0 663 KB conda-forge singledispatch-3.6.1 | pyh44b312d_0 12 KB conda-forge six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge sqlite-3.46.0 | h6d4b2fc_0 840 KB conda-forge subprocess32-3.5.4 | py27h516909a_0 46 KB conda-forge tornado-5.1.1 |py27h14c3975_1000 642 KB conda-forge urllib3-1.26.15 | pyhd8ed1ab_0 110 KB conda-forge wget-1.20.3 | ha56f1ee_1 804 KB conda-forge wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge xz-5.2.6 | h166bdaf_0 409 KB conda-forge zlib-1.2.13 | h4ab18f5_6 91 KB conda-forge ------------------------------------------------------------ Total: 409.1 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu backports conda-forge/noarch::backports-1.0-pyhd8ed1ab_3 backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0 backports_abc conda-forge/noarch::backports_abc-0.5-py_1 biom-format conda-forge/linux-64::biom-format-2.1.7-py27hc1659b7_1002 biopython conda-forge/linux-64::biopython-1.76-py27h516909a_0 blast bioconda/linux-64::blast-2.16.0-hc155240_3 bowtie2 bioconda/linux-64::bowtie2-2.5.4-h7071971_4 brotlipy conda-forge/linux-64::brotlipy-0.7.0-py27h516909a_1000 bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 c-ares conda-forge/linux-64::c-ares-1.34.4-hb9d3cd8_0 ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1 cffi conda-forge/linux-64::cffi-1.14.0-py27hd463f26_0 chardet conda-forge/linux-64::chardet-3.0.4-py27h8c360ce_1006 click conda-forge/noarch::click-7.1.2-pyh9f0ad1d_0 cryptography conda-forge/linux-64::cryptography-2.8-py27h2c19f6a_2 curl conda-forge/linux-64::curl-7.87.0-h6312ad2_0 cycler conda-forge/noarch::cycler-0.10.0-py_2 dendropy bioconda/noarch::dendropy-4.6.0-pyh7cba7a3_0 diamond bioconda/linux-64::diamond-2.1.10-h43eeafb_2 entrez-direct bioconda/linux-64::entrez-direct-22.4-he881be0_0 enum34 conda-forge/linux-64::enum34-1.1.10-py27h8c360ce_1 freetype conda-forge/linux-64::freetype-2.12.1-h267a509_2 functools32 conda-forge/noarch::functools32-3.2.3.2-py_3 future conda-forge/linux-64::future-0.18.2-py27h8c360ce_1 futures conda-forge/linux-64::futures-3.3.0-py27h8c360ce_1 gettext conda-forge/linux-64::gettext-0.23.1-h5888daf_0 gettext-tools conda-forge/linux-64::gettext-tools-0.23.1-h5888daf_0 glpk conda-forge/linux-64::glpk-5.0-h445213a_0 gmp conda-forge/linux-64::gmp-6.3.0-hac33072_2 humann biobakery/noarch::humann-4.0.0a1-py_0 icu conda-forge/linux-64::icu-64.2-he1b5a44_1 idna conda-forge/noarch::idna-2.10-pyh9f0ad1d_0 ipaddress conda-forge/noarch::ipaddress-1.0.23-py_0 keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 kiwisolver conda-forge/linux-64::kiwisolver-1.1.0-py27h9e3301b_1 krb5 conda-forge/linux-64::krb5-1.20.1-hf9c8cef_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 libasprintf conda-forge/linux-64::libasprintf-0.23.1-h8e693c7_0 libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.23.1-h8e693c7_0 libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas libcurl conda-forge/linux-64::libcurl-7.87.0-h6312ad2_0 libdeflate conda-forge/linux-64::libdeflate-1.23-h4ddbbb0_0 libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 libev conda-forge/linux-64::libev-4.33-hd590300_2 libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 libgettextpo conda-forge/linux-64::libgettextpo-0.23.1-h5888daf_0 libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.23.1-h5888daf_0 libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_20 libgfortran4 conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_20 libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2 libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 libidn2 conda-forge/linux-64::libidn2-2.3.7-hd590300_0 liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.51.0-hdcd2b5c_0 libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0 libpng conda-forge/linux-64::libpng-1.6.43-h2797004_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libssh2 conda-forge/linux-64::libssh2-1.10.0-haa6b8db_3 libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2 libunistring conda-forge/linux-64::libunistring-0.9.10-h7f98852_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6 matplotlib-base conda-forge/linux-64::matplotlib-base-2.2.5-py27h250f245_1 metaphlan bioconda/noarch::metaphlan-2.8.1-py_1 msgpack-python conda-forge/linux-64::msgpack-python-1.0.0-py27h9e3301b_1 muscle bioconda/linux-64::muscle-5.3-h4ac6f70_0 ncbi-vdb bioconda/linux-64::ncbi-vdb-3.2.0-h9948957_0 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3 numpy conda-forge/linux-64::numpy-1.16.5-py27h95a1406_0 openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0 pandas conda-forge/linux-64::pandas-0.24.2-py27hb3f55d8_0 perl conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 perl-archive-tar bioconda/noarch::perl-archive-tar-2.40-pl5321hdfd78af_0 perl-carp conda-forge/noarch::perl-carp-1.50-pl5321hd8ed1ab_0 perl-common-sense conda-forge/noarch::perl-common-sense-3.75-pl5321hd8ed1ab_0 perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-bzip2-2.201-pl5321hbf60520_0 perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-zlib-2.202-pl5321hadc24fc_0 perl-encode conda-forge/linux-64::perl-encode-3.21-pl5321hb9d3cd8_1 perl-exporter conda-forge/noarch::perl-exporter-5.74-pl5321hd8ed1ab_0 perl-exporter-tiny conda-forge/noarch::perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0 perl-extutils-mak~ conda-forge/noarch::perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 perl-io-compress bioconda/linux-64::perl-io-compress-2.201-pl5321h503566f_4 perl-io-zlib bioconda/noarch::perl-io-zlib-1.14-pl5321hdfd78af_0 perl-json bioconda/noarch::perl-json-4.10-pl5321hdfd78af_1 perl-json-xs bioconda/linux-64::perl-json-xs-4.03-pl5321h9948957_4 perl-list-moreuti~ bioconda/noarch::perl-list-moreutils-0.430-pl5321hdfd78af_0 perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.430-pl5321h7b50bb2_4 perl-parent conda-forge/noarch::perl-parent-0.243-pl5321hd8ed1ab_0 perl-pathtools conda-forge/linux-64::perl-pathtools-3.75-pl5321hb9d3cd8_1 perl-scalar-list-~ conda-forge/linux-64::perl-scalar-list-utils-1.68-pl5321hb9d3cd8_0 perl-storable conda-forge/linux-64::perl-storable-3.15-pl5321hb9d3cd8_0 perl-types-serial~ bioconda/noarch::perl-types-serialiser-1.01-pl5321hdfd78af_0 pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0 pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0 pyopenssl conda-forge/noarch::pyopenssl-19.1.0-py_1 pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 pyqi conda-forge/noarch::pyqi-0.3.2-py_0 pysam bioconda/linux-64::pysam-0.20.0-py27h7835474_0 pysocks conda-forge/linux-64::pysocks-1.7.1-py27h8c360ce_1 python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0 raxml bioconda/linux-64::raxml-8.2.13-h7b50bb2_3 readline conda-forge/linux-64::readline-8.2-h8c095d6_2 requests conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0 rpsbproc bioconda/linux-64::rpsbproc-0.5.0-h6a68c12_1 samtools bioconda/linux-64::samtools-0.1.19-h50ea8bc_11 scipy conda-forge/linux-64::scipy-1.2.1-py27h921218d_2 setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0 singledispatch conda-forge/noarch::singledispatch-3.6.1-pyh44b312d_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 subprocess32 conda-forge/linux-64::subprocess32-3.5.4-py27h516909a_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tornado conda-forge/linux-64::tornado-5.1.1-py27h14c3975_1000 urllib3 conda-forge/noarch::urllib3-1.26.15-pyhd8ed1ab_0 wget conda-forge/linux-64::wget-1.20.3-ha56f1ee_1 wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0 zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6 zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda install -q -y tbb=2020.2` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - tbb=2020.2 The following packages will be downloaded: package | build ---------------------------|----------------- tbb-2020.2 | h4bd325d_4 1.5 MB conda-forge ------------------------------------------------------------ Total: 1.5 MB The following NEW packages will be INSTALLED: tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_4 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda install -q -y kneaddata` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - kneaddata The following packages will be downloaded: package | build ---------------------------|----------------- alsa-lib-1.2.3.2 | h166bdaf_0 554 KB conda-forge cairo-1.16.0 | hcf35c78_1003 1.5 MB conda-forge expat-2.6.4 | h5888daf_0 135 KB conda-forge fastqc-0.12.1 | hdfd78af_0 11.1 MB bioconda font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge fontconfig-2.14.2 | h14ed4e7_0 266 KB conda-forge giflib-5.2.2 | hd590300_0 75 KB conda-forge glib-2.66.3 | h58526e2_0 500 KB conda-forge graphite2-1.3.13 | h59595ed_1003 95 KB conda-forge harfbuzz-2.4.0 | h9f30f68_3 1.5 MB conda-forge java-jdk-8.0.92 | 1 122.3 MB bioconda jpeg-9e | h0b41bf4_3 235 KB conda-forge kneaddata-0.7.6 | py27hbf8c060_0 591 KB biobakery lcms2-2.12 | hddcbb42_0 443 KB conda-forge libglib-2.66.3 | hbe7bbb4_0 3.0 MB conda-forge libiconv-1.18 | h4ce23a2_1 696 KB conda-forge libtiff-4.2.0 | hf544144_3 590 KB conda-forge libwebp-base-1.5.0 | h851e524_0 420 KB conda-forge libxcb-1.17.0 | h8a09558_0 387 KB conda-forge openjdk-11.0.8 | hacce0ff_0 173.3 MB conda-forge pcre-8.45 | h9c3ff4c_0 253 KB conda-forge pixman-0.38.0 | h516909a_1003 594 KB conda-forge pthread-stubs-0.4 | hb9d3cd8_1002 8 KB conda-forge trf-4.09.1 | h7b50bb2_7 68 KB bioconda xorg-libice-1.1.2 | hb9d3cd8_0 57 KB conda-forge xorg-libsm-1.2.5 | he73a12e_0 27 KB conda-forge xorg-libx11-1.8.11 | h4f16b4b_0 816 KB conda-forge xorg-libxau-1.0.12 | hb9d3cd8_0 14 KB conda-forge xorg-libxdmcp-1.1.5 | hb9d3cd8_0 19 KB conda-forge xorg-libxext-1.3.6 | hb9d3cd8_0 49 KB conda-forge xorg-libxfixes-6.0.1 | hb9d3cd8_0 19 KB conda-forge xorg-libxi-1.8.2 | hb9d3cd8_0 46 KB conda-forge xorg-libxrender-0.9.12 | hb9d3cd8_0 32 KB conda-forge xorg-libxtst-1.2.5 | hb9d3cd8_3 32 KB conda-forge ------------------------------------------------------------ Total: 319.9 MB The following NEW packages will be INSTALLED: alsa-lib conda-forge/linux-64::alsa-lib-1.2.3.2-h166bdaf_0 cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 expat conda-forge/linux-64::expat-2.6.4-h5888daf_0 fastqc bioconda/noarch::fastqc-0.12.1-hdfd78af_0 font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 giflib conda-forge/linux-64::giflib-5.2.2-hd590300_0 glib conda-forge/linux-64::glib-2.66.3-h58526e2_0 graphite2 conda-forge/linux-64::graphite2-1.3.13-h59595ed_1003 harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 java-jdk bioconda/linux-64::java-jdk-8.0.92-1 jpeg conda-forge/linux-64::jpeg-9e-h0b41bf4_3 kneaddata biobakery/linux-64::kneaddata-0.7.6-py27hbf8c060_0 lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0 libexpat conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 libglib conda-forge/linux-64::libglib-2.66.3-hbe7bbb4_0 libiconv conda-forge/linux-64::libiconv-1.18-h4ce23a2_1 libtiff conda-forge/linux-64::libtiff-4.2.0-hf544144_3 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libwebp-base conda-forge/linux-64::libwebp-base-1.5.0-h851e524_0 libxcb conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 openjdk conda-forge/linux-64::openjdk-11.0.8-hacce0ff_0 pcre conda-forge/linux-64::pcre-8.45-h9c3ff4c_0 pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 trf bioconda/linux-64::trf-4.09.1-h7b50bb2_7 xorg-libice conda-forge/linux-64::xorg-libice-1.1.2-hb9d3cd8_0 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.5-he73a12e_0 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.11-h4f16b4b_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.12-hb9d3cd8_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-6.0.1-hb9d3cd8_0 xorg-libxi conda-forge/linux-64::xorg-libxi-1.8.2-hb9d3cd8_0 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.12-hb9d3cd8_0 xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.5-hb9d3cd8_3 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ┌ Warning: Don't forget to add /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/bin to your PATH! │ │ This can be done in a julia session with: │ │ `ENV["PATH"] = ENV["PATH"] * ":" * "/home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/bin"`, │ or you can set it in your shell environment. └ @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:29 ┌ Error: Can not find `metaphlan`! If you think it should be installed, │ try running: │ │ ``` │ ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(env) │ ``` │ │ Where `env` is something like `:BiobakeryUtils`. └ @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:59 ┌ Error: Can not find `metaphlan`! If you think it should be installed, │ try running: │ │ ``` │ ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(env) │ ``` │ │ Where `env` is something like `:BiobakeryUtils`. └ @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:59 usage: merge_metaphlan_tables.py [-h] input.txt [input.txt ...] Please make sure to supply file paths to the files to combine. If combining 3 files (Table1.txt, Table2.txt, and Table3.txt) the call should be: python merge_metaphlan_tables.py Table1.txt Table2.txt Table3.txt > output.txt A wildcard to indicate all .txt files that start with Table can be used as follows: python merge_metaphlan_tables.py Table*.txt > output.txt merge_metaphlan_tables.py: error: unrecognized arguments: -o [ Info: Running command: `humann -i '' -o '' --help` usage: humann [-h] -i -o [--threads <1>] [--version] [-r] [--bypass-nucleotide-index] [--bypass-nucleotide-search] [--bypass-prescreen] [--bypass-translated-search] [--taxonomic-profile ] [--memory-use {minimum,maximum}] [--input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}] [-v] [--metaphlan ] [--metaphlan-options ] [--prescreen-threshold <0.5>] [--average-read-length <150.0>] [--bowtie2 ] [--bowtie-options ] [--nucleotide-database ] [--nucleotide-identity-threshold <0.0>] [--nucleotide-query-coverage-threshold <90.0>] [--nucleotide-subject-coverage-threshold <50.0>] [--diamond ] [--diamond-options ] [--evalue <1.0>] [--protein-database ] [--translated-alignment {diamond}] [--translated-identity-threshold <50.0>] [--translated-query-coverage-threshold <90.0>] [--translated-subject-coverage-threshold <50.0>] [--count-normalization {Adjusted CPMs,Adjusted RPKs,RPKs,Counts}] [--utility-database ] [--gap-fill {on,off}] [--minpath {on,off}] [--pathways {metacyc,unipathway}] [--pathways-database ] [--xipe {on,off}] [--annotation-gene-index <2>] [--id-mapping ] [--remove-temp-output] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--o-log ] [--output-basename ] [--output-format {tsv,biom}] [--output-max-decimals <10>] [--remove-column-description-output] [--remove-stratified-output] HUMAnN : HMP Unified Metabolic Analysis Network 3 optional arguments: -h, --help show this help message and exit [0] Common settings: -i , --input input file of type {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} [REQUIRED] -o , --output directory to write output files [REQUIRED] --threads <1> number of threads/processes [DEFAULT: 1] --version show program's version number and exit [1] Workflow refinement: -r, --resume bypass commands if the output files exist --bypass-nucleotide-index bypass the nucleotide index step and run on the indexed ChocoPhlAn database --bypass-nucleotide-search bypass the nucleotide search steps --bypass-prescreen bypass the prescreen step and run on the full ChocoPhlAn database --bypass-translated-search bypass the translated search step --taxonomic-profile a taxonomic profile (the output file created by metaphlan) [DEFAULT: file will be created] --memory-use {minimum,maximum} the amount of memory to use [DEFAULT: minimum] --input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} the format of the input file [DEFAULT: format identified by software] -v, --verbose additional output is printed [2] Configure tier 1: prescreen: --metaphlan directory containing the MetaPhlAn software [DEFAULT: $PATH] --metaphlan-options options to be provided to the MetaPhlAn software [DEFAULT: "-t rel_ab_w_read_stats"] --prescreen-threshold <0.5> minimum estimated genome coverage for inclusion in pangenome search [DEFAULT: 0.5] --average-read-length <150.0> average read length for input file [DEFAULT: 150.0] [3] Configure tier 2: nucleotide search: --bowtie2 directory containing the bowtie2 executable [DEFAULT: $PATH] --bowtie-options options to be provided to the bowtie software [DEFAULT: "--very-sensitive --no-hd --no-sq"] --nucleotide-database directory containing the nucleotide database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python2.7/site-packages/humann/data/chocophlan_DEMO] --nucleotide-identity-threshold <0.0> identity threshold for nucleotide alignments [DEFAULT: 0.0] --nucleotide-query-coverage-threshold <90.0> query coverage threshold for nucleotide alignments [DEFAULT: 90.0] --nucleotide-subject-coverage-threshold <50.0> subject coverage threshold for nucleotide alignments [DEFAULT: 50.0] [3] Configure tier 2: translated search: --diamond directory containing the diamond executable [DEFAULT: $PATH] --diamond-options options to be provided to the diamond software [DEFAULT: "--top 1 --sensitive --outfmt 6"] --evalue <1.0> the evalue threshold to use with the translated search [DEFAULT: 1.0] --protein-database directory containing the protein database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python2.7/site-packages/humann/data/uniref_DEMO] --translated-alignment {diamond} software to use for translated alignment [DEFAULT: diamond] --translated-identity-threshold <50.0> identity threshold for translated alignments [DEFAULT: 50.0] --translated-query-coverage-threshold <90.0> query coverage threshold for translated alignments [DEFAULT: 90.0] --translated-subject-coverage-threshold <50.0> subject coverage threshold for translated alignments [DEFAULT: 50.0] [5] Gene and pathway quantification: --count-normalization {Adjusted CPMs,Adjusted RPKs,RPKs,Counts} normalization mode for results from both nucleotide and translated search [DEFAULT: Adjusted CPMs] --utility-database directory containing the utility database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python2.7/site-packages/humann/data/utility_DEMO] --gap-fill {on,off} turn on/off the gap fill computation [DEFAULT: on] --minpath {on,off} turn on/off the minpath computation [DEFAULT: on] --pathways {metacyc,unipathway} the database to use for pathway computations [DEFAULT: metacyc] --pathways-database mapping file (or files, at most two in a comma-delimited list) to use for pathway computations [DEFAULT: metacyc database ] --xipe {on,off} turn on/off the xipe computation [DEFAULT: off] --annotation-gene-index <2> the index of the gene in the sequence annotation [DEFAULT: 2] --id-mapping id mapping file for alignments [DEFAULT: alignment reference used] [6] More output configuration: --remove-temp-output remove temp output files [DEFAULT: temp files are not removed] --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} level of messages to display in log [DEFAULT: DEBUG] --o-log log file [DEFAULT: sample_0.log] --output-basename the basename for the output files [DEFAULT: input file basename] --output-format {tsv,biom} the format of the output files [DEFAULT: tsv] --output-max-decimals <10> the number of decimals to output [DEFAULT: 10] --remove-column-description-output remove the description in the output column [DEFAULT: output column includes description] --remove-stratified-output remove stratification from output [DEFAULT: output is stratified] Pass Error Total CLI | 9 3 12 Utilities | 2 2 Metaphlan | 1 3 4 Humann | 6 6 Metaphlan: Error During Test at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 Test threw exception Expression: BiobakeryUtils.check_for_install("metaphlan") |> isnothing failed process: Process(`which metaphlan`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Base.CmdRedirect; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] check_for_install(tool::String) @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:56 [5] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined] [7] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 [inlined] [8] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [9] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 [inlined] [10] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 [inlined] [11] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:25 [inlined] [12] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [13] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:15 [inlined] [14] top-level scope @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 Metaphlan: Error During Test at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:29 Test threw exception Expression: (metaphlan("", ""; help = true)).exitcode == 0 failed process: Process(`which metaphlan`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Base.CmdRedirect; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] check_for_install(tool::String) @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:56 [5] metaphlan(inputfile::String, output::String; kwargs::@Kwargs{help::Bool}) @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/metaphlan.jl:33 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined] [7] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:29 [inlined] [8] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [9] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 [inlined] [10] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 [inlined] [11] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:25 [inlined] [12] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [13] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:15 [inlined] [14] top-level scope @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 Metaphlan: Error During Test at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:32 Test threw exception Expression: (metaphlan_merge(profiles, joinpath(#= /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:32 =# @__DIR__(), "files/metaphlan/merged_abundance_table.tsv"))).exitcode == 0 failed process: Process(`merge_metaphlan_tables.py -o /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/merged_abundance_table.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014459-Stool_profile.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014464-Anterior_nares_profile.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014470-Tongue_dorsum_profile.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014472-Buccal_mucosa_profile.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014476-Supragingival_plaque_profile.tsv /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/files/metaphlan/SRS014494-Posterior_fornix_profile.tsv`, ProcessExited(2)) [2] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] metaphlan_merge(paths::Vector{String}, output::String; kwargs::@Kwargs{}) @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/metaphlan.jl:67 [5] metaphlan_merge(paths::Vector{String}, output::String) @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/metaphlan.jl:54 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined] [7] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:32 [inlined] [8] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [9] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:26 [inlined] [10] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 [inlined] [11] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:25 [inlined] [12] macro expansion @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:670 [inlined] [13] macro expansion @ ~/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:15 [inlined] [14] top-level scope @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517 Main.BiobakeryUtilsTests | 9 3 12 ERROR: LoadError: Some tests did not pass: 9 passed, 0 failed, 3 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/runtests.jl:2 Testing failed after 358.12s ERROR: LoadError: Package BiobakeryUtils errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 437.9s: package tests unexpectedly errored