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Conda package #13

Closed
gallardoalba opened this issue Jun 22, 2023 · 16 comments
Closed

Conda package #13

gallardoalba opened this issue Jun 22, 2023 · 16 comments
Labels
enhancement

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@gallardoalba
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Hi,

I'm trying to create the Bioconda package, but not sure why it not working. Have you experience on that? Here is the PR bioconda/bioconda-recipes#41628

Regards
@HajkD
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HajkD commented Jun 24, 2023

Hi @gallardoalba

Thank you very much for reaching out!

@LotharukpongJS Would it be possible to help here?

If it is more tricky to solve, I will be back to office on 3rd July and will look into this.

With many thanks and very best wishes,
Hajk

@gallardoalba
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Contributor Author

Hi @gallardoalba

Thank you very much for reaching out!

@LotharukpongJS Would it be possible to help here?

If it is more tricky to solve, I will be back to office on 3rd July and will look into this.

With many thanks and very best wishes, Hajk

Thanks a lot! I'm planing to create a Galaxy training for the tool, so probably will stay in touch.

Regards

@LotharukpongJS
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Collaborator

Hi @gallardoalba ,

I had a look at your recipe file and building it was fine until there was an RcppArmadillo dependency error. I am not sure if this is due to the R version I am using. Is this an error you have noticed?

I will update my R and check again tomorrow. Conda-build takes a very long time so I sadly couldn't test a lot of things at once...

conda-build r-mytai

ERROR: dependency ‘RcppArmadillo’ is not available for package ‘myTAI’
See more 
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-mytai
INFO:conda_build.metadata:Attempting to finalize metadata for r-mytai
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh


The following NEW packages will be INSTALLED:

    _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:    2.40-hf600244_0            conda-forge
    bioconductor-edger:        3.40.0-r42hf17093f_1       bioconda   
    bioconductor-limma:        3.54.0-r42ha9d7317_1       bioconda   
    bwidget:                   1.9.14-ha770c72_1          conda-forge
    bzip2:                     1.0.8-h7f98852_4           conda-forge
    c-ares:                    1.19.1-hd590300_0          conda-forge
    ca-certificates:           2023.5.7-hbcca054_0        conda-forge
    cairo:                     1.16.0-hbbf8b49_1016       conda-forge
    curl:                      8.1.2-h409715c_0           conda-forge
    expat:                     2.5.0-hcb278e6_1           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:                2.14.2-h14ed4e7_0          conda-forge
    fonts-conda-ecosystem:     1-0                        conda-forge
    fonts-conda-forge:         1-0                        conda-forge
    freetype:                  2.12.1-hca18f0e_1          conda-forge
    fribidi:                   1.0.10-h36c2ea0_0          conda-forge
    gcc_impl_linux-64:         13.1.0-hc4be1a9_0          conda-forge
    gettext:                   0.21.1-h27087fc_0          conda-forge
    gfortran_impl_linux-64:    13.1.0-hd511a9b_0          conda-forge
    glpk:                      5.0-h445213a_0             conda-forge
    gmp:                       6.2.1-h58526e2_0           conda-forge
    graphite2:                 1.3.13-h58526e2_1001       conda-forge
    gsl:                       2.7-he838d99_0             conda-forge
    gxx_impl_linux-64:         13.1.0-hc4be1a9_0          conda-forge
    harfbuzz:                  7.3.0-hdb3a94d_0           conda-forge
    icu:                       72.1-hcb278e6_0            conda-forge
    kernel-headers_linux-64:   2.6.32-he073ed8_15         conda-forge
    keyutils:                  1.6.1-h166bdaf_0           conda-forge
    krb5:                      1.20.1-h81ceb04_0          conda-forge
    ld_impl_linux-64:          2.40-h41732ed_0            conda-forge
    lerc:                      4.0.0-h27087fc_0           conda-forge
    libblas:                   3.9.0-17_linux64_openblas  conda-forge
    libcblas:                  3.9.0-17_linux64_openblas  conda-forge
    libcurl:                   8.1.2-h409715c_0           conda-forge
    libdeflate:                1.18-h0b41bf4_0            conda-forge
    libedit:                   3.1.20191231-he28a2e2_2    conda-forge
    libev:                     4.33-h516909a_1            conda-forge
    libexpat:                  2.5.0-hcb278e6_1           conda-forge
    libffi:                    3.4.2-h7f98852_5           conda-forge
    libgcc-devel_linux-64:     13.1.0-he3cc6c4_0          conda-forge
    libgcc-ng:                 13.1.0-he5830b7_0          conda-forge
    libgfortran-ng:            13.1.0-h69a702a_0          conda-forge
    libgfortran5:              13.1.0-h15d22d2_0          conda-forge
    libglib:                   2.76.3-hebfc3b9_0          conda-forge
    libgomp:                   13.1.0-he5830b7_0          conda-forge
    libiconv:                  1.17-h166bdaf_0            conda-forge
    libjpeg-turbo:             2.1.5.1-h0b41bf4_0         conda-forge
    liblapack:                 3.9.0-17_linux64_openblas  conda-forge
    libnghttp2:                1.52.0-h61bc06f_0          conda-forge
    libopenblas:               0.3.23-pthreads_h80387f5_0 conda-forge
    libpng:                    1.6.39-h753d276_0          conda-forge
    libsanitizer:              13.1.0-hfd8a6a1_0          conda-forge
    libssh2:                   1.11.0-h0841786_0          conda-forge
    libstdcxx-devel_linux-64:  13.1.0-he3cc6c4_0          conda-forge
    libstdcxx-ng:              13.1.0-hfd8a6a1_0          conda-forge
    libtiff:                   4.5.1-h8b53f26_0           conda-forge
    libuuid:                   2.38.1-h0b41bf4_0          conda-forge
    libwebp-base:              1.3.0-h0b41bf4_0           conda-forge
    libxcb:                    1.15-h0b41bf4_0            conda-forge
    libxml2:                   2.11.4-h0d562d8_0          conda-forge
    libzlib:                   1.2.13-hd590300_5          conda-forge
    make:                      4.3-hd18ef5c_1             conda-forge
    ncurses:                   6.4-hcb278e6_0             conda-forge
    openssl:                   3.1.1-hd590300_1           conda-forge
    pandoc:                    2.19.2-h32600fe_2          conda-forge
    pango:                     1.50.14-heaa33ce_1         conda-forge
    pcre2:                     10.40-hc3806b6_0           conda-forge
    pixman:                    0.40.0-h36c2ea0_0          conda-forge
    pthread-stubs:             0.4-h36c2ea0_1001          conda-forge
    r-ape:                     5.7_1-r42h08d816e_1        conda-forge
    r-askpass:                 1.1-r42h57805ef_4          conda-forge
    r-assertthat:              0.2.1-r42hc72bb7e_4        conda-forge
    r-backports:               1.4.1-r42h57805ef_2        conda-forge
    r-base:                    4.2.3-hfabd6f2_3           conda-forge
    r-base64enc:               0.1_3-r42h57805ef_1006     conda-forge
    r-bit:                     4.0.5-r42h57805ef_1        conda-forge
    r-bit64:                   4.0.5-r42h57805ef_2        conda-forge
    r-bold:                    1.3.0-r42h785f33e_1        conda-forge
    r-bslib:                   0.5.0-r42hc72bb7e_1        conda-forge
    r-cachem:                  1.0.8-r42h57805ef_1        conda-forge
    r-checkmate:               2.2.0-r42h57805ef_1        conda-forge
    r-cli:                     3.6.1-r42ha503ecb_1        conda-forge
    r-clipr:                   0.8.0-r42hc72bb7e_2        conda-forge
    r-cluster:                 2.1.4-r42h61816a4_1        conda-forge
    r-codetools:               0.2_19-r42hc72bb7e_1       conda-forge
    r-colorspace:              2.1_0-r42h57805ef_1        conda-forge
    r-conditionz:              0.1.0-r42hc72bb7e_3        conda-forge
    r-cpp11:                   0.4.3-r42hc72bb7e_1        conda-forge
    r-crayon:                  1.5.2-r42hc72bb7e_2        conda-forge
    r-crul:                    1.4.0-r42h785f33e_1        conda-forge
    r-curl:                    5.0.1-r42hf9611b0_0        conda-forge
    r-data.table:              1.14.8-r42h029312a_2       conda-forge
    r-deldir:                  1.0_9-r42h61816a4_1        conda-forge
    r-digest:                  0.6.31-r42ha503ecb_1       conda-forge
    r-doparallel:              1.0.17-r42hc72bb7e_2       conda-forge
    r-dplyr:                   1.1.2-r42ha503ecb_1        conda-forge
    r-ellipsis:                0.3.2-r42h57805ef_2        conda-forge
    r-evaluate:                0.21-r42hc72bb7e_1         conda-forge
    r-fansi:                   1.0.4-r42h57805ef_1        conda-forge
    r-farver:                  2.1.1-r42ha503ecb_2        conda-forge
    r-fastmap:                 1.1.1-r42ha503ecb_1        conda-forge
    r-fastmatch:               1.1_3-r42h57805ef_2        conda-forge
    r-fitdistrplus:            1.1_11-r42hc72bb7e_1       conda-forge
    r-fontawesome:             0.5.1-r42hc72bb7e_1        conda-forge
    r-foreach:                 1.5.2-r42hc72bb7e_2        conda-forge
    r-foreign:                 0.8_84-r42h57805ef_1       conda-forge
    r-formula:                 1.2_5-r42hc72bb7e_1        conda-forge
    r-fs:                      1.6.2-r42ha503ecb_1        conda-forge
    r-generics:                0.1.3-r42hc72bb7e_2        conda-forge
    r-ggplot2:                 3.4.2-r42hc72bb7e_1        conda-forge
    r-glue:                    1.6.2-r42h57805ef_2        conda-forge
    r-gridextra:               2.3-r42hc72bb7e_1005       conda-forge
    r-gtable:                  0.3.3-r42hc72bb7e_1        conda-forge
    r-highr:                   0.10-r42hc72bb7e_1         conda-forge
    r-hmisc:                   5.1_0-r42h61816a4_1        conda-forge
    r-hms:                     1.1.3-r42hc72bb7e_1        conda-forge
    r-htmltable:               2.4.1-r42hc72bb7e_2        conda-forge
    r-htmltools:               0.5.5-r42ha503ecb_1        conda-forge
    r-htmlwidgets:             1.6.2-r42hc72bb7e_1        conda-forge
    r-httpcode:                0.3.0-r42ha770c72_3        conda-forge
    r-httr:                    1.4.6-r42hc72bb7e_1        conda-forge
    r-igraph:                  1.4.3-r42h9254619_1        conda-forge
    r-interp:                  1.1_4-r42ha503ecb_1        conda-forge
    r-isoband:                 0.2.7-r42ha503ecb_2        conda-forge
    r-iterators:               1.0.14-r42hc72bb7e_2       conda-forge
    r-jpeg:                    0.1_10-r42h0de940f_3       conda-forge
    r-jquerylib:               0.1.4-r42hc72bb7e_2        conda-forge
    r-jsonlite:                1.8.5-r42h57805ef_1        conda-forge
    r-knitr:                   1.43-r42hc72bb7e_1         conda-forge
    r-labeling:                0.4.2-r42hc72bb7e_3        conda-forge
    r-lattice:                 0.21_8-r42h57805ef_1       conda-forge
    r-latticeextra:            0.6_30-r42hc72bb7e_2       conda-forge
    r-lazyeval:                0.2.2-r42h57805ef_4        conda-forge
    r-lifecycle:               1.0.3-r42hc72bb7e_2        conda-forge
    r-locfit:                  1.5_9.8-r42h57805ef_1      conda-forge
    r-lsei:                    1.3_0-r42hd8f1df9_3        conda-forge
    r-magrittr:                2.0.3-r42h57805ef_2        conda-forge
    r-mass:                    7.3_60-r42h57805ef_1       conda-forge
    r-matrix:                  1.5_4.1-r42h316c678_1      conda-forge
    r-memoise:                 2.0.1-r42hc72bb7e_2        conda-forge
    r-mgcv:                    1.8_42-r42h316c678_2       conda-forge
    r-mime:                    0.12-r42h57805ef_2         conda-forge
    r-munsell:                 0.5.0-r42hc72bb7e_1006     conda-forge
    r-natserv:                 1.0.0-r42hc72bb7e_2        conda-forge
    r-nlme:                    3.1_162-r42h61816a4_1      conda-forge
    r-nnet:                    7.3_19-r42h57805ef_1       conda-forge
    r-nortest:                 1.0_4-r42hc72bb7e_1005     conda-forge
    r-npsurv:                  0.5_0-r42hc72bb7e_2        conda-forge
    r-openssl:                 2.0.6-r42hb353fa6_1        conda-forge
    r-pbapply:                 1.7_2-r42hc72bb7e_0        conda-forge
    r-phangorn:                2.11.1-r42h7ce84a7_1       conda-forge
    r-pillar:                  1.9.0-r42hc72bb7e_1        conda-forge
    r-pkgconfig:               2.0.3-r42hc72bb7e_3        conda-forge
    r-plyr:                    1.8.8-r42ha503ecb_1        conda-forge
    r-png:                     0.1_8-r42h81d01c5_1        conda-forge
    r-prettyunits:             1.1.1-r42hc72bb7e_3        conda-forge
    r-progress:                1.2.2-r42hc72bb7e_4        conda-forge
    r-purrr:                   1.0.1-r42h57805ef_1        conda-forge
    r-quadprog:                1.5_8-r42h13b3f57_5        conda-forge
    r-r.methodss3:             1.8.2-r42hc72bb7e_2        conda-forge
    r-r.oo:                    1.25.0-r42hc72bb7e_2       conda-forge
    r-r.utils:                 2.12.2-r42hc72bb7e_1       conda-forge
    r-r6:                      2.5.1-r42hc72bb7e_2        conda-forge
    r-rappdirs:                0.3.3-r42h57805ef_2        conda-forge
    r-ratelimitr:              0.4.1-r42hc72bb7e_2        conda-forge
    r-rcolorbrewer:            1.1_3-r42h785f33e_2        conda-forge
    r-rcpp:                    1.0.10-r42ha503ecb_1       conda-forge
    r-rcppeigen:               0.3.3.9.3-r42h08d816e_1    conda-forge
    r-readr:                   2.1.4-r42ha503ecb_1        conda-forge
    r-rentrez:                 1.2.3-r42h785f33e_2        conda-forge
    r-reshape:                 0.8.9-r42hc72bb7e_2        conda-forge
    r-reshape2:                1.4.4-r42ha503ecb_3        conda-forge
    r-rex:                     1.2.1-r42hc72bb7e_2        conda-forge
    r-ritis:                   1.0.0-r42hc72bb7e_2        conda-forge
    r-rlang:                   1.1.1-r42ha503ecb_1        conda-forge
    r-rmarkdown:               2.22-r42hc72bb7e_1         conda-forge
    r-rncl:                    0.8.7-r42ha503ecb_1        conda-forge
    r-rotl:                    3.1.0-r42hc72bb7e_1        conda-forge
    r-rpart:                   4.1.19-r42h57805ef_1       conda-forge
    r-rredlist:                0.7.1-r42hc72bb7e_1        conda-forge
    r-rstudioapi:              0.14-r42hc72bb7e_2         conda-forge
    r-sass:                    0.4.6-r42ha503ecb_1        conda-forge
    r-scales:                  1.2.1-r42hc72bb7e_2        conda-forge
    r-solrium:                 1.2.0-r42h785f33e_2        conda-forge
    r-stringi:                 1.7.12-r42hc0c3e09_2       conda-forge
    r-stringr:                 1.5.0-r42h785f33e_1        conda-forge
    r-survival:                3.5_5-r42h57805ef_1        conda-forge
    r-sys:                     3.4.2-r42h57805ef_1        conda-forge
    r-taxize:                  0.9.100-r42hc72bb7e_2      conda-forge
    r-tibble:                  3.2.1-r42h57805ef_2        conda-forge
    r-tidyselect:              1.2.0-r42hc72bb7e_1        conda-forge
    r-tinytex:                 0.45-r42hc72bb7e_1         conda-forge
    r-triebeard:               0.4.1-r42ha503ecb_1        conda-forge
    r-tzdb:                    0.4.0-r42ha503ecb_1        conda-forge
    r-urltools:                1.7.3-r42ha503ecb_4        conda-forge
    r-utf8:                    1.2.3-r42h57805ef_1        conda-forge
    r-uuid:                    1.1_0-r42h57805ef_2        conda-forge
    r-vctrs:                   0.6.3-r42ha503ecb_0        conda-forge
    r-viridis:                 0.6.3-r42hc72bb7e_1        conda-forge
    r-viridislite:             0.4.2-r42hc72bb7e_1        conda-forge
    r-vroom:                   1.6.3-r42ha503ecb_1        conda-forge
    r-wikidataqueryservicer:   1.0.0-r42hc72bb7e_2        conda-forge
    r-wikidatar:               2.3.3-r42hc72bb7e_2        conda-forge
    r-wikipedir:               1.5.0-r42hd8ed1ab_1005     conda-forge
    r-wikitaxa:                0.4.0-r42h785f33e_2        conda-forge
    r-withr:                   2.5.0-r42hc72bb7e_2        conda-forge
    r-worrms:                  0.4.3-r42h785f33e_0        conda-forge
    r-xfun:                    0.39-r42ha503ecb_1         conda-forge
    r-xml:                     3.99_0.14-r42hc38eee6_2    conda-forge
    r-xml2:                    1.3.4-r42h1ad5fc0_2        conda-forge
    r-yaml:                    2.3.7-r42h57805ef_1        conda-forge
    r-zoo:                     1.8_12-r42h57805ef_1       conda-forge
    readline:                  8.2-h8228510_1             conda-forge
    sed:                       4.8-he412f7d_0             conda-forge
    sysroot_linux-64:          2.12-he073ed8_15           conda-forge
    tk:                        8.6.12-h27826a3_0          conda-forge
    tktable:                   2.10-hb7b940f_3            conda-forge
    xorg-kbproto:              1.0.7-h7f98852_1002        conda-forge
    xorg-libice:               1.0.10-h7f98852_0          conda-forge
    xorg-libsm:                1.2.3-hd9c2040_1000        conda-forge
    xorg-libx11:               1.8.6-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:           0.9.10-h7f98852_1003       conda-forge
    xorg-libxt:                1.3.0-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:                      1.5.2-h3eb15da_6           conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_build_env


The following NEW packages will be INSTALLED:

    _libgcc_mutex:            0.1-conda_forge         conda-forge
    _openmp_mutex:            4.5-2_gnu               conda-forge
    autoconf:                 2.71-pl5321h2b4cb7a_1   conda-forge
    binutils_impl_linux-64:   2.40-hf600244_0         conda-forge
    binutils_linux-64:        2.40-hbdbef99_0         conda-forge
    gcc_impl_linux-64:        13.1.0-hc4be1a9_0       conda-forge
    gcc_linux-64:             13.1.0-hd2d1137_0       conda-forge
    gxx_impl_linux-64:        13.1.0-hc4be1a9_0       conda-forge
    gxx_linux-64:             13.1.0-h5006d2a_0       conda-forge
    kernel-headers_linux-64:  2.6.32-he073ed8_15      conda-forge
    ld_impl_linux-64:         2.40-h41732ed_0         conda-forge
    libgcc-devel_linux-64:    13.1.0-he3cc6c4_0       conda-forge
    libgcc-ng:                13.1.0-he5830b7_0       conda-forge
    libgomp:                  13.1.0-he5830b7_0       conda-forge
    libnsl:                   2.0.0-h7f98852_0        conda-forge
    libsanitizer:             13.1.0-hfd8a6a1_0       conda-forge
    libstdcxx-devel_linux-64: 13.1.0-he3cc6c4_0       conda-forge
    libstdcxx-ng:             13.1.0-hfd8a6a1_0       conda-forge
    m4:                       1.4.18-h516909a_1001    conda-forge
    perl:                     5.32.1-2_h7f98852_perl5 conda-forge
    sysroot_linux-64:         2.12-he073ed8_15        conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Source cache directory is: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/src_cache
INFO:conda_build.source:Source cache directory is: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/src_cache
Downloading source to cache: myTAI_0.9.3_9dc0ed24dd.tar.gz
INFO:conda_build.source:Downloading source to cache: myTAI_0.9.3_9dc0ed24dd.tar.gz
Downloading https://cran.r-project.org/src/contrib/myTAI_0.9.3.tar.gz
INFO:conda_build.source:Downloading https://cran.r-project.org/src/contrib/myTAI_0.9.3.tar.gz
Success
INFO:conda_build.source:Success
Extracting download
source tree in: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/work
export PREFIX=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
export BUILD_PREFIX=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_build_env
export SRC_DIR=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line
+AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar
+AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as
+CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++filt
+ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit
+GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof
+LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld
+LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold
+NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm
+OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy
+OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump
+RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib
+READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf
+SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size
+STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings
+STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+BUILD=x86_64-conda-linux-gnu
+CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
+CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-mytai-0.9.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
+CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
+CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr
+CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot
+CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
+CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
+CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp
+CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-mytai-0.9.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
+DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include
+GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc
+GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar
+GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm
+GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib
+HOST=x86_64-conda-linux-gnu
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib
+MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
+build_alias=x86_64-conda-linux-gnu
+host_alias=x86_64-conda-linux-gnu
-BUILD=x86_64-conda_cos6-linux-gnu
INFO: activate-gxx_linux-64.sh made the following environmental changes:
+CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++
+CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-mytai-0.9.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
+CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++
+DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-mytai-0.9.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
+GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g++
* installing to library ‘/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library’
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘myTAI’
* removing ‘/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/myTAI’
Traceback (most recent call last):
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/cli/main_build.py", line 593, in main
    execute(sys.argv[1:])
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/cli/main_build.py", line 573, in execute
    outputs = api.build(
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/api.py", line 253, in build
    return build_tree(
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/build.py", line 3799, in build_tree
    packages_from_this = build(
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/build.py", line 2668, in build
    utils.check_call_env(
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/utils.py", line 450, in check_call_env
    return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
  File "/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/lib/python3.9/site-packages/conda_build/utils.py", line 426, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/conda-bld/r-mytai_1688048714453/work/conda_build.sh']' returned non-zero exit status 1.

Regarding the error, Error in library("myTAI") : there is no package called ‘myTAI’ , my first guess is that it could be related to this commit? Let me know if it is related.

Apologies in advance for I haven't been able to solve it today.

Best,
Sodai

@LotharukpongJS
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Hi @gallardoalba,

After adding - r-rcpparmadillo to host and run, I tried to build the conda package again using

conda-build r-mytai

It finished with

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('myTAI')
> 
> 
+ exit 0

Resource usage statistics from testing r-mytai:
   Process count: 2
   CPU time: Sys=0:00:00.1, User=0:00:00.1
   Memory: 16.2M
   Disk usage: 12B
   Time elapsed: 0:00:04.1


TEST END: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
Renaming work directory '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work' to '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
INFO:conda_build.utils:Renaming work directory '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work' to '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
shutil.move(work)=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work, dest=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
INFO:conda_build.utils:shutil.move(work)=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work, dest=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:


# To have conda build upload to anaconda.org automatically, use
# conda config --set anaconda_upload yes
anaconda upload \
    /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
anaconda_upload is not set.  Not uploading wheels: []

INFO :: The inputs making up the hashes for the built packages are as follows:
{
  "r-mytai-0.9.3-r42h3fd9d12_0": {
    "recipe": {
      "c_compiler": "gcc",
      "cxx_compiler": "gxx",
      "target_platform": "linux-64"
    }
  }
}


####################################################################################
Resource usage summary:

Total time: 0:14:07.3
CPU usage: sys=0:00:32.4, user=0:00:07.6
Maximum memory usage observed: 706.0M
Total disk usage observed (not including envs): 9.2K


####################################################################################
Source and build intermediates have been left in /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld.
There are currently 2 accumulated.
To remove them, you can run the ```conda build purge``` command

Is this the behaviour you expected?

I tried doing the same using on another VM and got something similar

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('myTAI')
> 
> 
+ exit 0

Resource usage statistics from testing r-mytai:
   Process count: 2
   CPU time: Sys=-, User=0:00:00.0
   Memory: 14.3M
   Disk usage: 16B
   Time elapsed: 0:00:02.0


TEST END: /home/ubuntu/miniconda3/envs/pkgtest/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
Renaming work directory '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work' to '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
INFO:conda_build.utils:Renaming work directory '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work' to '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
shutil.move(work)=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work, dest=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
INFO:conda_build.utils:shutil.move(work)=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work, dest=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:


# To have conda build upload to anaconda.org automatically, use
# conda config --set anaconda_upload yes
anaconda upload \
    /home/ubuntu/miniconda3/envs/pkgtest/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
anaconda_upload is not set.  Not uploading wheels: []

INFO :: The inputs making up the hashes for the built packages are as follows:
{
  "r-mytai-0.9.3-r42h3fd9d12_0": {
    "recipe": {
      "c_compiler": "gcc",
      "cxx_compiler": "gxx",
      "target_platform": "linux-64"
    }
  }
}


####################################################################################
Resource usage summary:

Total time: 0:13:42.1
CPU usage: sys=0:00:05.7, user=0:00:09.7
Maximum memory usage observed: 700.3M
Total disk usage observed (not including envs): 8.0K


####################################################################################
Source and build intermediates have been left in /home/ubuntu/miniconda3/envs/pkgtest/conda-bld.
There are currently 6 accumulated.
To remove them, you can run the ```conda build purge``` command

Best,
Sodai

@LotharukpongJS LotharukpongJS mentioned this issue Jun 30, 2023
Closed
@HajkD
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HajkD commented Jul 1, 2023

Dear @LotharukpongJS

Thank you very much for pushing this forward! I think you solved it!

@gallardoalba Does the installation work for you now?

With very best wishes,
Hajk

@gallardoalba
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Yes, I think so. Thanks a lot!

@gallardoalba gallardoalba reopened this Jul 3, 2023
@gallardoalba
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Sorry for bothering you again. I tried to include the dependency, but I'm still not able to build the package locally. When I try to install myTAI locally, I get this dependency problem:

* installing *source* package ‘textshaping’ ...
** package ‘textshaping’ successfully unpacked and MD5 sums checked
** using staged installation
Inconsistency detected by ld.so: dl-call-libc-early-init.c: 37: _dl_call_libc_early_init: Assertion `sym != NULL' failed!
Inconsistency detected by ld.so: dl-call-libc-early-init.c: 37: _dl_call_libc_early_init: Assertion `sym != NULL' failed!
Using PKG_CFLAGS=
Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
 * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
 * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
 * csw: libharfbuzz_dev libfribidi_dev (Solaris)
 * brew: harfbuzz fribidi (OSX)
If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: hb-ft.h: No such file or directory
compilation terminated.

Do you think it could be related with the error?

Regards

@HajkD
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HajkD commented Jul 3, 2023

Hi @gallardoalba

Did you have a chance to try following the error message and install the suggested libraries?

Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
 * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
 * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
 * csw: libharfbuzz_dev libfribidi_dev (Solaris)
 * brew: harfbuzz fribidi (OSX)

Configuration failed to find the harfbuzz freetype2 fribidi library

Let me know if this helps.

@LotharukpongJS
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Hi @gallardoalba

Could you also let us know about your sessionInfo()?

Perhaps you can also add fribidi and harfbuzz via conda (perhaps with -c anaconda). Please double-check the link though.

However, I don't think these packages are typically required for users outside of Hebrew and Arabic languages - perhaps these are packages that should ideally be installed by individual users from these regions.

Description for fribidi:

One of the missing links stopping the penetration of free software in Middle East is the lack of support for the Arabic and Hebrew alphabets. In order to have proper Arabic and Hebrew support, the bidi algorithm needs to be implemented. It is our hope that this library will stimulate more free software in the Middle Eastern countries.

Description for harfbuzz:

HarfBuzz is a text shaping library. New Harbuzz targets various font technologies while Old HarfBuzz targets only OpenType fonts.

Also, see the Wikipedia article for harfbuzz.

A possible solution may be to indicate the channels when using conda-build, i.e.

conda-build r-mytai -c conda-forge -c bioconda -c anaconda

which I used with micromamba. Or perhaps it would help if you can install the packages prior to the build.

Let me know if this helps.

Best,
Sodai

@LotharukpongJS
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Hi again @gallardoalba ,

When making the conda recipe, could you change the package description as to satisfy the updates to the DESCRIPTION file in R? The exact change can be found here #15

Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) doi:10.1093/bioinformatics/btx835). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.

Many thanks in advance,
Sodai

@bgruening
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myTAI is now available as conda package from Bioconda https://anaconda.org/bioconda/r-mytai

@HajkD
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HajkD commented Jul 7, 2023

Wonderful!!! Thank you so much!

@gallardoalba
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myTAI is now available as conda package from Bioconda https://anaconda.org/bioconda/r-mytai

Thanks a lot.

@LotharukpongJS
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Dear @gallardoalba and @bgruening ,

Would it be possible for you to update the conda package description to the one provided here?

When making the conda recipe, could you change the package description as to satisfy the updates to the DESCRIPTION file in R? The exact change can be found here #15

Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) doi:10.1093/bioinformatics/btx835). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.

Best,
Sodai

@gallardoalba
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bioconda/bioconda-recipes#42850

@HajkD
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HajkD commented Sep 6, 2023

Wonderful, thank you so much for pushing this forward!

With very best wishes,
Hajk

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@bgruening @HajkD @gallardoalba @LotharukpongJS