libicui18n.so.64 missing in bioconda build

bernt-matthias commented 8 months ago

Solution to issue cannot be found in the documentation.

[X] I checked the documentation.

Issue

I'm experiencing problems with r-stringi during a bioconda build (https://github.com/bioconda/bioconda-recipes/pull/44971)

19:55:07 BIOCONDA INFO (OUT) > library('reshape2')
19:55:07 BIOCONDA INFO (OUT) Error: package or namespace load failed for ‘reshape2’ in dyn.load(file, DLLpath = DLLpath, ...):
19:55:07 BIOCONDA INFO (OUT)  unable to load shared object '/opt/conda/conda-bld/mitos_1704656792237/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/stringi/libs/stringi.so':
19:55:07 BIOCONDA INFO (OUT)   libicui18n.so.64: cannot open shared object file: No such file or directory
19:55:07 BIOCONDA INFO (OUT) In addition: Warning message:
19:55:07 BIOCONDA INFO (OUT) package ‘reshape2’ was built under R version 3.6.3

Any ideas how to fix this?

R version seems a bit old, but I have not managed to get a newer one: If I require R >3 then I get

20:30:42 BIOCONDA INFO (OUT) The reported errors are:
20:30:42 BIOCONDA INFO (OUT) - Encountered problems while solving:
20:30:42 BIOCONDA INFO (OUT) -   - package r-base-4.0.3-h349a78a_8 requires icu >=68.1,<69.0a0, but none of the providers can be installed

Installed packages

See linked PR

Environment info

Can't access this in the PR

mfansler commented 8 months ago

r-base-4.0.3-h349a78a_8 requires icu >=68.1,<69.0a0

Blame seems to imply that some of the other version constraints in the recipe are simply too old to use R v4.0+ because they haven't been built against newer versions of icu. Either loosen the constraints on anything that depends on icu, or generate new builds of the old versions that are required, but linking against newer icu versions.

mfansler commented 8 months ago

Also, could you please document here the solved environment used when encountering the library loading error? This probably needs some metadata patching to prevent future incompatible installs and I have a backlog of these to handle. The logs on the Bioconda will probably get deleted before I get around to this.

bernt-matthias commented 8 months ago

Thanks for the explanation. Loosening the pins helped.

An environment that failed was the following:

2024-01-07T19:53:25.8024332Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     _libgcc_mutex:            0.1-conda_forge             conda-forge[0m
2024-01-07T19:53:25.8024958Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     _openmp_mutex:            4.5-2_gnu                   conda-forge[0m
2024-01-07T19:53:25.8025486Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     _r-mutex:                 1.0.1-anacondar_1           conda-forge[0m
2024-01-07T19:53:25.8032191Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     alsa-lib:                 1.2.3.2-h166bdaf_0          conda-forge[0m
2024-01-07T19:53:25.8032659Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     binutils_impl_linux-64:   2.36.1-h193b22a_2           conda-forge[0m
2024-01-07T19:53:25.8035435Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     binutils_linux-64:        2.36-hf3e587d_33            conda-forge[0m
2024-01-07T19:53:25.8035857Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     biopython:                1.79-py37h540881e_2         conda-forge[0m
2024-01-07T19:53:25.8036323Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     blast:                    2.9.0-h20b68b9_1            bioconda[0m
2024-01-07T19:53:25.8036743Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     boost:                    1.68.0-py37h8619c78_1001    conda-forge[0m
2024-01-07T19:53:25.8040627Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     boost-cpp:                1.68.0-h11c811c_1000        conda-forge[0m
2024-01-07T19:53:25.8041037Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     bwidget:                  1.9.14-ha770c72_1           conda-forge[0m
2024-01-07T19:53:25.8041592Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     bzip2:                    1.0.8-hd590300_5            conda-forge[0m
2024-01-07T19:53:25.8042364Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     ca-certificates:          2023.11.17-hbcca054_0       conda-forge[0m
2024-01-07T19:53:25.8045046Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     cairo:                    1.16.0-h18b612c_1001        conda-forge[0m
2024-01-07T19:53:25.8045444Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     curl:                     7.68.0-hf8cf82a_0           conda-forge[0m
2024-01-07T19:53:25.8046080Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     expat:                    2.5.0-hcb278e6_1            conda-forge[0m
2024-01-07T19:53:25.8046482Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     fontconfig:               2.14.2-h14ed4e7_0           conda-forge[0m
2024-01-07T19:53:25.8049518Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     freetype:                 2.12.1-h267a509_2           conda-forge[0m
2024-01-07T19:53:25.8049983Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gcc_impl_linux-64:        7.5.0-habd7529_20           conda-forge[0m
2024-01-07T19:53:25.8050407Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gcc_linux-64:             7.5.0-h47867f9_33           conda-forge[0m
2024-01-07T19:53:25.8050977Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gettext:                  0.21.1-h27087fc_0           conda-forge[0m
2024-01-07T19:53:25.8051391Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gfortran_impl_linux-64:   7.5.0-h56cb351_20           conda-forge[0m
2024-01-07T19:53:25.8051874Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gfortran_linux-64:        7.5.0-h78c8a43_33           conda-forge[0m
2024-01-07T19:53:25.8052280Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     giflib:                   5.2.1-h0b41bf4_3            conda-forge[0m
2024-01-07T19:53:25.8058973Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     glib:                     2.78.3-hfc55251_0           conda-forge[0m
2024-01-07T19:53:25.8059408Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     glib-tools:               2.78.3-hfc55251_0           conda-forge[0m
2024-01-07T19:53:25.8059873Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gmp:                      6.3.0-h59595ed_0            conda-forge[0m
2024-01-07T19:53:25.8060274Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gnutls:                   3.6.13-h79a8f9a_0           conda-forge[0m
2024-01-07T19:53:25.8067408Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     graphite2:                1.3.13-h58526e2_1001        conda-forge[0m
2024-01-07T19:53:25.8067856Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gsl:                      2.5-h294904e_1              conda-forge[0m
2024-01-07T19:53:25.8068324Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gxx_impl_linux-64:        7.5.0-hd0bb8aa_20           conda-forge[0m
2024-01-07T19:53:25.8068743Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     gxx_linux-64:             7.5.0-h555fc39_33           conda-forge[0m
2024-01-07T19:53:25.8075045Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     harfbuzz:                 2.4.0-h37c48d4_1            conda-forge[0m
2024-01-07T19:53:25.8077714Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     hmmer:                    3.2.1-he1b5a44_2            bioconda[0m
2024-01-07T19:53:25.8089657Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     icu:                      58.2-hf484d3e_1000          conda-forge[0m
2024-01-07T19:53:25.8090310Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     infernal:                 1.1.4-pl5321h031d066_4      bioconda[0m
2024-01-07T19:53:25.8090795Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     jpeg:                     9e-h0b41bf4_3               conda-forge[0m
2024-01-07T19:53:25.8091228Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     kernel-headers_linux-64:  2.6.32-he073ed8_16          conda-forge[0m
2024-01-07T19:53:25.8095046Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     krb5:                     1.16.4-h2fd8d38_0           conda-forge[0m
2024-01-07T19:53:25.8095708Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     lcms2:                    2.14-h6ed2654_0             conda-forge[0m
2024-01-07T19:53:25.8096183Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     ld_impl_linux-64:         2.36.1-hea4e1c9_2           conda-forge[0m
2024-01-07T19:53:25.8096794Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     lerc:                     4.0.0-h27087fc_0            conda-forge[0m
2024-01-07T19:53:25.8102369Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libblas:                  3.9.0-8_openblas            conda-forge[0m
2024-01-07T19:53:25.8102800Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libcblas:                 3.9.0-8_openblas            conda-forge[0m
2024-01-07T19:53:25.8103380Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libcurl:                  7.68.0-hda55be3_0           conda-forge[0m
2024-01-07T19:53:25.8103785Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libdeflate:               1.14-h166bdaf_0             conda-forge[0m
2024-01-07T19:53:25.8104255Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libedit:                  3.1.20191231-he28a2e2_2     conda-forge[0m
2024-01-07T19:53:25.8104660Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libexpat:                 2.5.0-hcb278e6_1            conda-forge[0m
2024-01-07T19:53:25.8105273Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libffi:                   3.4.2-h7f98852_5            conda-forge[0m
2024-01-07T19:53:25.8105687Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libgcc-devel_linux-64:    7.5.0-hda03d7c_20           conda-forge[0m
2024-01-07T19:53:25.8110498Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libgcc-ng:                13.2.0-h807b86a_3           conda-forge[0m
2024-01-07T19:53:25.8111823Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libgfortran-ng:           7.5.0-h14aa051_20           conda-forge[0m
2024-01-07T19:53:25.8112354Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libgfortran4:             7.5.0-h14aa051_20           conda-forge[0m
2024-01-07T19:53:25.8112766Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libglib:                  2.78.3-h783c2da_0           conda-forge[0m
2024-01-07T19:53:25.8113225Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libgomp:                  13.2.0-h807b86a_3           conda-forge[0m
2024-01-07T19:53:25.8113631Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libiconv:                 1.17-hd590300_2             conda-forge[0m
2024-01-07T19:53:25.8114086Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     liblapack:                3.9.0-8_openblas            conda-forge[0m
2024-01-07T19:53:25.8114485Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libnsl:                   2.0.1-hd590300_0            conda-forge[0m
2024-01-07T19:53:25.8121009Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libopenblas:              0.3.12-pthreads_hb3c22a3_1  conda-forge[0m
2024-01-07T19:53:25.8121437Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libpng:                   1.6.39-h753d276_0           conda-forge[0m
2024-01-07T19:53:25.8121902Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libsqlite:                3.44.2-h2797004_0           conda-forge[0m
2024-01-07T19:53:25.8122303Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libssh2:                  1.10.0-haa6b8db_3           conda-forge[0m
2024-01-07T19:53:25.8122782Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libstdcxx-devel_linux-64: 7.5.0-hb016644_20           conda-forge[0m
2024-01-07T19:53:25.8123205Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libstdcxx-ng:             13.2.0-h7e041cc_3           conda-forge[0m
2024-01-07T19:53:25.8123808Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libtiff:                  4.4.0-h82bc61c_5            conda-forge[0m
2024-01-07T19:53:25.8124204Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libuuid:                  2.38.1-h0b41bf4_0           conda-forge[0m
2024-01-07T19:53:25.8128025Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libwebp-base:             1.3.2-hd590300_0            conda-forge[0m
2024-01-07T19:53:25.8128441Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libxcb:                   1.13-h7f98852_1004          conda-forge[0m
2024-01-07T19:53:25.8128906Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libxcrypt:                4.4.36-hd590300_1           conda-forge[0m
2024-01-07T19:53:25.8129310Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libxml2:                  2.9.9-h13577e0_2            conda-forge[0m
2024-01-07T19:53:25.8129938Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     libzlib:                  1.2.13-hd590300_5           conda-forge[0m
2024-01-07T19:53:25.8130432Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     make:                     4.3-hd18ef5c_1              conda-forge[0m
2024-01-07T19:53:25.8130886Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     mitos:                    2.1.6-pyhdfd78af_0          local[0m
2024-01-07T19:53:25.8131380Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     ncurses:                  6.4-h59595ed_2              conda-forge[0m
2024-01-07T19:53:25.8136483Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     nettle:                   3.4.1-h1bed415_1002         conda-forge[0m
2024-01-07T19:53:25.8136899Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     numpy:                    1.21.6-py37h976b520_0       conda-forge[0m
2024-01-07T19:53:25.8137474Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     openjdk:                  11.0.8-hacce0ff_0           conda-forge[0m
2024-01-07T19:53:25.8137883Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     openjpeg:                 2.5.0-h7d73246_1            conda-forge[0m
2024-01-07T19:53:25.8138342Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     openssl:                  1.1.1w-hd590300_0           conda-forge[0m
2024-01-07T19:53:25.8138751Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pango:                    1.40.14-he7ab937_1005       conda-forge[0m
2024-01-07T19:53:25.8139207Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pcre:                     8.45-h9c3ff4c_0             conda-forge[0m
2024-01-07T19:53:25.8139599Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pcre2:                    10.42-hcad00b1_0            conda-forge[0m
2024-01-07T19:53:25.8142599Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl:                     5.32.1-7_hd590300_perl5     conda-forge[0m
2024-01-07T19:53:25.8143016Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-archive-tar:         2.40-pl5321hdfd78af_0       bioconda[0m
2024-01-07T19:53:25.8143531Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-carp:                1.50-pl5321hd8ed1ab_0       conda-forge[0m
2024-01-07T19:53:25.8143951Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-common-sense:        3.75-pl5321hd8ed1ab_0       conda-forge[0m
2024-01-07T19:53:25.8144444Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-compress-raw-bzip2:  2.201-pl5321h166bdaf_0      conda-forge[0m
2024-01-07T19:53:25.8145036Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-compress-raw-zlib:   2.202-pl5321h166bdaf_0      conda-forge[0m
2024-01-07T19:53:25.8145533Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-encode:              3.19-pl5321h166bdaf_0       conda-forge[0m
2024-01-07T19:53:25.8146042Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-exporter:            5.74-pl5321hd8ed1ab_0       conda-forge[0m
2024-01-07T19:53:25.8149432Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-exporter-tiny:       1.002002-pl5321hd8ed1ab_0   conda-forge[0m
2024-01-07T19:53:25.8149865Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-extutils-makemaker:  7.70-pl5321hd8ed1ab_0       conda-forge[0m
2024-01-07T19:53:25.8150364Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-io-compress:         2.201-pl5321hdbdd923_2      bioconda[0m
2024-01-07T19:53:25.8150781Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-io-zlib:             1.14-pl5321hdfd78af_0       bioconda[0m
2024-01-07T19:53:25.8151249Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-json:                4.10-pl5321hdfd78af_0       bioconda[0m
2024-01-07T19:53:25.8151759Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-json-xs:             2.34-pl5321h4ac6f70_6       bioconda[0m
2024-01-07T19:53:25.8152239Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-list-moreutils:      0.430-pl5321hdfd78af_0      bioconda[0m
2024-01-07T19:53:25.8152664Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-list-moreutils-xs:   0.430-pl5321h031d066_2      bioconda[0m
2024-01-07T19:53:25.8157458Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-parent:              0.241-pl5321hd8ed1ab_0      conda-forge[0m
2024-01-07T19:53:25.8158022Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-pathtools:           3.75-pl5321h166bdaf_0       conda-forge[0m
2024-01-07T19:53:25.8158517Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-scalar-list-utils:   1.63-pl5321h166bdaf_0       conda-forge[0m
2024-01-07T19:53:25.8158943Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-storable:            3.15-pl5321h166bdaf_0       conda-forge[0m
2024-01-07T19:53:25.8159424Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     perl-types-serialiser:    1.01-pl5321hdfd78af_0       bioconda[0m
2024-01-07T19:53:25.8159928Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pillow:                   9.2.0-py37h850a105_2        conda-forge[0m
2024-01-07T19:53:25.8160386Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pip:                      23.3.2-pyhd8ed1ab_0         conda-forge[0m
2024-01-07T19:53:25.8160793Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pixman:                   0.38.0-h516909a_1003        conda-forge[0m
2024-01-07T19:53:25.8166690Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     pthread-stubs:            0.4-h36c2ea0_1001           conda-forge[0m
2024-01-07T19:53:25.8167111Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     python:                   3.7.12-hb7a2778_100_cpython conda-forge[0m
2024-01-07T19:53:25.8167673Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     python_abi:               3.7-4_cp37m                 conda-forge[0m
2024-01-07T19:53:25.8168086Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     r-assertthat:             0.2.1-r36h6115d3f_2         conda-forge[0m
2024-01-07T19:53:25.8168568Z 19:53:25 [32mBIOCONDA INFO[0m (OUT)     r-backports:              1.2.1-r36hcfec24a_0         conda-forge[0m
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conda-forge / r-stringi-feedstock