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July 6, 2020 15:15
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Error log for snakemake_alevin_10x using `renv`
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| * Restoring project ... | |
| The following package(s) will be updated: | |
| # Bioconductor ======================= | |
| - Biobase [* -> 2.48.0] | |
| - BiocGenerics [* -> 0.34.0] | |
| - BiocParallel [* -> 1.22.0] | |
| - BiocVersion [* -> 3.11.1] | |
| - Biostrings [* -> 2.56.0] | |
| - DelayedArray [* -> 0.14.0] | |
| - DelayedMatrixStats [* -> 1.10.1] | |
| - GenomeInfoDb [* -> 1.24.2] | |
| - GenomeInfoDbData [* -> 1.2.3] | |
| - GenomicAlignments [* -> 1.24.0] | |
| - GenomicRanges [* -> 1.40.0] | |
| - HDF5Array [* -> 1.16.1] | |
| - IRanges [* -> 2.22.2] | |
| - Rhdf5lib [* -> 1.10.0] | |
| - Rhtslib [* -> 1.20.0] | |
| - Rsamtools [* -> 2.4.0] | |
| - S4Vectors [* -> 0.26.1] | |
| - SummarizedExperiment [* -> 1.18.1] | |
| - XVector [* -> 0.28.0] | |
| - rhdf5 [* -> 2.32.2] | |
| - rtracklayer [* -> 1.48.0] | |
| - tximport [* -> 1.16.1] | |
| - zlibbioc [* -> 1.34.0] | |
| # CRAN =============================== | |
| - BH [* -> 1.72.0-3] | |
| - BiocManager [* -> 1.30.10] | |
| - DBI [* -> 1.1.0] | |
| - MASS [* -> 7.3-51.6] | |
| - Matrix [* -> 1.2-18] | |
| - R6 [* -> 2.4.1] | |
| - RColorBrewer [* -> 1.1-2] | |
| - RCurl [* -> 1.98-1.2] | |
| - Rcpp [* -> 1.0.4.6] | |
| - XML [* -> 3.99-0.4] | |
| - askpass [* -> 1.1] | |
| - assertthat [* -> 0.2.1] | |
| - backports [* -> 1.1.8] | |
| - base64enc [* -> 0.1-3] | |
| - bitops [* -> 1.0-6] | |
| - blob [* -> 1.2.1] | |
| - broom [* -> 0.5.6] | |
| - callr [* -> 3.4.3] | |
| - cellranger [* -> 1.1.0] | |
| - cli [* -> 2.0.2] | |
| - clipr [* -> 0.7.0] | |
| - colorspace [* -> 1.4-1] | |
| - cowplot [* -> 1.0.0] | |
| - crayon [* -> 1.3.4] | |
| - curl [* -> 4.3] | |
| - dbplyr [* -> 1.4.4] | |
| - desc [* -> 1.2.0] | |
| - digest [* -> 0.6.25] | |
| - dplyr [* -> 1.0.0] | |
| - ellipsis [* -> 0.3.1] | |
| - evaluate [* -> 0.14] | |
| - fansi [* -> 0.4.1] | |
| - farver [* -> 2.0.3] | |
| - forcats [* -> 0.5.0] | |
| - formatR [* -> 1.7] | |
| - fs [* -> 1.4.2] | |
| - futile.logger [* -> 1.4.3] | |
| - futile.options [* -> 1.0.1] | |
| - generics [* -> 0.0.2] | |
| - ggplot2 [* -> 3.3.2] | |
| - glue [* -> 1.4.1] | |
| - gtable [* -> 0.3.0] | |
| - haven [* -> 2.3.1] | |
| - highr [* -> 0.8] | |
| - hms [* -> 0.5.3] | |
| - htmltools [* -> 0.5.0] | |
| - httr [* -> 1.4.1] | |
| - isoband [* -> 0.2.2] | |
| - jsonlite [* -> 1.7.0] | |
| - knitr [* -> 1.29] | |
| - labeling [* -> 0.3] | |
| - lambda.r [* -> 1.2.4] | |
| - lattice [* -> 0.20-41] | |
| - lifecycle [* -> 0.2.0] | |
| - lubridate [* -> 1.7.9] | |
| - magrittr [* -> 1.5] | |
| - markdown [* -> 1.1] | |
| - matrixStats [* -> 0.56.0] | |
| - mgcv [* -> 1.8-31] | |
| - mime [* -> 0.9] | |
| - modelr [* -> 0.1.8] | |
| - munsell [* -> 0.5.0] | |
| - nlme [* -> 3.1-148] | |
| - openssl [* -> 1.4.2] | |
| - pillar [* -> 1.4.4] | |
| - pkgbuild [* -> 1.0.8] | |
| - pkgconfig [* -> 2.0.3] | |
| - pkgload [* -> 1.1.0] | |
| - plyr [* -> 1.8.6] | |
| - praise [* -> 1.0.0] | |
| - prettyunits [* -> 1.1.1] | |
| - processx [* -> 3.4.3] | |
| - progress [* -> 1.2.2] | |
| - ps [* -> 1.3.3] | |
| - purrr [* -> 0.3.4] | |
| - readr [* -> 1.3.1] | |
| - readxl [* -> 1.3.1] | |
| - rematch [* -> 1.0.1] | |
| - renv [* -> 0.11.0] | |
| - reprex [* -> 0.3.0] | |
| - reshape2 [* -> 1.4.4] | |
| - rlang [* -> 0.4.6] | |
| - rmarkdown [* -> 2.3] | |
| - rprojroot [* -> 1.3-2] | |
| - rstudioapi [* -> 0.11] | |
| - rvest [* -> 0.3.5] | |
| - scales [* -> 1.1.1] | |
| - selectr [* -> 0.4-2] | |
| - sessioninfo [* -> 1.1.1] | |
| - snow [* -> 0.4-3] | |
| - stringi [* -> 1.4.6] | |
| - stringr [* -> 1.4.0] | |
| - sys [* -> 3.3] | |
| - testthat [* -> 2.3.2] | |
| - tibble [* -> 3.0.1] | |
| - tidyr [* -> 1.1.0] | |
| - tidyselect [* -> 1.1.0] | |
| - tidyverse [* -> 1.3.0] | |
| - tinytex [* -> 0.24] | |
| - utf8 [* -> 1.1.4] | |
| - vctrs [* -> 0.3.1] | |
| - viridisLite [* -> 0.3.0] | |
| - whisker [* -> 0.4] | |
| - withr [* -> 2.2.0] | |
| - xfun [* -> 0.15] | |
| - xml2 [* -> 1.3.2] | |
| - yaml [* -> 2.2.1] | |
| Installing BiocManager [1.30.10] ... | |
| OK (linked cache) | |
| * Querying repositories for available source packages ... Done! | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/DelayedMatrixStats_1.10.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/HDF5Array_1.16.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/rhdf5_2.32.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Rhdf5lib_1.10.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/GenomeInfoDb_1.24.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/RCurl_1.98-1.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/GenomicAlignments_1.24.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/GenomicRanges_1.40.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Rsamtools_2.4.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Rhtslib_1.20.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/SummarizedExperiment_1.18.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/MASS_7.3-51.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/R6_2.4.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/RColorBrewer_1.1-2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.4.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/XML_3.99-0.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/askpass_1.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/sys_3.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/backports_1.1.8.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/base64enc_0.1-3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/blob_1.2.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rlang_0.4.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/vctrs_0.3.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/ellipsis_0.3.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/digest_0.6.25.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/broom_0.5.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/dplyr_1.0.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/generics_0.0.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/lifecycle_0.2.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/tibble_3.0.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/pillar_1.4.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/utf8_1.1.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/pkgconfig_2.0.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/tidyselect_1.1.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/purrr_0.3.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/nlme_3.1-148.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/reshape2_1.4.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/plyr_1.8.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/stringr_1.4.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/stringi_1.4.6.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/tidyr_1.1.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/callr_3.4.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/processx_3.4.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/ps_1.3.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rematch_1.0.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/clipr_0.7.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/colorspace_1.4-1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/cowplot_1.0.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/gtable_0.3.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/isoband_0.2.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/testthat_2.3.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/evaluate_0.14.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/pkgload_1.1.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/desc_1.2.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rprojroot_1.3-2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/pkgbuild_1.0.8.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/prettyunits_1.1.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rstudioapi_0.11.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/praise_1.0.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/mgcv_1.8-31.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/scales_1.1.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/farver_2.0.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/labeling_0.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/munsell_0.5.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/viridisLite_0.3.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/curl_4.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/dbplyr_1.4.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/forcats_0.5.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/fs_1.4.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/haven_2.3.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/hms_0.5.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/readr_1.3.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/highr_0.8.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/htmltools_0.5.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/httr_1.4.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/jsonlite_1.7.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/mime_0.9.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/openssl_1.4.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/knitr_1.29.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/markdown_1.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/xfun_0.15.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/yaml_2.2.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/lubridate_1.7.9.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/modelr_0.1.8.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/progress_1.2.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/readxl_1.3.1.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/reprex_0.3.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rmarkdown_2.3.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/tinytex_0.24.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/whisker_0.4.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/rtracklayer_1.48.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/rvest_0.3.5.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/selectr_0.4-2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/xml2_1.3.2.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://cran.rstudio.com/src/contrib/tidyverse_1.3.0.tar.gz' ... | |
| OK [file is up to date] | |
| Retrieving 'https://bioconductor.org/packages/3.11/bioc/src/contrib/tximport_1.16.1.tar.gz' ... | |
| OK [file is up to date] | |
| Installing BH [1.72.0-3] ... | |
| OK (linked cache) | |
| Installing BiocGenerics [0.34.0] ... | |
| OK (linked cache) | |
| Installing Biobase [2.48.0] ... | |
| OK (linked cache) | |
| Installing BiocManager [1.30.10] ... | |
| OK (linked cache) | |
| Installing formatR [1.7] ... | |
| OK (linked cache) | |
| Installing lambda.r [1.2.4] ... | |
| OK (linked cache) | |
| Installing futile.options [1.0.1] ... | |
| OK (linked cache) | |
| Installing futile.logger [1.4.3] ... | |
| OK (linked cache) | |
| Installing snow [0.4-3] ... | |
| OK (linked cache) | |
| Installing BiocParallel [1.22.0] ... | |
| OK (linked cache) | |
| Installing BiocVersion [3.11.1] ... | |
| OK (linked cache) | |
| Installing crayon [1.3.4] ... | |
| OK (linked cache) | |
| Installing S4Vectors [0.26.1] ... | |
| OK (linked cache) | |
| Installing IRanges [2.22.2] ... | |
| OK (linked cache) | |
| Installing zlibbioc [1.34.0] ... | |
| OK (linked cache) | |
| Installing XVector [0.28.0] ... | |
| OK (linked cache) | |
| Installing Biostrings [2.56.0] ... | |
| OK (linked cache) | |
| Installing DBI [1.1.0] ... | |
| OK (linked cache) | |
| Installing lattice [0.20-41] ... | |
| OK (linked cache) | |
| Installing Matrix [1.2-18] ... | |
| OK (linked cache) | |
| Installing matrixStats [0.56.0] ... | |
| OK (linked cache) | |
| Installing DelayedArray [0.14.0] ... | |
| OK (linked cache) | |
| Installing Rhdf5lib [1.10.0] ... | |
| FAILED | |
| Error installing package 'Rhdf5lib': | |
| ==================================== | |
| * installing *source* package ‘Rhdf5lib’ ... | |
| ** using staged installation | |
| checking for gcc... x86_64-apple-darwin13.4.0-clang | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes | |
| checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed | |
| checking whether we are using the GNU C++ compiler... yes | |
| checking whether x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 accepts -g... yes | |
| checking whether C++ compiler accepts -w... yes | |
| checking how to run the C++ preprocessor... x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -E | |
| checking for grep that handles long lines and -e... /usr/bin/grep | |
| checking for egrep... /usr/bin/grep -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking for zlib.h... yes | |
| checking curl/curl.h usability... yes | |
| checking curl/curl.h presence... yes | |
| checking for curl/curl.h... yes | |
| checking openssl/evp.h usability... yes | |
| checking openssl/evp.h presence... no | |
| configure: WARNING: openssl/evp.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/evp.h: proceeding with the compiler's result | |
| checking for openssl/evp.h... yes | |
| checking openssl/hmac.h usability... yes | |
| checking openssl/hmac.h presence... no | |
| configure: WARNING: openssl/hmac.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/hmac.h: proceeding with the compiler's result | |
| checking for openssl/hmac.h... yes | |
| checking openssl/sha.h usability... yes | |
| checking openssl/sha.h presence... no | |
| configure: WARNING: openssl/sha.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/sha.h: proceeding with the compiler's result | |
| checking for openssl/sha.h... yes | |
| checking for curl_global_init in -lcurl... yes | |
| checking for EVP_sha256 in -lcrypto... yes | |
| untarring hdf5small_cxx_hl_1.10.6.tar.gz ... | |
| building the szip library... | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... bin/install-sh -c -d | |
| checking for gawk... no | |
| checking for mawk... no | |
| checking for nawk... no | |
| checking for awk... awk | |
| checking whether make sets $(MAKE)... yes | |
| checking whether make supports nested variables... yes | |
| checking whether to enable maintainer-specific portions of Makefiles... no | |
| checking build system type... x86_64-apple-darwin19.5.0 | |
| checking host system type... x86_64-apple-darwin19.5.0 | |
| checking for config x86_64-apple-darwin19.5.0... no | |
| checking for config x86_64-apple-darwin19.5.0... no | |
| checking for config apple-darwin19.5.0... no | |
| checking for config apple-darwin19.5.0... no | |
| checking for config x86_64-darwin19.5.0... no | |
| checking for config x86_64-darwin19.5.0... no | |
| checking for config x86_64-apple... no | |
| checking for config darwin19.5.0... no | |
| checking for config darwin19.5.0... no | |
| checking for config apple... no | |
| checking for config x86_64... no | |
| checking for gcc... x86_64-apple-darwin13.4.0-clang | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes | |
| checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed | |
| checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes | |
| checking for style of include used by make... GNU | |
| checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 | |
| checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E | |
| checking whether make sets $(MAKE)... (cached) yes | |
| checking how to print strings... printf | |
| checking for a sed that does not truncate output... /usr/bin/sed | |
| checking for grep that handles long lines and -e... /usr/bin/grep | |
| checking for egrep... /usr/bin/grep -E | |
| checking for fgrep... /usr/bin/grep -F | |
| checking for ld used by x86_64-apple-darwin13.4.0-clang... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld | |
| checking if the linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) is GNU ld... no | |
| checking for BSD- or MS-compatible name lister (nm)... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm | |
| checking the name lister (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm) interface... BSD nm | |
| checking whether ln -s works... yes | |
| checking the maximum length of command line arguments... 196608 | |
| checking how to convert x86_64-apple-darwin19.5.0 file names to x86_64-apple-darwin19.5.0 format... func_convert_file_noop | |
| checking how to convert x86_64-apple-darwin19.5.0 file names to toolchain format... func_convert_file_noop | |
| checking for /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld option to reload object files... -r | |
| checking for objdump... objdump | |
| checking how to recognize dependent libraries... pass_all | |
| checking for dlltool... no | |
| checking how to associate runtime and link libraries... printf %s\n | |
| checking for archiver @FILE support... no | |
| checking for strip... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-strip | |
| checking for ranlib... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ranlib | |
| checking command to parse /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm output from x86_64-apple-darwin13.4.0-clang object... ok | |
| checking for sysroot... no | |
| checking for a working dd... /bin/dd | |
| checking how to truncate binary pipes... /bin/dd bs=4096 count=1 | |
| checking for mt... no | |
| checking if : is a manifest tool... no | |
| checking for dsymutil... dsymutil | |
| checking for nmedit... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nmedit | |
| checking for lipo... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-lipo | |
| checking for otool... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-otool | |
| checking for otool64... no | |
| checking for -single_module linker flag... yes | |
| checking for -exported_symbols_list linker flag... yes | |
| checking for -force_load linker flag... yes | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking for dlfcn.h... yes | |
| checking for objdir... .libs | |
| checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes | |
| checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC | |
| checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes | |
| checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no | |
| checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes | |
| checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes | |
| checking whether the x86_64-apple-darwin13.4.0-clang linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes | |
| checking dynamic linker characteristics... darwin19.5.0 dyld | |
| checking how to hardcode library paths into programs... immediate | |
| checking for dlopen in -ldl... yes | |
| checking whether a program can dlopen itself... yes | |
| checking whether a statically linked program can dlopen itself... yes | |
| checking whether stripping libraries is possible... yes | |
| checking if libtool supports shared libraries... yes | |
| checking whether to build shared libraries... no | |
| checking whether to build static libraries... yes | |
| checking for build mode... production | |
| checking for math library support... no | |
| checking for ANSI C header files... (cached) yes | |
| checking fcntl.h usability... yes | |
| checking fcntl.h presence... yes | |
| checking for fcntl.h... yes | |
| checking for stdlib.h... (cached) yes | |
| checking for string.h... (cached) yes | |
| checking for an ANSI C-conforming const... yes | |
| checking for size_t... yes | |
| checking for error_at_line... no | |
| checking for working memcmp... yes | |
| checking for vprintf... yes | |
| checking for _doprnt... no | |
| checking for memset... yes | |
| checking if encoding enabled... yes | |
| checking that generated files are newer than configure... done | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating src/Makefile | |
| config.status: creating src/SZconfig.h | |
| config.status: executing depfiles commands | |
| config.status: executing libtool commands | |
| Making all in src | |
| make[1]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make all-am | |
| make[2]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| /bin/sh ../libtool --tag=CC --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c | |
| libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c -fno-common -DPIC -o rice.o | |
| mv -f .deps/rice.Tpo .deps/rice.Plo | |
| /bin/sh ../libtool --tag=CC --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c | |
| libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c -fno-common -DPIC -o sz_api.o | |
| mv -f .deps/sz_api.Tpo .deps/sz_api.Plo | |
| /bin/sh ../libtool --tag=CC --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c | |
| libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I/usr/local/opt/imagemagick@6/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c -fno-common -DPIC -o encoding.o | |
| mv -f .deps/encoding.Tpo .deps/encoding.Plo | |
| /bin/sh ../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC -version-info 2:0:0 -L/usr/local/opt/imagemagick@6/lib -o libsz.la -rpath /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo -lm | |
| libtool: link: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ar cru .libs/libsz.a rice.o sz_api.o encoding.o | |
| libtool: link: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ranlib .libs/libsz.a | |
| libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" ) | |
| make[2]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make[1]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make[1]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| make[1]: Nothing to be done for 'all-am'. | |
| make[1]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| Making install in src | |
| make[1]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make[2]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| ../bin/install-sh -c -d '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib' | |
| /bin/sh ../libtool --mode=install /usr/bin/install -c libsz.la '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib' | |
| libtool: install: /usr/bin/install -c .libs/libsz.lai /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la | |
| libtool: install: /usr/bin/install -c .libs/libsz.a /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a | |
| libtool: install: chmod 644 /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a | |
| libtool: install: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ranlib /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a | |
| ../bin/install-sh -c -d '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/include' | |
| /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/include' | |
| make[2]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make[1]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/src' | |
| make[1]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| make[2]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| make[2]: Nothing to be done for 'install-exec-am'. | |
| make[2]: Nothing to be done for 'install-data-am'. | |
| make[2]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| make[1]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip' | |
| building the hdf5 library... | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... bin/install-sh -c -d | |
| checking for gawk... no | |
| checking for mawk... no | |
| checking for nawk... no | |
| checking for awk... awk | |
| checking whether make sets $(MAKE)... yes | |
| checking whether make supports nested variables... yes | |
| checking whether make supports nested variables... (cached) yes | |
| checking whether to enable maintainer-specific portions of Makefiles... no | |
| checking build system type... x86_64-apple-darwin19.5.0 | |
| checking host system type... x86_64-apple-darwin19.5.0 | |
| checking shell variables initial values... done | |
| checking if basename works... yes | |
| checking if xargs works... yes | |
| checking for cached host... none | |
| checking for config x86_64-apple-darwin19.5.0... no | |
| checking for config x86_64-apple-darwin19.5.0... no | |
| checking for config apple-darwin19.5.0... no | |
| checking for config apple-darwin19.5.0... no | |
| checking for config x86_64-darwin19.5.0... no | |
| checking for config x86_64-darwin19.5.0... no | |
| checking for config x86_64-apple... no | |
| checking for config darwin19.5.0... no | |
| checking for config darwin19.5.0... no | |
| checking for config apple... found | |
| No match to get cc_version_info for x86_64-apple-darwin13.4.0-clang | |
| compiler '/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-gfortran' is GNU gfortran-7.3.0 | |
| checking for config ./config/site-specific/host-Kevins-MacBook-Pro.local... no | |
| checking for config ./config/site-specific/host-local... no | |
| checking build mode... production | |
| checking for gcc... x86_64-apple-darwin13.4.0-clang | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes | |
| checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed | |
| checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes | |
| checking for style of include used by make... GNU | |
| checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 | |
| checking if unsupported combinations of configure options are allowed... no | |
| checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E | |
| checking for grep that handles long lines and -e... /usr/bin/grep | |
| checking for egrep... /usr/bin/grep -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking for off_t... yes | |
| checking for size_t... yes | |
| checking for ssize_t... yes | |
| checking for ptrdiff_t... yes | |
| checking whether byte ordering is bigendian... no | |
| checking size of char... 1 | |
| checking size of short... 2 | |
| checking size of int... 4 | |
| checking size of unsigned... 4 | |
| checking size of long... 8 | |
| checking size of long long... 8 | |
| checking size of __int64... 0 | |
| checking size of float... 4 | |
| checking size of double... 8 | |
| checking size of long double... 16 | |
| checking size of __float128... 0 | |
| checking size of _Quad... 0 | |
| checking quadmath.h usability... no | |
| checking quadmath.h presence... no | |
| checking for quadmath.h... no | |
| checking maximum decimal precision for C... 21 | |
| checking if Fortran interface enabled... no | |
| checking whether we are using the GNU C++ compiler... yes | |
| checking whether x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 accepts -g... yes | |
| checking dependency style of x86_64-apple-darwin13.4.0-clang++ -std=gnu++11... gcc3 | |
| checking how to run the C++ preprocessor... x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -E | |
| checking if c++ interface enabled... yes | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 needs old style header files in includes... no | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 can handle namespaces... yes | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 can handle static cast... yes | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 has offsetof extension... yes | |
| checking if the high-level library is enabled... yes | |
| checking whether make sets $(MAKE)... (cached) yes | |
| checking for tr... /usr/bin/tr | |
| checking if srcdir= and time commands work together... yes | |
| checking if Java JNI interface enabled... no | |
| checking if building tests is disabled... checking if building tools is disabled... checking how to print strings... printf | |
| checking for a sed that does not truncate output... /usr/bin/sed | |
| checking for fgrep... /usr/bin/grep -F | |
| checking for ld used by x86_64-apple-darwin13.4.0-clang... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld | |
| checking if the linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) is GNU ld... no | |
| checking for BSD- or MS-compatible name lister (nm)... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm | |
| checking the name lister (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm) interface... BSD nm | |
| checking whether ln -s works... yes | |
| checking the maximum length of command line arguments... 196608 | |
| checking how to convert x86_64-apple-darwin19.5.0 file names to x86_64-apple-darwin19.5.0 format... func_convert_file_noop | |
| checking how to convert x86_64-apple-darwin19.5.0 file names to toolchain format... func_convert_file_noop | |
| checking for /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld option to reload object files... -r | |
| checking for objdump... objdump | |
| checking how to recognize dependent libraries... pass_all | |
| checking for dlltool... no | |
| checking how to associate runtime and link libraries... printf %s\n | |
| checking for archiver @FILE support... no | |
| checking for strip... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-strip | |
| checking for ranlib... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ranlib | |
| checking command to parse /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nm output from x86_64-apple-darwin13.4.0-clang object... ok | |
| checking for sysroot... no | |
| checking for a working dd... /bin/dd | |
| checking how to truncate binary pipes... /bin/dd bs=4096 count=1 | |
| checking for mt... no | |
| checking if : is a manifest tool... no | |
| checking for dsymutil... dsymutil | |
| checking for nmedit... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-nmedit | |
| checking for lipo... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-lipo | |
| checking for otool... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-otool | |
| checking for otool64... no | |
| checking for -single_module linker flag... yes | |
| checking for -exported_symbols_list linker flag... yes | |
| checking for -force_load linker flag... yes | |
| checking for dlfcn.h... yes | |
| checking for objdir... .libs | |
| checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes | |
| checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC | |
| checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes | |
| checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no | |
| checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes | |
| checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes | |
| checking whether the x86_64-apple-darwin13.4.0-clang linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes | |
| checking dynamic linker characteristics... darwin19.5.0 dyld | |
| checking how to hardcode library paths into programs... immediate | |
| checking for dlopen in -ldl... yes | |
| checking whether a program can dlopen itself... yes | |
| checking whether a statically linked program can dlopen itself... yes | |
| checking whether stripping libraries is possible... yes | |
| checking if libtool supports shared libraries... yes | |
| checking whether to build shared libraries... no | |
| checking whether to build static libraries... yes | |
| checking how to run the C++ preprocessor... x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -E | |
| checking for ld used by x86_64-apple-darwin13.4.0-clang++ -std=gnu++11... /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld | |
| checking if the linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) is GNU ld... no | |
| checking whether the x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes | |
| checking for x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 option to produce PIC... -fno-common -DPIC | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 PIC flag -fno-common -DPIC works... yes | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 static flag -static works... no | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 supports -c -o file.o... yes | |
| checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 supports -c -o file.o... (cached) yes | |
| checking whether the x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 linker (/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes | |
| checking dynamic linker characteristics... darwin19.5.0 dyld | |
| checking how to hardcode library paths into programs... immediate | |
| checking if we should install only statically linked executables... no | |
| checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes | |
| checking for ceil in -lm... yes | |
| checking for dlopen in -ldl... (cached) yes | |
| checking for ANSI C header files... (cached) yes | |
| checking whether time.h and sys/time.h may both be included... yes | |
| checking sys/resource.h usability... yes | |
| checking sys/resource.h presence... yes | |
| checking for sys/resource.h... yes | |
| checking sys/time.h usability... yes | |
| checking sys/time.h presence... yes | |
| checking for sys/time.h... yes | |
| checking for unistd.h... (cached) yes | |
| checking sys/ioctl.h usability... yes | |
| checking sys/ioctl.h presence... yes | |
| checking for sys/ioctl.h... yes | |
| checking for sys/stat.h... (cached) yes | |
| checking sys/socket.h usability... yes | |
| checking sys/socket.h presence... yes | |
| checking for sys/socket.h... yes | |
| checking for sys/types.h... (cached) yes | |
| checking sys/file.h usability... yes | |
| checking sys/file.h presence... yes | |
| checking for sys/file.h... yes | |
| checking stddef.h usability... yes | |
| checking stddef.h presence... yes | |
| checking for stddef.h... yes | |
| checking setjmp.h usability... yes | |
| checking setjmp.h presence... yes | |
| checking for setjmp.h... yes | |
| checking features.h usability... no | |
| checking features.h presence... no | |
| checking for features.h... no | |
| checking dirent.h usability... yes | |
| checking dirent.h presence... yes | |
| checking for dirent.h... yes | |
| checking for stdint.h... (cached) yes | |
| checking stdbool.h usability... yes | |
| checking stdbool.h presence... yes | |
| checking for stdbool.h... yes | |
| checking mach/mach_time.h usability... yes | |
| checking mach/mach_time.h presence... yes | |
| checking for mach/mach_time.h... yes | |
| checking io.h usability... no | |
| checking io.h presence... no | |
| checking for io.h... no | |
| checking winsock2.h usability... no | |
| checking winsock2.h presence... no | |
| checking for winsock2.h... no | |
| checking sys/timeb.h usability... yes | |
| checking sys/timeb.h presence... yes | |
| checking for sys/timeb.h... yes | |
| checking for _FILE_OFFSET_BITS value needed for large files... no | |
| checking size of int8_t... 1 | |
| checking size of uint8_t... 1 | |
| checking size of int_least8_t... 1 | |
| checking size of uint_least8_t... 1 | |
| checking size of int_fast8_t... 1 | |
| checking size of uint_fast8_t... 1 | |
| checking size of int16_t... 2 | |
| checking size of uint16_t... 2 | |
| checking size of int_least16_t... 2 | |
| checking size of uint_least16_t... 2 | |
| checking size of int_fast16_t... 2 | |
| checking size of uint_fast16_t... 2 | |
| checking size of int32_t... 4 | |
| checking size of uint32_t... 4 | |
| checking size of int_least32_t... 4 | |
| checking size of uint_least32_t... 4 | |
| checking size of int_fast32_t... 4 | |
| checking size of uint_fast32_t... 4 | |
| checking size of int64_t... 8 | |
| checking size of uint64_t... 8 | |
| checking size of int_least64_t... 8 | |
| checking size of uint_least64_t... 8 | |
| checking size of int_fast64_t... 8 | |
| checking size of uint_fast64_t... 8 | |
| checking size of size_t... 8 | |
| checking size of ssize_t... 8 | |
| checking size of ptrdiff_t... 8 | |
| checking size of off_t... 8 | |
| checking size of bool... 1 | |
| checking size of time_t... 8 | |
| checking if dev_t is scalar... yes | |
| checking for dmalloc library... suppressed | |
| checking zlib.h usability... yes | |
| checking zlib.h presence... yes | |
| checking for zlib.h... yes | |
| checking for compress2 in -lz... yes | |
| checking for compress2... yes | |
| checking szlib.h usability... yes | |
| checking szlib.h presence... yes | |
| checking for szlib.h... yes | |
| checking for SZ_BufftoBuffCompress in -lsz... yes | |
| checking for szlib encoder... yes | |
| checking for thread safe support... no | |
| checking whether CLOCK_MONOTONIC is declared... yes | |
| checking for tm_gmtoff in struct tm... yes | |
| checking for global timezone variable... yes | |
| checking for st_blocks in struct stat... no | |
| checking for _getvideoconfig... no | |
| checking for gettextinfo... no | |
| checking for GetConsoleScreenBufferInfo... no | |
| checking for getpwuid... yes | |
| checking for _scrsize... no | |
| checking for ioctl... yes | |
| checking for struct videoconfig... no | |
| checking for struct text_info... no | |
| checking for TIOCGWINSZ... yes | |
| checking for TIOCGETD... yes | |
| checking for library containing clock_gettime... none required | |
| checking for alarm... yes | |
| checking for clock_gettime... yes | |
| checking for difftime... yes | |
| checking for fcntl... yes | |
| checking for flock... yes | |
| checking for fork... yes | |
| checking for frexpf... yes | |
| checking for frexpl... yes | |
| checking for gethostname... yes | |
| checking for getrusage... yes | |
| checking for gettimeofday... yes | |
| checking for lstat... yes | |
| checking for rand_r... yes | |
| checking for random... yes | |
| checking for setsysinfo... no | |
| checking for signal... yes | |
| checking for longjmp... yes | |
| checking for setjmp... yes | |
| checking for siglongjmp... yes | |
| checking for sigsetjmp... yes | |
| checking for sigprocmask... yes | |
| checking for snprintf... yes | |
| checking for srandom... yes | |
| checking for strdup... yes | |
| checking for symlink... yes | |
| checking for system... yes | |
| checking for strtoll... yes | |
| checking for strtoull... yes | |
| checking for tmpfile... yes | |
| checking for asprintf... yes | |
| checking for vasprintf... yes | |
| checking for vsnprintf... yes | |
| checking for waitpid... yes | |
| checking for roundf... yes | |
| checking for lroundf... yes | |
| checking for llroundf... yes | |
| checking for round... yes | |
| checking for lround... yes | |
| checking for llround... yes | |
| checking for an ANSI C-conforming const... yes | |
| checking if the compiler understands __inline__... yes | |
| checking if the compiler understands __inline... yes | |
| checking if the compiler understands inline... yes | |
| checking for __attribute__ extension... yes | |
| checking for __func__ extension... yes | |
| checking for __FUNCTION__ extension... yes | |
| checking for C99 designated initialization support... yes | |
| checking how to print long long... %ld and %lu | |
| checking enable debugging symbols... no | |
| checking enable asserts... no | |
| checking enable developer warnings... no | |
| checking profiling... no | |
| checking optimization level... high | |
| checking for internal debug output... none | |
| checking whether function stack tracking is enabled... no | |
| checking for API tracing... no | |
| checking whether a memory checking tool will be used... no | |
| checking whether internal memory allocation sanity checking is used... no | |
| checking for parallel support files... skipped | |
| checking whether O_DIRECT is declared... no | |
| checking for posix_memalign... yes | |
| checking if the direct I/O virtual file driver (VFD) is enabled... no | |
| checking curl/curl.h usability... yes | |
| checking curl/curl.h presence... yes | |
| checking for curl/curl.h... yes | |
| checking openssl/evp.h usability... yes | |
| checking openssl/evp.h presence... no | |
| configure: WARNING: openssl/evp.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/evp.h: proceeding with the compiler's result | |
| checking for openssl/evp.h... yes | |
| checking openssl/hmac.h usability... yes | |
| checking openssl/hmac.h presence... no | |
| configure: WARNING: openssl/hmac.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/hmac.h: proceeding with the compiler's result | |
| checking for openssl/hmac.h... yes | |
| checking openssl/sha.h usability... yes | |
| checking openssl/sha.h presence... no | |
| configure: WARNING: openssl/sha.h: accepted by the compiler, rejected by the preprocessor! | |
| configure: WARNING: openssl/sha.h: proceeding with the compiler's result | |
| checking for openssl/sha.h... yes | |
| checking for curl_global_init in -lcurl... yes | |
| checking for EVP_sha256 in -lcrypto... yes | |
| checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes | |
| checking for libhdfs... suppressed | |
| checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin | |
| checking whether exception handling functions is checked during data conversions... yes | |
| checking whether data accuracy is guaranteed during data conversions... yes | |
| checking if the machine has window style path name... no | |
| checking if using special algorithm to convert long double to (unsigned) long values... no | |
| checking if using special algorithm to convert (unsigned) long to long double values... no | |
| checking if correctly converting long double to (unsigned) long long values... no | |
| checking if correctly converting (unsigned) long long to long double values... no | |
| checking if the system is IBM ppc64le and cannot correctly convert some long double values... no | |
| checking additional programs should be built... no | |
| checking if deprecated public symbols are available... yes | |
| checking which version of public symbols to use by default... v110 | |
| checking whether to perform strict file format checks... no | |
| checking for pread... yes | |
| checking for pwrite... yes | |
| checking whether to use pread/pwrite instead of read/write in certain VFDs... yes | |
| checking whether to have library information embedded in the executables... yes | |
| checking if alignment restrictions are strictly enforced... yes | |
| configure: creating ./config.lt | |
| config.lt: creating libtool | |
| checking that generated files are newer than configure... done | |
| configure: creating ./config.status | |
| config.status: creating src/libhdf5.settings | |
| config.status: creating Makefile | |
| config.status: creating src/Makefile | |
| config.status: creating bin/h5cc | |
| config.status: creating bin/Makefile | |
| config.status: creating c++/Makefile | |
| config.status: creating c++/src/Makefile | |
| config.status: creating c++/src/h5c++ | |
| config.status: creating hl/Makefile | |
| config.status: creating hl/src/Makefile | |
| config.status: creating hl/c++/Makefile | |
| config.status: creating hl/c++/src/Makefile | |
| config.status: creating src/H5config.h | |
| config.status: executing pubconf commands | |
| creating src/H5pubconf.h | |
| Post process src/libhdf5.settings | |
| config.status: executing depfiles commands | |
| config.status: executing libtool commands | |
| config.status: executing .classes commands | |
| sed: -i may not be used with stdin | |
| SUMMARY OF THE HDF5 CONFIGURATION | |
| ================================= | |
| General Information: | |
| ------------------- | |
| HDF5 Version: 1.10.6 | |
| Configured on: Mon Jul 6 15:09:26 BST 2020 | |
| Configured by: kevin@Kevins-MacBook-Pro.local | |
| Host system: x86_64-apple-darwin19.5.0 | |
| Uname information: Darwin Kevins-MacBook-Pro.local 19.5.0 Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64 x86_64 | |
| Byte sex: little-endian | |
| Installation point: /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/hdf5 | |
| Compiling Options: | |
| ------------------ | |
| Build Mode: production | |
| Debugging Symbols: no | |
| Asserts: no | |
| Profiling: no | |
| Optimization Level: high | |
| Linking Options: | |
| ---------------- | |
| Libraries: static | |
| Statically Linked Executables: | |
| LDFLAGS: -L/usr/local/opt/imagemagick@6/lib | |
| H5_LDFLAGS: | |
| AM_LDFLAGS: -L/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/lib | |
| Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm | |
| Archiver: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ar | |
| AR_FLAGS: cr | |
| Ranlib: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-ranlib | |
| Languages: | |
| ---------- | |
| C: yes | |
| C Compiler: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-clang | |
| CPPFLAGS: -I/usr/local/opt/imagemagick@6/include | |
| H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API | |
| AM_CPPFLAGS: -I/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/szip/szip/include | |
| C Flags: -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC | |
| H5 C Flags: | |
| AM C Flags: | |
| Shared C Library: no | |
| Static C Library: yes | |
| Fortran: no | |
| C++: yes | |
| C++ Compiler: /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/bin/x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 | |
| C++ Flags: -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base_1593070335561/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/private/tmp/snakemake_alevin_10x/.snakemake/conda/6b62eeb9=/usr/local/src/conda-prefix -w -fPIC | |
| H5 C++ Flags: | |
| AM C++ Flags: | |
| Shared C++ Library: no | |
| Static C++ Library: yes | |
| Java: no | |
| Features: | |
| --------- | |
| Parallel HDF5: no | |
| Parallel Filtered Dataset Writes: no | |
| Large Parallel I/O: no | |
| High-level library: yes | |
| Build HDF5 Tests: yes | |
| Build HDF5 Tools: yes | |
| Threadsafety: no | |
| Default API mapping: v110 | |
| With deprecated public symbols: yes | |
| I/O filters (external): deflate(zlib),szip(encoder) | |
| MPE: no | |
| Direct VFD: no | |
| (Read-Only) S3 VFD: yes | |
| (Read-Only) HDFS VFD: no | |
| dmalloc: no | |
| Packages w/ extra debug output: none | |
| API tracing: no | |
| Using memory checker: no | |
| Memory allocation sanity checks: no | |
| Function stack tracing: no | |
| Strict file format checks: no | |
| Optimization instrumentation: no | |
| for d in src . c++ hl; do \ | |
| if test $d != .; then \ | |
| (cd $d && make lib) || exit 1; \ | |
| fi; \ | |
| done | |
| make[1]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/src' | |
| make[2]: Entering directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/src' | |
| CC H5.lo | |
| CC H5checksum.lo | |
| CC H5dbg.lo | |
| CC H5system.lo | |
| CC H5timer.lo | |
| CC H5trace.lo | |
| CC H5A.lo | |
| CC H5Abtree2.lo | |
| CC H5Adense.lo | |
| CC H5Adeprec.lo | |
| CC H5Aint.lo | |
| CC H5Atest.lo | |
| CC H5AC.lo | |
| CC H5ACdbg.lo | |
| CC H5ACproxy_entry.lo | |
| CC H5B.lo | |
| CC H5Bcache.lo | |
| CC H5Bdbg.lo | |
| CC H5B2.lo | |
| CC H5B2cache.lo | |
| CC H5B2dbg.lo | |
| CC H5B2hdr.lo | |
| CC H5B2int.lo | |
| CC H5B2internal.lo | |
| CC H5B2leaf.lo | |
| CC H5B2stat.lo | |
| CC H5B2test.lo | |
| CC H5C.lo | |
| CC H5Cdbg.lo | |
| CC H5Cepoch.lo | |
| CC H5Cimage.lo | |
| CC H5Clog.lo | |
| CC H5Clog_json.lo | |
| CC H5Clog_trace.lo | |
| CC H5Cprefetched.lo | |
| CC H5Cquery.lo | |
| CC H5Ctag.lo | |
| CC H5Ctest.lo | |
| CC H5CS.lo | |
| CC H5CX.lo | |
| CC H5D.lo | |
| CC H5Dbtree.lo | |
| CC H5Dbtree2.lo | |
| CC H5Dchunk.lo | |
| CC H5Dcompact.lo | |
| CC H5Dcontig.lo | |
| CC H5Ddbg.lo | |
| CC H5Ddeprec.lo | |
| CC H5Dearray.lo | |
| CC H5Defl.lo | |
| CC H5Dfarray.lo | |
| CC H5Dfill.lo | |
| CC H5Dint.lo | |
| CC H5Dio.lo | |
| CC H5Dlayout.lo | |
| CC H5Dnone.lo | |
| CC H5Doh.lo | |
| CC H5Dscatgath.lo | |
| CC H5Dselect.lo | |
| CC H5Dsingle.lo | |
| CC H5Dtest.lo | |
| CC H5Dvirtual.lo | |
| CC H5E.lo | |
| CC H5Edeprec.lo | |
| CC H5Eint.lo | |
| CC H5EA.lo | |
| CC H5EAcache.lo | |
| CC H5EAdbg.lo | |
| CC H5EAdblkpage.lo | |
| CC H5EAdblock.lo | |
| CC H5EAhdr.lo | |
| CC H5EAiblock.lo | |
| CC H5EAint.lo | |
| CC H5EAsblock.lo | |
| CC H5EAstat.lo | |
| CC H5EAtest.lo | |
| CC H5F.lo | |
| CC H5Faccum.lo | |
| CC H5Fcwfs.lo | |
| CC H5Fdbg.lo | |
| CC H5Fdeprec.lo | |
| CC H5Fefc.lo | |
| CC H5Ffake.lo | |
| CC H5Fint.lo | |
| CC H5Fio.lo | |
| CC H5Fmount.lo | |
| CC H5Fquery.lo | |
| CC H5Fsfile.lo | |
| CC H5Fspace.lo | |
| CC H5Fsuper.lo | |
| CC H5Fsuper_cache.lo | |
| CC H5Ftest.lo | |
| CC H5FA.lo | |
| CC H5FAcache.lo | |
| CC H5FAdbg.lo | |
| CC H5FAdblock.lo | |
| CC H5FAdblkpage.lo | |
| CC H5FAhdr.lo | |
| CC H5FAint.lo | |
| CC H5FAstat.lo | |
| CC H5FAtest.lo | |
| CC H5FD.lo | |
| CC H5FDcore.lo | |
| CC H5FDfamily.lo | |
| CC H5FDhdfs.lo | |
| CC H5FDint.lo | |
| CC H5FDlog.lo | |
| CC H5FDmulti.lo | |
| CC H5FDsec2.lo | |
| CC H5FDspace.lo | |
| CC H5FDstdio.lo | |
| CC H5FDtest.lo | |
| CC H5FL.lo | |
| CC H5FO.lo | |
| CC H5FS.lo | |
| CC H5FScache.lo | |
| CC H5FSdbg.lo | |
| CC H5FSint.lo | |
| CC H5FSsection.lo | |
| CC H5FSstat.lo | |
| CC H5FStest.lo | |
| CC H5G.lo | |
| CC H5Gbtree2.lo | |
| CC H5Gcache.lo | |
| CC H5Gcompact.lo | |
| CC H5Gdense.lo | |
| CC H5Gdeprec.lo | |
| CC H5Gent.lo | |
| CC H5Gint.lo | |
| CC H5Glink.lo | |
| CC H5Gloc.lo | |
| CC H5Gname.lo | |
| CC H5Gnode.lo | |
| CC H5Gobj.lo | |
| CC H5Goh.lo | |
| CC H5Groot.lo | |
| CC H5Gstab.lo | |
| CC H5Gtest.lo | |
| CC H5Gtraverse.lo | |
| CC H5HF.lo | |
| CC H5HFbtree2.lo | |
| CC H5HFcache.lo | |
| CC H5HFdbg.lo | |
| CC H5HFdblock.lo | |
| CC H5HFdtable.lo | |
| CC H5HFhdr.lo | |
| CC H5HFhuge.lo | |
| CC H5HFiblock.lo | |
| CC H5HFiter.lo | |
| CC H5HFman.lo | |
| CC H5HFsection.lo | |
| CC H5HFspace.lo | |
| CC H5HFstat.lo | |
| CC H5HFtest.lo | |
| CC H5HFtiny.lo | |
| CC H5HG.lo | |
| CC H5HGcache.lo | |
| CC H5HGdbg.lo | |
| CC H5HGquery.lo | |
| CC H5HL.lo | |
| CC H5HLcache.lo | |
| CC H5HLdbg.lo | |
| CC H5HLint.lo | |
| CC H5HLprfx.lo | |
| CC H5HLdblk.lo | |
| CC H5HP.lo | |
| CC H5I.lo | |
| CC H5Itest.lo | |
| CC H5L.lo | |
| CC H5Lexternal.lo | |
| CC H5make_libsettings.o | |
| CCLD H5make_libsettings | |
| LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/opt/imagemagick@6/lib | \ | |
| sed -e 's/-L/:/g' -e 's/ //g'`" \ | |
| ./H5make_libsettings > H5lib_settings.c || \ | |
| (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ | |
| (rm -f H5lib_settings.c ; exit 1) | |
| dyld: Library not loaded: @rpath/libcrypto.1.1.dylib | |
| Referenced from: /private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/src/./H5make_libsettings | |
| Reason: image not found | |
| /bin/sh: line 4: 94579 Abort trap: 6 LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/opt/imagemagick@6/lib | sed -e 's/-L/:/g' -e 's/ //g'`" ./H5make_libsettings > H5lib_settings.c | |
| make[2]: *** [Makefile:1939: H5lib_settings.c] Error 1 | |
| make[2]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/src' | |
| make[1]: *** [Makefile:1989: lib] Error 1 | |
| make[1]: Leaving directory '/private/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T/RtmpDvehtP/R.INSTALL13e51337443be/Rhdf5lib/src/hdf5/src' | |
| make: *** [Makefile:1088: lib] Error 1 | |
| configure: HDF5_INCLUDE=hdf5/src | |
| configure: HDF5_CXX_INCLUDE=hdf5/c++/src | |
| configure: HDF5_HL_INCLUDE=hdf5/hl/src | |
| configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src | |
| configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a | |
| configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a | |
| configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a | |
| configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a | |
| configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| mkdir -p "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" | |
| cp "hdf5/src/"*.h "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" | |
| cp "hdf5/c++/src/"*.h "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" | |
| cp "hdf5/hl/src/"*.h "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" | |
| cp "hdf5/hl/c++/src/"*.h "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" | |
| mkdir -p "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" | |
| cp "hdf5/src/.libs/libhdf5.a" "/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" | |
| cp: hdf5/src/.libs/libhdf5.a: No such file or directory | |
| make: *** [Makevars:38: copying] Error 1 | |
| ERROR: compilation failed for package ‘Rhdf5lib’ | |
| * removing ‘/private/tmp/snakemake_alevin_10x/renv/library/R-4.0/x86_64-apple-darwin13.4.0/.renv/1/Rhdf5lib’ |
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