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Bioconductor / Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://bioconductor.org/packages/Rsamtools
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installing error #29

Closed sunnyyakima closed 2 years ago

sunnyyakima commented 3 years ago

here is the error message:

installing to /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rsamtools/00new/Rsamtools/libs R inst byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so': /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: tbx_conf_gff Error: loading failed Execution halted ERROR: loading failed

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=C.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] Rhtslib_1.22.0 devtools_2.3.1 usethis_1.6.1

loaded via a namespace (and not attached): [1] magrittr_2.0.1 zlibbioc_1.36.0 pkgload_1.1.0
[4] R6_2.5.1 rlang_0.4.12 tools_4.0.2
[7] pkgbuild_1.0.8 sessioninfo_1.1.1 cli_3.1.0
[10] withr_2.4.2 ellipsis_0.3.2 remotes_2.4.1
[13] digest_0.6.28 assertthat_0.2.1 rprojroot_2.0.2
[16] crayon_1.4.2 processx_3.4.3 BiocManager_1.30.16 [19] callr_3.4.3 fs_1.5.0 ps_1.3.3
[22] testthat_2.3.2 curl_4.3.2 memoise_1.1.0
[25] glue_1.4.2 compiler_4.0.2 desc_1.2.0
[28] prettyunits_1.1.1

Here is output from ldd: ldd Rsamtools.so linux-vdso.so.1 (0x00007fffe8fc0000) libR.so => /usr/lib/libR.so (0x00007f162daba000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f162d8cc000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f162d8b1000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f162d6c0000) libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007f162d465000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f162d316000) libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8 (0x00007f162d2c4000) libpcre2-8.so.0 => /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007f162d23f000) liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f162d019000) libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f162ce09000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f162cbec000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f162cbe6000) libicuuc.so.67 => /usr/lib/x86_64-linux-gnu/libicuuc.so.67 (0x00007f162c9f8000) libicui18n.so.67 => /usr/lib/x86_64-linux-gnu/libicui18n.so.67 (0x00007f162c6e6000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f162c6ac000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f162c689000) /lib64/ld-linux-x86-64.so.2 (0x00007f162dfcd000) libopenblas.so.0 => /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007f162a3e3000) libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00007f162a3b1000) libicudata.so.67 => /usr/lib/x86_64-linux-gnu/libicudata.so.67 (0x00007f1628898000) libgfortran.so.4 => /usr/lib/x86_64-linux-gnu/libgfortran.so.4 (0x00007f16284b9000) libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f162846f000)

sunnyyakima commented 3 years ago

more info:

so_file <- file.path(installed.packages()['Rhtslib','LibPath'], 'Rhtslib', 'usrlib', 'libhts.so.2') grep(pattern = "tbx_conf_gff", x = system2("nm", so_file, stdout = TRUE), value = TRUE ) [1] "0000000000097830 R tbx_conf_gff"

seems tbx_conf_gff is not missing.

mtmorgan commented 3 years ago

Is this because BiocManager::valid() reports problems, eg. with Rhtslib?

sunnyyakima commented 3 years ago

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cloud.r-project.org

R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=C.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] Rhtslib_1.22.0 devtools_2.3.1 usethis_1.6.1

loaded via a namespace (and not attached): [1] magrittr_2.0.1 zlibbioc_1.36.0 pkgload_1.1.0
[4] R6_2.5.1 rlang_0.4.12 tools_4.0.2
[7] pkgbuild_1.0.8 sessioninfo_1.1.1 cli_3.1.0
[10] withr_2.4.2 ellipsis_0.3.2 remotes_2.4.1
[13] digest_0.6.28 assertthat_0.2.1 rprojroot_2.0.2
[16] crayon_1.4.2 processx_3.4.3 BiocManager_1.30.16 [19] callr_3.4.3 fs_1.5.0 ps_1.3.3
[22] testthat_2.3.2 curl_4.3.2 memoise_1.1.0
[25] glue_1.4.2 compiler_4.0.2 desc_1.2.0
[28] prettyunits_1.1.1

Bioconductor version '3.12'

create a valid installation with

BiocManager::install(c( "ape", "backports", "BH", "Biobase", "BiocGenerics", "bit", "bit64", "bitops", "blob", "broom", "callr", "car", "caTools", "cli", "clipr", "coda", "colorspace", "colourpicker", "conquer", "corrplot", "covr", "cowplot", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "deldir", "DEoptimR", "desc", "devtools", "diffobj", "digest", "diptest", "DNAcopy", "doParallel", "dplyr", "dqrng", "DT", "e1071", "ellipsis", "expm", "fansi", "farver", "fastICA", "fastmap", "fitdistrplus", "flexmix", "forcats", "foreach", "Formula", "fpc", "fs", "future", "future.apply", "gdtools", "generics", "ggplot2", "ggrepel", "ggridges", "ggsignif", "gh", "git2r", "globals", "glue", "gplots", "graph", "gtools", "haven", "hdf5r", "hexbin", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "igraph", "isoband", "iterators", "jpeg", "jsonlite", "knitr", "labeling", "later", "leiden", "lifecycle", "limma", "littler", "lme4", "lmtest", "lubridate", "magrittr", "maptools", "MatrixModels", "matrixStats", "mclust", "memoise", "mime", "mvtnorm", "openssl", "openxlsx", "patchwork", "pbapply", "pbkrtest", "pillar", "pkgbuild", "pkgKitten", "pkgload", "plotly", "processx", "promises", "proxy", "ps", "quantreg", "R.methodsS3", "R.oo", "R6", "rappdirs", "RBGL", "rcmdcheck", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppParallel", "readr", "remotes", "reprex", "reticulate", "rio", "rjags", "rlang", "rmarkdown", "robustbase", "roxygen2", "rprojroot", "rstatix", "rstudioapi", "rsvd", "rversions", "rvest", "sandwich", "sctransform", "Seurat", "sf", "shiny", "shinyjs", "sitmo", "slam", "sodium", "sp", "SparseM", "statmod", "stringi", "svglite", "sys", "systemfonts", "testit", "testthat", "tibble", "tidyr", "tidyselect", "tidyverse", "tinytex", "units", "usethis", "utf8", "uwot", "vctrs", "vdiffr", "vegan", "VennDiagram", "VGAM", "viridis", "viridisLite", "withr", "xfun", "XML", "zip", "zoo" ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 184 packages out-of-date; 0 packages too new

mtmorgan commented 3 years ago

Yikes! If it were me and I did not have critical work pending, I would start by updating package BiocManager::install(ask = FALSE). But actually when I look at the out-of-date packages I do not see the most likely culprit -- Rhtslib -- so I might first make sure that there was just a single installation of this package in .libPaths(). And I might also want to know whether there were network file systems involved.

sunnyyakima commented 3 years ago

Rhtslib is only installed in my /home it is a remote system in which I tried to install "Rsamtools", and I am a regular user, I guess there are network file systems

sunnyyakima commented 3 years ago

a little progress:

ls -lrth /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/*/*.so -rwxr-xr-- 1 yu_liu yu_liu 3.7M Oct 30 10:47 /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/usrlib/libhts.so -rwxr-xr-- 1 yu_liu yu_liu 2.7M Oct 30 10:47 /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/libs/Rhtslib.so

nm /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/usrlib/libhts.so | grep tbx_conf_gff 0000000000097830 R tbx_conf_gff nm /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/libs/Rhtslib.so | grep tbx_conf_gff nothing from last command

so there are two Rhtslib.so in my /home, one of them has "tbx_conf_gff", but it is not reachable. Also, seems all other lib have similar path: x86_64-pc-linux-gnu-library/4.0/XXXXlib/lib/XXXX.so the Rhtslib with "tbx_conf_gff" has path with different pattern: /home/yu_liu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib/usrlib/libhts.so

hpages commented 2 years ago

Hi @sunnyyakima , were you able to solve this? Thanks