Installation fails: "Error: object ‘filter_obs’ is not exported by 'namespace:taxa'"

[sielerjm]

---

Hi all,

I'm attempting to install MicrobiomeR on R Studio Server Pro. It's a cloud based GUI of Rstudio. I'm getting stuck on this error, that I haven't been able to troubleshoot successfully. I suspect it's related to the taxa package, but I'm not sure how to proceed. I'd appreciate any help you all may have.

I've tried installing from source locally as well as using devtools::install_github, but each returns the same error.

Thanks!

> install.packages("/home/sielerjm/Projects/Downloads/MicrobiomeR_0.7.0.tar", repos = NULL, type ="source")
Installing package into ‘/home/sielerjm/R/x86_64-redhat-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘MicrobiomeR’ ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘filter_obs’ is not exported by 'namespace:taxa'
Execution halted
ERROR: lazy loading failed for package ‘MicrobiomeR’
* removing ‘/home/sielerjm/R/x86_64-redhat-linux-gnu-library/4.0/MicrobiomeR’
Warning in install.packages :
  installation of package ‘/home/sielerjm/Projects/Downloads/MicrobiomeR_0.7.0.tar’ had non-zero exit status

I've also tried installing via devtools and I receive a similar error attempting to install:

> devtools::install_github("vallenderlab/MicrobiomeR")
Installing package into ‘/home/sielerjm/R/x86_64-redhat-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘MicrobiomeR’ ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘filter_obs’ is not exported by 'namespace:taxa'
Execution halted
ERROR: lazy loading failed for package ‘MicrobiomeR’
* removing ‘/home/sielerjm/R/x86_64-redhat-linux-gnu-library/4.0/MicrobiomeR’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmphkTX0J/file28a83b3b35d015/MicrobiomeR_0.6.1.tar.gz’ had non-zero exit status

Session Information

R version 4.0.5 (2021-03-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.so

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

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

other attached packages:
 [1] taxa_0.4.0              picante_1.8.2           nlme_3.1-153            ape_5.5                 rcompanion_2.4.1        phyloseqCompanion_0.2.1 GUniFrac_1.4            doParallel_1.0.16      
 [9] iterators_1.0.13        foreach_1.5.1           magrittr_2.0.1          vegan_2.5-7             lattice_0.20-45         permute_0.9-5           phyloseq_1.39.1         roperators_1.1.0       
[17] readxl_1.3.1            nortest_1.0-4           flextable_0.6.10        cowplot_1.1.1           reshape2_1.4.4          data.table_1.14.2       RColorBrewer_1.1-2      forcats_0.5.1          
[25] stringr_1.4.0           dplyr_1.0.7             purrr_0.3.4             readr_2.1.1             tidyr_1.1.4             tibble_3.1.6            tidyverse_1.3.1         tinytex_0.35           
[33] ggplot2_3.3.5           knitr_1.36              vctrs_0.3.8             metacoder_0.3.5.001    

loaded via a namespace (and not attached):
  [1] uuid_1.0-3          backports_1.4.0     systemfonts_1.0.3   plyr_1.8.6          igraph_1.2.9        splines_4.0.5       usethis_2.0.1       TH.data_1.1-0       digest_0.6.29       htmltools_0.5.2    
 [11] lmerTest_3.1-3      fansi_0.5.0         memoise_2.0.0       cluster_2.1.2       remotes_2.4.0       tzdb_0.2.0          Biostrings_2.58.0   modelr_0.1.8        matrixStats_0.61.0  officer_0.4.1      
 [21] stabledist_0.7-1    sandwich_3.0-1      prettyunits_1.1.1   colorspace_2.0-2    rvest_1.0.2         ggrepel_0.9.1       haven_2.4.3         xfun_0.28           callr_3.7.0         libcoin_1.0-9      
 [31] crayon_1.4.2        jsonlite_1.7.2      Exact_3.0           lme4_1.1-27.1       zoo_1.8-9           survival_3.2-13     glue_1.5.1          gtable_0.3.0        zlibbioc_1.36.0     XVector_0.30.0     
 [41] pkgbuild_1.2.0      Rhdf5lib_1.12.1     BiocGenerics_0.36.1 scales_1.1.1        mvtnorm_1.1-2       DBI_1.1.1           Rcpp_1.0.7          clue_0.3-60         proxy_0.4-26        stats4_4.0.5       
 [51] timeSeries_3062.100 httr_1.4.2          modeltools_0.2-23   ellipsis_0.3.2      spatial_7.3-14      pkgconfig_2.0.3     multcompView_0.1-8  dbplyr_2.1.1        utf8_1.2.2          tidyselect_1.1.1   
 [61] rlang_0.4.12        cachem_1.0.6        munsell_0.5.0       cellranger_1.1.0    tools_4.0.5         cli_3.1.0           generics_0.1.1      ade4_1.7-18         devtools_2.4.2      broom_0.7.10       
 [71] evaluate_0.14       biomformat_1.18.0   fastmap_1.1.0       processx_3.5.2      fs_1.5.0            zip_2.2.0           packrat_0.7.0       coin_1.4-2          rootSolve_1.8.2.3   xml2_1.3.3         
 [81] compiler_4.0.5      rstudioapi_0.13     curl_4.3.2          testthat_3.0.4      e1071_1.7-9         reprex_2.0.1        statmod_1.4.36      DescTools_0.99.43   stringi_1.7.6       statip_0.2.3       
 [91] ps_1.6.0            desc_1.3.0          gdtools_0.2.3       modeest_2.4.0       fBasics_3042.89.1   Matrix_1.3-4        nloptr_1.2.2.3      multtest_2.46.0     pillar_1.6.4        lifecycle_1.0.1    
[101] rhdf5filters_1.2.1  lmtest_0.9-38       lmom_2.8            R6_2.5.1            stable_1.1.4        IRanges_2.24.1      gld_2.6.2           sessioninfo_1.1.1   codetools_0.2-18    pkgload_1.2.2      
[111] boot_1.3-28         MASS_7.3-54         assertthat_0.2.1    rhdf5_2.34.0        rprojroot_2.0.2     withr_2.4.3         multcomp_1.4-17     S4Vectors_0.28.1    mgcv_1.8-37         expm_0.999-6       
[121] hms_1.1.1           grid_4.0.5          rpart_4.1-15        timeDate_3043.102   class_7.3-19        minqa_1.2.4         rmarkdown_2.11      rmutil_1.1.5        numDeriv_2016.8-1.1 Biobase_2.50.0     
[131] lubridate_1.8.0     base64enc_0.1-3 

[sdhutchins]

Hey, @sielerjm. Thanks for pointing this out.

I'll try to get to this next week.

[sielerjm]

Thanks, no rush! I understand these are busy times for folks.

[grabear]

It seems that the taxa package is undergoing a rework, so there are many of the taxmap related functions that aren't available in the current version of their package (0.4.0). I didn't have time to test, but I made a pre-release https://github.com/vallenderlab/MicrobiomeR/releases that depends on any version of taxa under 0.3.4.

Please try this and let us know how it goes @sielerjm

[sielerjm]

Hi @grabear,

I'll be conducting some new analyses in the coming weeks and will report back the . Thanks for your help!

[sdhutchins]

Thanks for taking a look @grabear !