Question

Advice on ANCOMBC 'R CMD build' error for BioC 3.16

0

Entering edit mode

HULFRED ▴ 10

@hul40-23955

Last seen 7 months ago

United States

Hi,

I recently received an email notifying me that the ANCOMBC package I maintained encountered an error for BioC 3.16.

The error message is:

--- re-building ‘ANCOMBC2.Rmd’ using rmarkdown
The number of taxa after filtering is: 91
`tax_level` is not speficified 
The lowest taxonomic level will be used: Species
Otherwise, please speficy `tax_level` by one of the following: 
Species
Obtaining initial estimates ...
Estimating sample-specific biases ...
ANCOM-BC2 primary results ...
The sensitivity analysis for the pseudo-count addition ...
Quitting from lines 240-274 (ANCOMBC2.Rmd) 
Error: processing vignette 'ANCOMBC2.Rmd' failed with diagnostics:
Input includes an object that is not 'SummarizedExperiment'.
--- failed re-building ‘ANCOMBC2.Rmd’

It seems the issue is related to a SummarizedExperiment object. However, I am not able to reproduce this error locally. The ANCOMBC2 vignette ran without an error from my end, and the package has passed both R CMD check and BiocCheck.

I wonder if it is because another package (e.g., SummarizedExperiment) breaks ANCOMBC. May you please advice how to fix this issue? Thank you!

Here is the session info for my local machine:

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DT_0.23                        caret_6.0-92                   lattice_0.20-45                mia_1.4.0                     
 [5] MultiAssayExperiment_1.22.0    TreeSummarizedExperiment_2.4.0 Biostrings_2.64.0              XVector_0.36.0                
 [9] SingleCellExperiment_1.18.1    SummarizedExperiment_1.26.1    Biobase_2.56.0                 GenomicRanges_1.48.0          
[13] GenomeInfoDb_1.32.2            IRanges_2.30.0                 S4Vectors_0.34.0               BiocGenerics_0.42.0           
[17] MatrixGenerics_1.8.1           matrixStats_0.62.0             forcats_0.5.1                  stringr_1.4.0                 
[21] dplyr_1.0.9                    purrr_0.3.4                    readr_2.1.2                    tidyr_1.2.0                   
[25] tibble_3.1.7                   ggplot2_3.3.6                  tidyverse_1.3.1                ANCOMBC_1.99.3                

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  tidyselect_1.1.2            lme4_1.1-29                 RSQLite_2.2.17             
  [5] htmlwidgets_1.5.4           grid_4.2.0                  BiocParallel_1.30.3         gmp_0.6-5                  
  [9] pROC_1.18.0                 munsell_0.5.0               ScaledMatrix_1.4.1          codetools_0.2-18           
 [13] future_1.26.1               withr_2.5.0                 colorspace_2.0-3            energy_1.7-10              
 [17] knitr_1.39                  rstudioapi_0.13             DescTools_0.99.45           listenv_0.8.0              
 [21] labeling_0.4.2              Rdpack_2.3.1                emmeans_1.8.1-1             GenomeInfoDbData_1.2.8     
 [25] farver_2.1.0                bit64_4.0.5                 parallelly_1.32.0           vctrs_0.4.1                
 [29] treeio_1.20.2               generics_0.1.2              ipred_0.9-13                xfun_0.31                  
 [33] R6_2.5.1                    doParallel_1.0.17           ggbeeswarm_0.6.0            rsvd_1.0.5                 
 [37] bitops_1.0-7                cachem_1.0.6                DelayedArray_0.22.0         assertthat_0.2.1           
 [41] scales_1.2.0                nnet_7.3-17                 beeswarm_0.4.0              rootSolve_1.8.2.3          
 [45] gtable_0.3.0                beachmat_2.12.0             globals_0.15.1              lmom_2.9                   
 [49] timeDate_3043.102           rlang_1.0.2                 splines_4.2.0               lazyeval_0.2.2             
 [53] ModelMetrics_1.2.2.2        broom_0.8.0                 checkmate_2.1.0             yaml_2.3.5                 
 [57] modelr_0.1.8                reshape2_1.4.4              backports_1.4.1             Hmisc_4.7-0                
 [61] tools_4.2.0                 lava_1.6.10                 ellipsis_0.3.2              decontam_1.16.0            
 [65] RColorBrewer_1.1-3          proxy_0.4-27                Rcpp_1.0.8.3                plyr_1.8.7                 
 [69] base64enc_0.1-3             sparseMatrixStats_1.8.0     zlibbioc_1.42.0             RCurl_1.98-1.7             
 [73] rpart_4.1.16                viridis_0.6.2               haven_2.5.0                 ggrepel_0.9.1              
 [77] cluster_2.1.3               fs_1.5.2                    DECIPHER_2.24.0             magrittr_2.0.3             
 [81] data.table_1.14.2           lmerTest_3.1-3              reprex_2.0.1                mvtnorm_1.1-3              
 [85] gsl_2.1-7.1                 evaluate_0.15               hms_1.1.1                   xtable_1.8-4               
 [89] jpeg_0.1-9                  readxl_1.4.0                gridExtra_2.3               compiler_4.2.0             
 [93] scater_1.24.0               crayon_1.5.1                minqa_1.2.4                 htmltools_0.5.2            
 [97] tzdb_0.3.0                  mgcv_1.8-40                 Formula_1.2-4               expm_0.999-6               
[101] Exact_3.1                   lubridate_1.8.0             DBI_1.1.3                   dbplyr_2.2.0               
[105] MASS_7.3-57                 boot_1.3-28                 Matrix_1.5-1                permute_0.9-7              
[109] cli_3.3.0                   rbibutils_2.2.8             parallel_4.2.0              gower_1.0.0                
[113] pkgconfig_2.0.3             numDeriv_2016.8-1.1         foreign_0.8-82              scuttle_1.6.3              
[117] recipes_0.2.0               xml2_1.3.3                  foreach_1.5.2               vipor_0.4.5                
[121] DirichletMultinomial_1.38.0 hardhat_1.1.0               rngtools_1.5.2              estimability_1.4.1         
[125] prodlim_2019.11.13          rvest_1.0.2                 CVXR_1.0-10                 doRNG_1.8.2                
[129] yulab.utils_0.0.5           digest_0.6.29               vegan_2.6-2                 rmarkdown_2.14             
[133] cellranger_1.1.0            tidytree_0.4.1              htmlTable_2.4.0             gld_2.6.4                  
[137] DelayedMatrixStats_1.18.1   nloptr_2.0.3                lifecycle_1.0.1             nlme_3.1-158               
[141] jsonlite_1.8.0              BiocNeighbors_1.14.0        viridisLite_0.4.0           fansi_1.0.3                
[145] pillar_1.7.0                fastmap_1.1.0               httr_1.4.3                  survival_3.3-1             
[149] glue_1.6.2                  png_0.1-7                   iterators_1.0.14            bit_4.0.4                  
[153] class_7.3-20                stringi_1.7.6               blob_1.2.3                  BiocSingular_1.12.0        
[157] latticeExtra_0.6-29         memoise_2.0.1               Rmpfr_0.8-9                 irlba_2.3.5                
[161] e1071_1.7-11                future.apply_1.9.0          ape_5.6-2

BuildReport • 1.1k views

ADD COMMENT • link updated 18 months ago by shepherl 3.8k • written 18 months ago by HULFRED ▴ 10

1

Entering edit mode

I can reproduce this locally on my computer. Please make sure you are using Bioconductor devel and have updated all packages. BiocManager::valid() and BiocManager::install() . Also questions on debugging and package development are generally better asked on bioc-devel@r-project ; where the support site should be for more user related errors and questions.

FWIW I tracked down exact code failing running the vignette manually:

> sens_cat = tab_sens %>%
+     transmute(sens_cat = cat_cov2) %>%
+     rownames_to_column("tax_id") %>%
+     left_join(res_prim %>%
+                   rownames_to_column("tax_id") %>%
+                   transmute(tax_id, diff_cat = diff_cat_cov2), 
+               by = "tax_id") %>%
+     mutate(group = "Cat2 vs. Cat1") %>%
+     bind_rows(
+         tab_sens %>%
+             transmute(sens_cat = cat_cov3) %>%
+             rownames_to_column("tax_id") %>%
+             left_join(res_prim %>%
+                           rownames_to_column("tax_id") %>%
+                           transmute(tax_id, diff_cat = diff_cat_cov3), 
+                       by = "tax_id") %>%
+             mutate(group = "Cat3 vs. Cat1")
+     )
Error: Input includes an object that is not 'SummarizedExperiment'.

My guess is, you might have to specify exactly which package function to use in this chunk of code using package::function

ADD REPLY • link 18 months ago shepherl 3.8k

0

Entering edit mode

Thanks for your advice! I really appreciate it!

ADD REPLY • link 18 months ago HULFRED ▴ 10

0

Entering edit mode

Hi,

I resolved the issue and was trying to push the changes to Bioconductor. However, I encountered the following error:

(base) ➜  ANCOMBC git:(devel) git push upstream master 
To git.bioconductor.org:packages/ANCOMBC.git
 ! [rejected]        master -> master (non-fast-forward)
error: failed to push some refs to 'git@git.bioconductor.org:packages/ANCOMBC.git'
hint: Updates were rejected because a pushed branch tip is behind its remote
hint: counterpart. Check out this branch and integrate the remote changes
hint: (e.g. 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

I have tried git pull as it suggested, but it showed that:

(base) ➜  ANCOMBC git:(devel) git pull
Already up-to-date.

The git merge upstream/master command did not work either

(base) ➜  ANCOMBC git:(devel) git merge upstream/master
Already up-to-date.

Any suggestions on how to deal with this error? Thanks a lot!

ADD REPLY • link 18 months ago HULFRED ▴ 10

1

Entering edit mode

Please ask these types on questions on bioc-devel@r-project.org

ADD REPLY • link 18 months ago shepherl 3.8k