Error with package installation failed

[ghost]

I ran into the following problems when installing this package, and got an error message coming out as:

> BiocManager::install("waldronlab/subtypeHeterogeneity", dependencies = TRUE, build_vignettes = TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details`

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

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing github package(s) 'waldronlab/subtypeHeterogeneity'
Downloading GitHub repo waldronlab/subtypeHeterogeneity@HEAD
✓ checking for file ‘/tmp/Rtmp7rjiir/remotes19a4b7fa83ada/waldronlab-subtypeHeterogeneity-0f275d2/DESCRIPTION’ ...
─ preparing ‘subtypeHeterogeneity’:
✓ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
-----------------------------------
─ installing source package ‘subtypeHeterogeneity’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error : 'diseaseCodes' is not an exported object from 'namespace:TCGAutils'
Error: unable to load R code in package ‘subtypeHeterogeneity’
Execution halted
ERROR: lazy loading failed for package ‘subtypeHeterogeneity’
─ removing ‘/tmp/RtmpSqLNH6/Rinst1ac9065d11f54/subtypeHeterogeneity’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'subtypeHeterogeneity' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ** R
E> ** inst
E> ** byte-compile and prepare package for lazy loading
E> Error : 'diseaseCodes' is not an exported object from 'namespace:TCGAutils'
E> Error: unable to load R code in package ‘subtypeHeterogeneity’
E> Execution halted
E> ERROR: lazy loading failed for package ‘subtypeHeterogeneity’
E> * removing ‘/tmp/RtmpSqLNH6/Rinst1ac9065d11f54/subtypeHeterogeneity’
E> -----------------------------------
E> ERROR: package installation failed

I would be appreciated with any help.

> sessionInfo()

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

loaded via a namespace (and not attached):
[1] MatrixGenerics_1.4.3 Biobase_2.52.0
[3] httr_1.4.2 bit64_4.0.5
[5] jsonlite_1.7.2 assertthat_0.2.1
[7] TCGAutils_1.12.0 BiocManager_1.30.16
[9] stats4_4.1.1 BiocFileCache_2.0.0
[11] blob_1.2.2 Rsamtools_2.8.0
[13] GenomeInfoDbData_1.2.6 yaml_2.2.1
[15] remotes_2.4.1 progress_1.2.2
[17] pillar_1.6.4 RSQLite_2.2.8
[19] lattice_0.20-45 glue_1.4.2
[21] digest_0.6.28 GenomicRanges_1.44.0
[23] XVector_0.32.0 rvest_1.0.2
[25] Matrix_1.3-4 XML_3.99-0.8
[27] pkgconfig_2.0.3 biomaRt_2.48.3
[29] zlibbioc_1.38.0 purrr_0.3.4
[31] processx_3.5.2 MultiAssayExperiment_1.18.0
[33] BiocParallel_1.26.2 tzdb_0.2.0
[35] tibble_3.1.5 KEGGREST_1.32.0
[37] generics_0.1.1 IRanges_2.26.0
[39] ellipsis_0.3.2 cachem_1.0.6
[41] withr_2.4.2 SummarizedExperiment_1.22.0
[43] GenomicFeatures_1.44.2 BiocGenerics_0.38.0
[45] cli_3.1.0 magrittr_2.0.1
[47] crayon_1.4.1 memoise_2.0.0
[49] ps_1.6.0 fansi_0.5.0
[51] xml2_1.3.2 pkgbuild_1.2.0
[53] tools_4.1.1 prettyunits_1.1.1
[55] hms_1.1.1 BiocIO_1.2.0
[57] lifecycle_1.0.1 matrixStats_0.61.0
[59] stringr_1.4.0 S4Vectors_0.30.2
[61] DelayedArray_0.18.0 AnnotationDbi_1.54.1
[63] callr_3.7.0 Biostrings_2.60.2
[65] compiler_4.1.1 GenomeInfoDb_1.28.4
[67] rlang_0.4.12 grid_4.1.1
[69] GenomicDataCommons_1.16.0 RCurl_1.98-1.5
[71] rstudioapi_0.13 rjson_0.2.20
[73] rappdirs_0.3.3 bitops_1.0-7
[75] restfulr_0.0.13 DBI_1.1.1
[77] curl_4.3.2 R6_2.5.1
[79] GenomicAlignments_1.28.0 rtracklayer_1.52.1
[81] dplyr_1.0.7 fastmap_1.1.0
[83] bit_4.0.4 utf8_1.2.2
[85] filelock_1.0.2 rprojroot_2.0.2
[87] readr_2.0.2 stringi_1.7.5
[89] parallel_4.1.1 Rcpp_1.0.7
[91] vctrs_0.3.8 png_0.1-7
[93] dbplyr_2.1.1 tidyselect_1.1.1

[lgeistlinger]

Please note that analysis as documented in this repository was carried out using R-4.0.2 and Bioconductor-3.11.

It looks like you are using R.4.1.1 and Bioconductor version 3.13, so you would need to install the corresponding R and Bioconductor versions listed above. Packages and functions change over time, as we observe here for the TCGAutils package.

[lwaldron]

I think I can fix that, it's a small update from TCGAutils.

[lgeistlinger]

I am not sure we want to go down that road though, as somebody trying to restore the analysis environment as used for the paper (R-4.0.2 / Bioc 3.11) will then encounter an error when using the updated code. On the other hand, there is no guarantee that TCGAutils is the only package that has changed, and your are then keeping on updating a repo with many dependencies as opposed to freezing reproducibility to a given R and Bioc version at the time of publication.

[ghost]

Thanks for your reply.
I plan to change to 'R-4.0.2' and 'Bioconductor-3.11' according to your comments. But for now, downgrading to 'TCGAutils-1.8.1' solved the problem temporarily.

[lwaldron]

FWIW, I think the only change in TCGAutils was beginning to lazy-load diseaseCodes, so removing TCGAutils::diseaseCodes from this package's Imports and adding a line data("diseaseCodes", package="TCGAutils") to use the diseaseCodes object should fix this error for the current R/Bioconductor. I don't think such a change would cause any errors in the previous TCGAutils version either, and I think would in general be preferable to importing data objects.

[LiNk-NY]

Thanks Levi, this should be resolved by #5