autonomics: example("read_somascan", package = "autonomics") fails, but not on Bioc check servers
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@henrik-bengtsson-4333
Last seen 10 weeks ago
United States

Hello, I'm trying to understand why Bioc checks don't pick up what my reverse-dependency checks on different systems detect:

> example("read_somascan", package = "autonomics")
rd_sms> file <- download_data('atkin18.somascan.adat')
rd_sms> read_somascan(file, pca = TRUE, fit = 'limma', block = 'Subject_ID')
Error in (1 + f_col):n_col : NA/NaN argument

Details: Debugging this reveals that the download file at line endings with CRCRLF (sic!), which I don't think is expected by read_somascan(), which uses readLines() to read the lines. My guess is that the the source data file is corrupt;

$ wget https://bitbucket.org/graumannlabtools/autonomics/downloads/atkin18.somascan.adat
$ ls -l atkin18.somascan.adat 
-rw-rw-r-- 1 henrik henrik 674340 Jul 12 03:02 atkin18.somascan.adat
$ md5sum atkin18.somascan.adat 
6253e8fe04448fc1c43b73baf45ba62e  atkin18.somascan.adat
$ file atkin18.somascan.adat 
atkin18.somascan.adat: ASCII text, with very long lines (11067), with CRLF, CR line terminators
$ cat -A atkin18.somascan.adat
[ shows line endings ^M^M$ == CRCRLF ]

My questions:

  1. Is this just me? I can reproduce it on a CentOS 7, a Rocky 8, and an Ubuntu 22.04 system at different sites, all running R 4.3.2 and Bioc 3.18 (autonomics 1.10.2).

  2. Why isn't this error occurring on the Bioconductor check servers ( https://bioconductor.org/checkResults/release/bioc-LATEST/autonomics/ )?

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.8 (Green Obsidian)

Matrix products: default
BLAS:   /wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib/libRblas.so
LAPACK: /wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

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

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

other attached packages:
[1] autonomics_1.10.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0            dplyr_1.1.4
 [3] blob_1.2.4                  filelock_1.0.2
 [5] R.utils_2.12.3              bitops_1.0-7
 [7] fastmap_1.1.1               RCurl_1.98-1.13
 [9] BiocFileCache_2.10.1        assertive.files_0.0-2
[11] digest_0.6.33               lifecycle_1.0.4
[13] statmod_1.5.0               RSQLite_2.3.3
[15] magrittr_2.0.3              compiler_4.3.2
[17] rlang_1.1.2                 tools_4.3.2
[19] utf8_1.2.4                  assertive.base_0.0-9
[21] data.table_1.14.8           assertive.sets_0.0-3
[23] S4Arrays_1.2.0              bit_4.0.5
[25] curl_5.1.0                  DelayedArray_0.28.0
[27] abind_1.4-5                 withr_2.5.2
[29] purrr_1.0.2                 BiocGenerics_0.48.1
[31] desc_1.4.2                  R.oo_1.25.0
[33] grid_4.3.2                  stats4_4.3.2
[35] fansi_1.0.5                 colorspace_2.1-0
[37] progressr_0.14.0            edgeR_4.0.2
[39] ggplot2_3.4.4               scales_1.3.0
[41] MultiAssayExperiment_1.28.0 SummarizedExperiment_1.32.0
[43] debugme_1.1.0               cli_3.6.1
[45] crayon_1.5.2                generics_0.1.3
[47] parsedate_1.3.1             cranlike_1.0.2
[49] httr_1.4.7                  readxl_1.4.3
[51] DBI_1.1.3                   cachem_1.0.8
[53] zlibbioc_1.48.0             parallel_4.3.2
[55] cellranger_1.1.0            XVector_0.42.0
[57] matrixStats_1.1.0           vctrs_0.6.4
[59] Matrix_1.6-3                IRanges_2.36.0
[61] S4Vectors_0.40.2            bit64_4.0.5
[63] ggrepel_0.9.4               locfit_1.5-9.8
[65] limma_3.58.1                tidyr_1.3.0
[67] glue_1.6.2                  crancache_0.0.0.9001
[69] rematch2_2.1.2              stringi_1.8.2
[71] gtable_0.3.4                GenomeInfoDb_1.38.1
[73] GenomicRanges_1.54.1        munsell_0.5.0
[75] tibble_3.2.1                pillar_1.9.0
[77] rappdirs_0.3.3              GenomeInfoDbData_1.2.11
[79] R6_2.5.1                    dbplyr_2.4.0
[81] rprojroot_2.0.4             lattice_0.22-5
[83] Biobase_2.62.0              R.methodsS3_1.8.2
[85] memoise_2.0.1               Rcpp_1.0.11
[87] gridExtra_2.3               SparseArray_1.2.2
[89] MatrixGenerics_1.14.0       assertive.numbers_0.0-2
[91] pkgconfig_2.0.3

EDIT: Replaced example("create_design", package = "autonomics") with example("read_somascan", package = "autonomics"), which has the same problem.

autonomics • 280 views
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Entering edit mode
Mike Smith ★ 6.4k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg

It looks like autonomics uses BiocFileCache to create a local copy of the data and save repeat downloading. Given the (relatively) recent last update on that file, I'd guess that the build system is using a cached version from before it was changed on the remote server. As far as I can see autonomics:::download_data() has a commented out call to bfcneedsupdate(). My understanding is that should address this issue, but maybe it wasn't working as expected.

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Entering edit mode

Thanks Mike for diving deeper into this. Your findings make sense. It sounds like the Bioconductor checks need to be modified so that they do not have a memory from previous runs and rely on side effects such as file caches. It would probably better to test with a temporary file cache, so the cache is only active during a single package check. I'll try to find the proper issue tracker to post this proposal.

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