ococrook
commented
2 years ago @lgatto will have a look at this. I have no problem locally so I'll reinstall R and try again.
Closed lgatto closed 2 years ago
ococrook
commented
2 years ago @lgatto will have a look at this. I have no problem locally so I'll reinstall R and try again.
lgatto
commented
2 years ago Thank you for looking into it.
Here's the Bioconductor check report and my local session info
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.10.0
LAPACK: /usr/lib/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] pRoloc_1.33.0 BiocParallel_1.27.16 MLInterfaces_1.73.0
[4] cluster_2.1.2 annotate_1.71.0 XML_3.99-0.8
[7] AnnotationDbi_1.55.1 IRanges_2.27.2 MSnbase_2.19.2
[10] ProtGenerics_1.25.2 S4Vectors_0.31.5 mzR_2.27.1
[13] Rcpp_1.0.7 Biobase_2.53.0 BiocGenerics_0.39.2
loaded via a namespace (and not attached):
[1] colorspace_2.0-2 ellipsis_0.3.2 class_7.3-19
[4] mclust_5.4.7 XVector_0.33.0 clue_0.3-59
[7] rstudioapi_0.13 proxy_0.4-26 listenv_0.8.0
[10] hexbin_1.28.2 affyio_1.63.2 bit64_4.0.5
[13] lubridate_1.7.10 prodlim_2019.11.13 fansi_0.5.0
[16] mvtnorm_1.1-2 xml2_1.3.2 codetools_0.2-18
[19] splines_4.1.0 ncdf4_1.17 doParallel_1.0.16
[22] cachem_1.0.6 impute_1.67.0 knitr_1.36
[25] LaplacesDemon_16.1.6 pROC_1.18.0 caret_6.0-89
[28] kernlab_0.9-29 vsn_3.61.2 dbplyr_2.1.1
[31] png_0.1-7 BiocManager_1.30.16 compiler_4.1.0
[34] httr_1.4.2 sampling_2.9 assertthat_0.2.1
[37] Matrix_1.3-4 fastmap_1.1.0 limma_3.49.4
[40] prettyunits_1.1.1 tools_4.1.0 coda_0.19-4
[43] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.7
[46] affy_1.71.0 reshape2_1.4.4 dplyr_1.0.7
[49] rappdirs_0.3.3 MALDIquant_1.20 vctrs_0.3.8
[52] Biostrings_2.61.2 preprocessCore_1.55.2 nlme_3.1-153
[55] iterators_1.0.13 timeDate_3043.102 gower_0.2.2
[58] xfun_0.26 stringr_1.4.0 globals_0.14.0
[61] lpSolve_5.6.15 lifecycle_1.0.1 gtools_3.9.2
[64] dendextend_1.15.1 future_1.22.1 zlibbioc_1.39.0
[67] MASS_7.3-54 scales_1.1.1 ipred_0.9-12
[70] pcaMethods_1.85.0 hms_1.1.1 parallel_4.1.0
[73] RColorBrewer_1.1-2 curl_4.3.2 memoise_2.0.0
[76] gridExtra_2.3 ggplot2_3.3.5 rpart_4.1-15
[79] biomaRt_2.49.4 segmented_1.3-4 stringi_1.7.5
[82] RSQLite_2.2.8 randomForest_4.6-14 foreach_1.5.1
[85] e1071_1.7-9 filelock_1.0.2 lava_1.6.10
[88] GenomeInfoDb_1.29.8 rlang_0.4.11 pkgconfig_2.0.3
[91] bitops_1.0-7 mzID_1.31.0 lattice_0.20-45
[94] purrr_0.3.4 recipes_0.1.17 bit_4.0.4
[97] tidyselect_1.1.1 parallelly_1.28.1 plyr_1.8.6
[100] magrittr_2.0.1
[ reached getOption("max.print") -- omitted 27 entries ]hmm no problem on windows at the moment, with the following sessioninfo. @lmsimp anything on your end?
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocCheck_1.28.0 pRoloc_1.33.0 BiocParallel_1.26.2 MLInterfaces_1.72.0 cluster_2.1.2 annotate_1.70.0
[7] XML_3.99-0.8 AnnotationDbi_1.54.1 IRanges_2.26.0 testthat_3.1.0 pRolocdata_1.30.0 MSnbase_2.18.0
[13] ProtGenerics_1.24.0 S4Vectors_0.30.2 mzR_2.26.1 Rcpp_1.0.7 Biobase_2.52.0 BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] BiocFileCache_2.0.0 plyr_1.8.6 splines_4.1.1 listenv_0.8.0 usethis_2.0.1
[6] GenomeInfoDb_1.28.4 ggplot2_3.3.5 digest_0.6.28 foreach_1.5.1 viridis_0.6.1
[11] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0 doParallel_1.0.16 mixtools_1.2.0
[16] limma_3.48.3 remotes_2.4.1 globals_0.14.0 recipes_0.1.17 Biostrings_2.60.2
[21] gower_0.2.2 lpSolve_5.6.15 prettyunits_1.1.1 colorspace_2.0-2 blob_1.2.2
[26] rappdirs_0.3.3 xfun_0.26 dplyr_1.0.7 callr_3.7.0 crayon_1.4.1
[31] RCurl_1.98-1.5 hexbin_1.28.2 graph_1.70.0 impute_1.66.0 survival_3.2-11
[36] iterators_1.0.13 glue_1.4.2 gtable_0.3.0 ipred_0.9-12 zlibbioc_1.38.0
[41] XVector_0.32.0 pkgbuild_1.2.0 kernlab_0.9-29 future.apply_1.8.1 scales_1.1.1
[46] vsn_3.60.0 mvtnorm_1.1-2 DBI_1.1.1 viridisLite_0.4.0 xtable_1.8-4
[51] progress_1.2.2 clue_0.3-59 bit_4.0.4 proxy_0.4-26 mclust_5.4.7
[56] preprocessCore_1.54.0 MsCoreUtils_1.4.0 lava_1.6.10 prodlim_2019.11.13 getopt_1.20.3
[61] sampling_2.9 httr_1.4.2 FNN_1.1.3 RColorBrewer_1.1-2 ellipsis_0.3.2
[66] pkgconfig_2.0.3 nnet_7.3-16 dbplyr_2.1.1 utf8_1.2.2 caret_6.0-89
[71] reshape2_1.4.4 tidyselect_1.1.1 rlang_0.4.11 biocViews_1.60.0 munsell_0.5.0
[76] tools_4.1.1 LaplacesDemon_16.1.6 cachem_1.0.6 cli_3.0.1 generics_0.1.0
[81] RSQLite_2.2.8 devtools_2.4.2 stringr_1.4.0 fastmap_1.1.0 mzID_1.30.0
[86] ModelMetrics_1.2.2.2 processx_3.5.2 knitr_1.36 bit64_4.0.5 fs_1.5.0
[91] randomForest_4.6-14 purrr_0.3.4 KEGGREST_1.32.0 dendextend_1.15.1 ncdf4_1.17
[96] RBGL_1.68.0 future_1.22.1 nlme_3.1-152 xml2_1.3.2 biomaRt_2.48.3
[101] compiler_4.1.1 rstudioapi_0.13 filelock_1.0.2 curl_4.3.2 png_0.1-7
[106] e1071_1.7-9 affyio_1.62.0 tibble_3.1.5 stringi_1.7.5 ps_1.6.0
[111] desc_1.4.0 lattice_0.20-44 Matrix_1.3-4 vctrs_0.3.8 stringdist_0.9.8
[116] pillar_1.6.3 lifecycle_1.0.1 RUnit_0.4.32 optparse_1.6.6 BiocManager_1.30.16
[121] MALDIquant_1.20 data.table_1.14.2 bitops_1.0-7 R6_2.5.1 pcaMethods_1.84.0
[126] affy_1.70.0 gridExtra_2.3 parallelly_1.28.1 sessioninfo_1.1.1 codetools_0.2-18
[131] gtools_3.9.2 MASS_7.3-54 assertthat_0.2.1 pkgload_1.2.2 rprojroot_2.0.2
[136] withr_2.4.2 GenomeInfoDbData_1.2.6 hms_1.1.1 grid_4.1.1 rpart_4.1-15
[141] timeDate_3043.102 coda_0.19-4 class_7.3-19 segmented_1.3-4 pROC_1.18.0
[146] lubridate_1.7.10 Could you try to install the devel version of BiocParallel.
lgatto
commented
2 years ago Great, thank you!
The MCMC chains in TAGM MCMC consistency test aren't equal anymore. This might be related to recent changes in [BiocParallel] (even though we use
SerialParams).@ococrook - could you have a look. This is actually quite urgent and critical, as package code will be frozen next week for the new release, and
pRolocis failing.