Closed lgatto closed 2 years ago
@lgatto will have a look at this. I have no problem locally so I'll reinstall R and try again.
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.
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
pRoloc
is failing.