Open sarah91-RA opened 3 months ago
I think this has now become a really urgent issue.
(delayed)matrixstats up to recently was giving the following warnings when running detP:
> detP <- detectionP(rgSet)
Warning messages:
1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
2: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
3: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
4: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
However, as of the latest version (matrixStats 1.2.*), the deprecation warning has become a fatal error and detectionP cannot be performed anymore.
I am not sure where/how this relates to the entire dependency structure, so I do not have the capabilities to resolve it myself. Is there anyone who can look into this?
kind regards,
Youri
I cannot replicate this error with a recent install of minfi. Could you please report both
1) the output of sessionInfo()
2) the output of
library(BiocManager)
BiocManager::valid()
I am guessing this may be related to you mixing an older version of minfi with a newer version of matrixStats
Dear Kasper,
Thank you for the quick response. We're running on a system that is running for 2 years, probably with some R packages installed through Red Hat. The issue appeared on a brand new user with brand new home directory after his first time installing minfi (BiocManager::install("minfi")
), yesterday or the day before.
Here is the output of your requested commands (please note that matrixStats is new back to 1.1.0, I copied it from another user as work-around for the issue):
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.4.3 dplyr_1.1.4
[3] stringr_1.5.1 minfiData_0.44.0
[5] IlluminaHumanMethylation450kmanifest_0.4.0 missMethyl_1.32.1
[7] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 RColorBrewer_1.1-3
[9] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 limma_3.54.2
[11] knitr_1.46 IlluminaHumanMethylationEPICmanifest_0.3.0
[13] minfi_1.44.0 bumphunter_1.40.0
[15] locfit_1.5-9.9 iterators_1.0.14
[17] foreach_1.5.2 Biostrings_2.66.0
[19] XVector_0.38.0 SummarizedExperiment_1.28.0
[21] Biobase_2.58.0 MatrixGenerics_1.10.0
[23] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[25] IRanges_2.32.0 S4Vectors_0.36.2
[27] BiocGenerics_0.44.0 matrixStats_1.1.0
loaded via a namespace (and not attached):
[1] rjson_0.2.21 siggenes_1.72.0 mclust_6.1 base64_2.0.1
[5] bit64_4.0.5 AnnotationDbi_1.60.2 fansi_1.0.6 xml2_1.3.6
[9] codetools_0.2-20 splines_4.2.2 sparseMatrixStats_1.10.0 cachem_1.0.8
[13] scrime_1.3.5 Rsamtools_2.14.0 annotate_1.76.0 dbplyr_2.5.0
[17] png_0.1-8 HDF5Array_1.26.0 BiocManager_1.30.22 readr_2.1.5
[21] compiler_4.2.2 httr_1.4.7 Matrix_1.6-5 fastmap_1.1.1
[25] cli_3.6.2 prettyunits_1.2.0 tools_4.2.2 glue_1.7.0
[29] GenomeInfoDbData_1.2.9 rappdirs_0.3.3 doRNG_1.8.6 Rcpp_1.0.12
[33] cellranger_1.1.0 vctrs_0.6.5 rhdf5filters_1.10.1 multtest_2.54.0
[37] preprocessCore_1.60.2 nlme_3.1-164 rtracklayer_1.58.0 DelayedMatrixStats_1.20.0
[41] xfun_0.43 lifecycle_1.0.4 restfulr_0.0.15 rngtools_1.5.2
[45] statmod_1.5.0 XML_3.99-0.16.1 beanplot_1.3.1 org.Hs.eg.db_3.16.0
[49] zlibbioc_1.44.0 MASS_7.3-60.0.1 hms_1.1.3 rhdf5_2.42.1
[53] GEOquery_2.66.0 yaml_2.3.8 curl_5.2.1 memoise_2.0.1
[57] biomaRt_2.54.1 reshape_0.8.9 stringi_1.8.3 RSQLite_2.3.6
[61] genefilter_1.80.3 BiocIO_1.8.0 GenomicFeatures_1.50.4 filelock_1.0.3
[65] BiocParallel_1.32.6 rlang_1.1.3 pkgconfig_2.0.3 bitops_1.0-7
[69] nor1mix_1.3-3 lattice_0.22-6 purrr_1.0.2 Rhdf5lib_1.20.0
[73] GenomicAlignments_1.34.1 bit_4.0.5 tidyselect_1.2.1 plyr_1.8.9
[77] magrittr_2.0.3 R6_2.5.1 generics_0.1.3 DelayedArray_0.24.0
[81] DBI_1.2.2 withr_3.0.0 pillar_1.9.0 survival_3.6-4
[85] KEGGREST_1.38.0 RCurl_1.98-1.14 tibble_3.2.1 crayon_1.5.2
[89] utf8_1.2.4 BiocFileCache_2.6.1 tzdb_0.4.0 progress_1.2.3
[93] grid_4.2.2 data.table_1.15.4 blob_1.2.4 digest_0.6.35
[97] xtable_1.8-4 tidyr_1.3.1 illuminaio_0.40.0 openssl_2.1.2
[101] askpass_1.2.0 quadprog_1.5-8
> library(BiocManager)
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31)
Bioconductor version '3.16' is out-of-date; the current release version '3.18' is available with R version '4.3'; see
https://bioconductor.org/install
> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
* sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.22 readxl_1.4.3
[3] dplyr_1.1.4 stringr_1.5.1
[5] minfiData_0.44.0 IlluminaHumanMethylation450kmanifest_0.4.0
[7] missMethyl_1.32.1 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[9] RColorBrewer_1.1-3 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[11] limma_3.54.2 knitr_1.46
[13] IlluminaHumanMethylationEPICmanifest_0.3.0 minfi_1.44.0
[15] bumphunter_1.40.0 locfit_1.5-9.9
[17] iterators_1.0.14 foreach_1.5.2
[19] Biostrings_2.66.0 XVector_0.38.0
[21] SummarizedExperiment_1.28.0 Biobase_2.58.0
[23] MatrixGenerics_1.10.0 GenomicRanges_1.50.2
[25] GenomeInfoDb_1.34.9 IRanges_2.32.0
[27] S4Vectors_0.36.2 BiocGenerics_0.44.0
[29] matrixStats_1.1.0
loaded via a namespace (and not attached):
[1] rjson_0.2.21 siggenes_1.72.0 mclust_6.1 base64_2.0.1
[5] bit64_4.0.5 AnnotationDbi_1.60.2 fansi_1.0.6 xml2_1.3.6
[9] codetools_0.2-20 splines_4.2.2 sparseMatrixStats_1.10.0 cachem_1.0.8
[13] scrime_1.3.5 Rsamtools_2.14.0 annotate_1.76.0 dbplyr_2.5.0
[17] png_0.1-8 HDF5Array_1.26.0 readr_2.1.5 compiler_4.2.2
[21] httr_1.4.7 Matrix_1.6-5 fastmap_1.1.1 cli_3.6.2
[25] prettyunits_1.2.0 tools_4.2.2 glue_1.7.0 GenomeInfoDbData_1.2.9
[29] rappdirs_0.3.3 doRNG_1.8.6 Rcpp_1.0.12 cellranger_1.1.0
[33] vctrs_0.6.5 rhdf5filters_1.10.1 multtest_2.54.0 preprocessCore_1.60.2
[37] nlme_3.1-164 rtracklayer_1.58.0 DelayedMatrixStats_1.20.0 xfun_0.43
[41] lifecycle_1.0.4 restfulr_0.0.15 rngtools_1.5.2 statmod_1.5.0
[45] XML_3.99-0.16.1 beanplot_1.3.1 org.Hs.eg.db_3.16.0 zlibbioc_1.44.0
[49] MASS_7.3-60.0.1 hms_1.1.3 rhdf5_2.42.1 GEOquery_2.66.0
[53] yaml_2.3.8 curl_5.2.1 memoise_2.0.1 biomaRt_2.54.1
[57] reshape_0.8.9 stringi_1.8.3 RSQLite_2.3.6 genefilter_1.80.3
[61] BiocIO_1.8.0 GenomicFeatures_1.50.4 filelock_1.0.3 BiocParallel_1.32.6
[65] rlang_1.1.3 pkgconfig_2.0.3 bitops_1.0-7 nor1mix_1.3-3
[69] lattice_0.22-6 purrr_1.0.2 Rhdf5lib_1.20.0 GenomicAlignments_1.34.1
[73] bit_4.0.5 tidyselect_1.2.1 plyr_1.8.9 magrittr_2.0.3
[77] R6_2.5.1 generics_0.1.3 DelayedArray_0.24.0 DBI_1.2.2
[81] withr_3.0.0 pillar_1.9.0 survival_3.6-4 KEGGREST_1.38.0
[85] RCurl_1.98-1.14 tibble_3.2.1 crayon_1.5.2 utf8_1.2.4
[89] BiocFileCache_2.6.1 tzdb_0.4.0 progress_1.2.3 grid_4.2.2
[93] data.table_1.15.4 blob_1.2.4 digest_0.6.35 xtable_1.8-4
[97] tidyr_1.3.1 illuminaio_0.40.0 openssl_2.1.2 askpass_1.2.0
[101] quadprog_1.5-8
Bioconductor version '3.16'
* 2 packages out-of-date
* 0 packages too new
create a valid installation with
BiocManager::install(c(
"matrixStats", "mclust"
), update = TRUE, ask = FALSE, force = TRUE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
Warning message:
2 packages out-of-date; 0 packages too new
If we need to do any testing or can be of help in any other way, feel free to ask.
Youri
Hi Everyone,
I am currently experiencing an error while performing EPIC methylation analysis. This has not happened before and recently I encountered this error which happened when I was trying to perform "detectionP " on methyl channels. The error is as follow;
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE
I am sharing the commands and packages
library(limma) library(minfi) library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) library(IlluminaHumanMethylationEPICmanifest) library(missMethyl) library(minfiData) library(RColorBrewer) library(Gviz) library(DMRcate) library(stringr)
Commands are ; Epic850k= getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) head(Epic850k)
targets <- read.metharray.sheet(dataDirectory, pattern="ILMLEPIC-16516_SampleSheet_updated150124.csv") targets
rgSet <-read.metharray.exp(targets=targets) rgSet
pData(rgSet) getManifest(rgSet)
targets$ID <- paste(targets$Sample_Group,targets$Sample_Name,sep=".")
sampleNames(rgSet) <- targets$ID rgSet
calculate the detection P-values
>0.01 p-value indicatepoor samples
detP<- detectionP(rgSet)
After applying the detection command, I got the error that I mentioned above. If anyone knows how to resolve this issue please let me know.