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Dear All,
I am installing my package (abciba4) in R and during the installation I got this message
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
But the installation was successful.
When I call the library
library(abciba4)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
The sessionInfo() is
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] abciba4_1.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ellipsis_0.3.1 siggenes_1.64.0 mclust_5.4.6 XVector_0.30.0 GenomicRanges_1.42.0 base64_2.0 ffpe_1.34.0 affyio_1.60.0
[10] bit64_4.0.5 AnnotationDbi_1.52.0 xml2_1.3.2 codetools_0.2-18 splines_4.0.3 sparseMatrixStats_1.2.0 scrime_1.3.5 methylumi_2.36.0 Rsamtools_2.6.0
[19] annotate_1.68.0 dbplyr_2.0.0 sfsmisc_1.1-7 NormalGamma_1.1 HDF5Array_1.18.0 readr_1.4.0 BiocManager_1.30.10 compiler_4.0.3 httr_1.4.2
[28] assertthat_0.2.1 Matrix_1.2-18 limma_3.46.0 prettyunits_1.1.1 tools_4.0.3 glue_1.4.2 GenomeInfoDbData_1.2.4 affy_1.68.0 dplyr_1.0.2
[37] rappdirs_0.3.1 doRNG_1.8.2 Rcpp_1.0.5 Biobase_2.50.0 bumphunter_1.32.0 MBCB_1.44.0 vctrs_0.3.4 Biostrings_2.58.0 rhdf5filters_1.2.0
[46] multtest_2.46.0 nlme_3.1-150 preprocessCore_1.52.0 rtracklayer_1.50.0 iterators_1.0.13 DelayedMatrixStats_1.12.0 stringr_1.4.0 lifecycle_0.2.0 rngtools_1.5
[55] XML_3.99-0.5 beanplot_1.2 nleqslv_3.3.2 zlibbioc_1.36.0 MASS_7.3-53 zoo_1.8-8 hms_0.5.3 MatrixGenerics_1.2.0 parallel_4.0.3
[64] SummarizedExperiment_1.20.0 GEOquery_2.58.0 minfi_1.36.0 rhdf5_2.34.0 RColorBrewer_1.1-2 curl_4.3 memoise_1.1.0 biomaRt_2.46.0 reshape_0.8.8
[73] stringi_1.5.3 RSQLite_2.2.1 genefilter_1.72.0 S4Vectors_0.28.0 foreach_1.5.1 lumi_2.42.0 TTR_0.24.2 GenomicFeatures_1.42.0 BiocGenerics_0.36.0
[82] BiocParallel_1.24.1 GenomeInfoDb_1.26.0 rlang_0.4.8 pkgconfig_2.0.3 matrixStats_0.57.0 bitops_1.0-6 nor1mix_1.3-0 lattice_0.20-41 purrr_0.3.4
[91] Rhdf5lib_1.12.0 GenomicAlignments_1.26.0 bit_4.0.4 tidyselect_1.1.0 plyr_1.8.6 magrittr_1.5 R6_2.5.0 IRanges_2.24.0 generics_0.1.0
[100] DelayedArray_0.16.0 DBI_1.1.0 mgcv_1.8-33 pillar_1.4.6 xts_0.12.1 survival_3.2-7 RCurl_1.98-1.2 tibble_3.0.4 crayon_1.3.4
[109] KernSmooth_2.23-18 BiocFileCache_1.14.0 progress_1.2.2 locfit_1.5-9.4 grid_4.0.3 data.table_1.13.2 blob_1.2.1 digest_0.6.27 xtable_1.8-4
[118] tidyr_1.1.2 illuminaio_0.32.0 openssl_1.4.3 stats4_4.0.3 quadprog_1.5-8 askpass_1.1
>
I have read some discussions here, but I could not find the right clue. Please, anyone help me.
Thank you very much in advance
With kind regards, Ema
This appears to be an issue with the lumi package NAMESPACE. I have reached out to the maintainers to fix the issue.
Thank you!