No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Entering edit mode
Rohmatul • 0
Last seen 3.1 years ago

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

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

[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

RSQLite lumi • 2.2k views
Entering edit mode

This appears to be an issue with the lumi package NAMESPACE. I have reached out to the maintainers to fix the issue.

Entering edit mode

Thank you!


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