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tanya
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@tanya-24893
Last seen 3.7 years ago
Hi, Can you please help me with using Oligo package. I am using Oligo Package to read celfiles. I donwloaded the data from GEOquery and now want to read the celfiles. But reading celfiles using read.celfiles gives an error. So I thought maybe its linked with the error that comes with loading the oligo library. I have included the code and the following errors. Code should be placed in three backticks as shown below
library(oligo)
Loading required package: oligoClasses
Error: package or namespace load failed for ‘oligoClasses’:
object 'maxindex' not found whilst loading namespace 'ff'
Error: package ‘oligoClasses’ could not be loaded
rawData<- read.celfiles(celfiles)
Error in read.celfiles(celfiles) : could not find function "read.celfiles"
sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 lattice_0.20-41 prettyunits_1.1.1 Rsamtools_2.4.0 Biostrings_2.56.0
[6] assertthat_0.2.1 digest_0.6.25 BiocFileCache_1.12.0 R6_2.4.1 GenomeInfoDb_1.24.2
[11] stats4_4.0.2 RSQLite_2.2.0 httr_1.4.2 pillar_1.4.4 zlibbioc_1.34.0
[16] rlang_0.4.9 GenomicFeatures_1.40.1 progress_1.2.2 curl_4.3 rstudioapi_0.13
[21] blob_1.2.1 S4Vectors_0.26.1 Matrix_1.2-18 BiocParallel_1.22.0 stringr_1.4.0
[26] RCurl_1.98-1.2 bit_1.1-15.2 biomaRt_2.44.4 DelayedArray_0.14.0 compiler_4.0.2
[31] rtracklayer_1.48.0 pkgconfig_2.0.3 askpass_1.1 openssl_1.4.1 tidyselect_1.1.0
[36] SummarizedExperiment_1.18.1 tibble_3.0.1 GenomeInfoDbData_1.2.3 IRanges_2.22.2 matrixStats_0.56.0
[41] XML_3.99-0.3 crayon_1.3.4 dplyr_1.0.0 dbplyr_1.4.4 GenomicAlignments_1.24.0
[46] bitops_1.0-6 rappdirs_0.3.1 grid_4.0.2 lifecycle_0.2.0 DBI_1.1.0
[51] magrittr_1.5 stringi_1.4.6 XVector_0.28.0 affyio_1.58.0 xml2_1.3.2
[56] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.1 tools_4.0.2 bit64_0.9-7
[61] Biobase_2.48.0 glue_1.4.1 purrr_0.3.4 hms_0.5.3 AnnotationDbi_1.50.3
[66] GenomicRanges_1.40.0 memoise_1.1.0
I have installed oligoClasses but to no avail, It is still showing the same error above. I tried installing ff from CRAN but its not available for the R version I am using.
This type of error usually means that you are mixing Bioconductor packages from different releases. Try
ff
is available under 'Windows binaries' at https://cran.r-project.org/package=ff, so probably R is trying to tell you something else; posting the full installation attempt and message would help.