Taylor gex data about curatedpcadata HOT 2 CLOSED

> CELs <- oligo::read.celfiles(affy::list.celfiles())
Loading required package: pd.huex.1.0.st.v2
Attempting to obtain 'pd.huex.1.0.st.v2' from BioConductor website.
Checking to see if your internet connection works...
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/src/contrib:
  cannot open destfile 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e\file396c362b6579', reason 'No such file or directory'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
  cannot open destfile 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e\file396c10c97694', reason 'No such file or directory'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/src/contrib:
  cannot open destfile 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e\file396c1015170b', reason 'No such file or directory'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/workflows/src/contrib:
  cannot open destfile 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e\file396c520a2235', reason 'No such file or directory'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open destfile 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e\file396c7c93361f', reason 'No such file or directory'
Package 'pd.huex.1.0.st.v2' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in oligo::read.celfiles(affy::list.celfiles()) : 
  The annotation package, pd.huex.1.0.st.v2, could not be loaded.
> library(pd.huex.1.0.st.v2)
Error in library(pd.huex.1.0.st.v2) : 
  there is no package called ‘pd.huex.1.0.st.v2’
> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("pd.huex.1.0.st.v2")
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file 'C:\Users\teemu\AppData\Local\Temp\RtmpYjdG8e/libloc_193_c5921c9.rds', probable reason 'No such file or directory'
# At this point I started a new R session and installed "pd.huex.1.0.st.v2" separate with BiocManager
> library("pd.huex.1.0.st.v2")
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.48.0
Loading required package: oligo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

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Welcome to oligo version 1.50.0
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Loading required package: DBI
Warning messages:
1: package ‘S4Vectors’ was built under R version 3.6.2 
2: package ‘IRanges’ was built under R version 3.6.2 
3: package ‘RSQLite’ was built under R version 3.6.3 
4: package ‘DBI’ was built under R version 3.6.3