alexvnesta
commented
6 years ago My apologies, It looks like the latest version 1.25.1 fixes this. I didn't realize I had to update bioconductor to get it.
Closed alexvnesta closed 6 years ago
alexvnesta
commented
6 years ago My apologies, It looks like the latest version 1.25.1 fixes this. I didn't realize I had to update bioconductor to get it.
kasperdanielhansen
commented
6 years ago NP. Did you confirm it is fixed, or do you just think it might be fixed?
On Fri, Jan 26, 2018 at 9:57 PM, alexvnesta notifications@github.com wrote:
My apologies, It looks like the latest version 1.25.1 fixes this. I didn't realize I had to update bioconductor to get it.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/minfi/issues/127#issuecomment-360954687, or mute the thread https://github.com/notifications/unsubscribe-auth/AEuhn3WEO_kKAFCjljdy--xg4n9wSQFBks5tOpCUgaJpZM4RvHZj .
alexvnesta
commented
6 years ago looking into it now. Will update once verified.
alexvnesta
commented
6 years ago Updated to 1.25.1 All Fixed and verified with a quick data plot! Thank you for this package, and your prompt support!
Note: Latest release version is 1.24.0 which still has this issue. Had to install 1.25.1 from source via R CMD INSTALL. Also had to reinstall readr and tinyverse because of a weird install corruption issue.
R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
library("minfi", lib.loc="~/Library/R/3.4/library") 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, parSapplyLBThe following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabsThe following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.minLoading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.gridLoading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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")'.Loading required package: DelayedArray Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMediansAttaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRangesThe following object is masked from ‘package:base’:
applyLoading required package: Biostrings Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
typeThe following object is masked from ‘package:base’:
strsplitLoading required package: bumphunter Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE)
mSetSq <- getGenomicRatioSetFromGEO(GSE = "GSE30654") Found 3 file(s) GSE30654-GPL13534_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/GSE30654-GPL13534_series_matrix.txt.gz' Content type 'application/x-gzip' length 309790493 bytes (295.4 MB)
downloaded 295.4 MB
Error in date_names_lang(date_names) : cannot open file '~/Library/R/3.4/library/readr/R/sysdata.rdb': No such file or directory
library(readr) library(minfi) install.packages("tidyverse") Installing package into ‘/Users/Alex/Library/R/3.4/library’ (as ‘lib’ is unspecified) also installing the dependencies ‘rematch’, ‘cellranger’, ‘callr’, ‘rmarkdown’, ‘selectr’, ‘dbplyr’, ‘forcats’, ‘haven’, ‘modelr’, ‘readxl’, ‘reprex’, ‘rvest’
There is a binary version available but the source version is later: binary source needs_compilation reprex 0.1.1 0.1.2 FALSE
downloaded 10 KB
downloaded 71 KB
downloaded 33 KB
downloaded 2.1 MB
downloaded 171 KB
downloaded 309 KB
downloaded 159 KB
downloaded 819 KB
downloaded 130 KB
downloaded 1.3 MB
downloaded 832 KB
downloaded 75 KB
The downloaded binary packages are in /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpU16695/downloaded_packages installing the source package ‘reprex’
downloaded 22 KB
The downloaded source packages are in ‘/private/var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T/RtmpU16695/downloaded_packages’
install.packages("readr") Error in install.packages : Updating loaded packages
Restarting R session...
install.packages("readr") Installing package into ‘/Users/Alex/Library/R/3.4/library’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/readr_1.1.1.tgz' Content type 'application/x-gzip' length 1967561 bytes (1.9 MB)
downloaded 1.9 MB
The downloaded binary packages are in /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpXDUcEv/downloaded_packages
library(minfi) 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, parSapplyLBThe following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabsThe following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.minLoading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.gridLoading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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")'.Loading required package: DelayedArray Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMediansAttaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRangesThe following object is masked from ‘package:base’:
applyLoading required package: Biostrings Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
typeThe following object is masked from ‘package:base’:
strsplitLoading required package: bumphunter Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE)
mSetSq <- getGenomicRatioSetFromGEO(GSE = "GSE30654") Found 3 file(s) GSE30654-GPL13534_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/GSE30654-GPL13534_series_matrix.txt.gz' Content type 'application/x-gzip' length 309790493 bytes (295.4 MB)
downloaded 295.4 MB
downloaded 36.5 MB
downloaded 31.5 MB
Parsed with column specification: cols( .default = col_double(), ID_REF = col_character() ) See spec(...) for full column specifications. |=================================================================| 100% 77 MB File stored at: /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpXDUcEv/GPL8490.soft Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 Warning message: In getGenomicRatioSetFromGEO(GSE = "GSE30654") : More than one ExpressionSet found: GSE30654-GPL13534_series_matrix.txt.gzGSE30654-GPL6947_series_matrix.txt.gzGSE30654-GPL8490_series_matrix.txt.gz Using entry 1
densityPlot(getBeta(mSetSq),
- main="Normalized", legend=FALSE)
kasperdanielhansen
commented
6 years ago Thanks. I was planning on backporting the fix to the stable branch, but I had forgotten about it. Thanks for closing the issue.
On Fri, Jan 26, 2018 at 10:32 PM, alexvnesta notifications@github.com wrote:
Closed #127 https://github.com/kasperdanielhansen/minfi/issues/127.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/minfi/issues/127#event-1444681128, or mute the thread https://github.com/notifications/unsubscribe-auth/AEuhn3qE3Ud2qzz7ygXx0udwvhEu3yBrks5tOpiwgaJpZM4RvHZj .
mSetSq <- getGenomicRatioSetFromGEO(GSE = "GSE30654") https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/ OK Found 3 file(s) GSE30654-GPL13534_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/GSE30654-GPL13534_series_matrix.txt.gz' Content type 'application/x-gzip' length 309790493 bytes (295.4 MB)
downloaded 295.4 MB
File stored at: /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpQ6jdxd/GPL13534.soft GSE30654-GPL6947_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/GSE30654-GPL6947_series_matrix.txt.gz' Content type 'application/x-gzip' length 38255623 bytes (36.5 MB)
downloaded 36.5 MB
File stored at: /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpQ6jdxd/GPL6947.soft GSE30654-GPL8490_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30654/matrix/GSE30654-GPL8490_series_matrix.txt.gz' Content type 'application/x-gzip' length 33013631 bytes (31.5 MB)
downloaded 31.5 MB
File stored at: /var/folders/14/zdpg3tzd1kq5_w7qybng_49r0000gn/T//RtmpQ6jdxd/GPL8490.soft Error in .local(assays, ...) : unused argument (pData = list(title = c(16, 17, 7, 2, 3, 1, 13, 11, 12, 9, 10, 4, 5, 6, 8, 15, 14, 18, 19, 23, 25, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 37, 36, 49, 48, 51, 50, 53, 52, 55, 54, 56, 58, 57, 39, 38, 40, 41, 43, 42, 45, 44, 47, 46, 60, 59, 33, 34, 32, 35, 63, 64, 66, 61, 62, 65, 67, 68, 69, 70, 71, 72, 90, 92, 80, 81, 75, 78, 79, 85, 82, 89, 88, 86, 87, 74, 83, 76, 77, 84, 91, 93, 73, 101, 132, 131, 147, 144, 145, 142, 146, 143, 103, 104, 114, 111, 112, 113, 110, 151, 150, 119, 116, 117, 118, 115, 123, 121, 122, 120, 109, 106, 107, 108, 105, 134, 133, 149, 148, 141, 139, 140, 137, 138, 153, 152, 130, 126, 127, 128, 124, 129, 125, 100, 98, 96, 99, 97, 136, 135, 95, 94, 102), geo_accession = 1:153, status = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, In addition: Warning messages: 1: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist 2: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist 3: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist 4: In getGenomicRatioSetFromGEO(GSE = "GSE30654") : More than one ExpressionSet found: GSE30654-GPL13534_series_matrix.txt.gzGSE30654-GPL6947_series_matrix.txt.gzGSE30654-GPL8490_series_matrix.txt.gz Using entry 1