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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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loading DADA2 #30

Closed spholmes closed 9 years ago

spholmes commented 9 years ago

Error in unloadNamespace(package) : namespace ‘S4Vectors’ is imported by ‘GenomeInfoDb’, ‘Biostrings’, ‘AnnotationDbi’, ‘IRanges’, ‘DESeq2’, ‘XVector’, ‘GenomicRanges’ so cannot be unloaded

benjjneb commented 9 years ago

How did this error come up? Loading dada2?

On Thu, Aug 6, 2015 at 10:43 AM, spholmes notifications@github.com wrote:

Error in unloadNamespace(package) : namespace ‘S4Vectors’ is imported by ‘GenomeInfoDb’, ‘Biostrings’, ‘AnnotationDbi’, ‘IRanges’, ‘DESeq2’, ‘XVector’, ‘GenomicRanges’ so cannot be unloaded

— Reply to this email directly or view it on GitHub https://github.com/benjjneb/dada2/issues/30.

spholmes commented 9 years ago

Sorry, yes, it was at my first load ofthe package.

benjjneb commented 9 years ago

Joey, any wisdom to share on this issue?

On Thu, Aug 6, 2015 at 11:03 AM, spholmes notifications@github.com wrote:

Sorry, yes, it was at my first load ofthe package.

— Reply to this email directly or view it on GitHub https://github.com/benjjneb/dada2/issues/30#issuecomment-128404963.

spholmes commented 9 years ago

Here are a few more details, also require(dada2) loaded the package and load(dada2) doesn't.

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 object is masked from ‘package:stats’:

xtabs

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

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

Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges

Attaching package: ‘IRanges’

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

distance

Loading required package: XVector Loading required package: Rcpp Warning messages: 1: package ‘Biostrings’ was built under R version 3.2.1 2: package ‘S4Vectors’ was built under R version 3.2.1 3: package ‘IRanges’ was built under R version 3.2.1 4: replacing previous import by ‘data.table::tables’ when loading ‘dada2’

benjjneb commented 9 years ago

Load won't work, but library(dada2) and require(dada2) should work.

So it did successfully load after the above output (albeit with the listed complaints?) Or it failed to load?

On Thu, Aug 6, 2015 at 11:27 AM, spholmes notifications@github.com wrote:

Here are a few more details, also require(dada2) loaded the package and load(dada2) doesn't.

  • DONE (dada2) > load(dada2) Error in load(dada2) : object 'dada2' not found > load("dada2") Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'dada2', probable reason 'No such file or directory' > require("dada2") Loading required package: dada2 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 object is masked from ‘package:stats’:

xtabs

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

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

Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges

Attaching package: ‘IRanges’

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

distance

Loading required package: XVector Loading required package: Rcpp Warning messages: 1: package ‘Biostrings’ was built under R version 3.2.1 2: package ‘S4Vectors’ was built under R version 3.2.1 3: package ‘IRanges’ was built under R version 3.2.1 4: replacing previous import by ‘data.table::tables’ when loading ‘dada2’

— Reply to this email directly or view it on GitHub https://github.com/benjjneb/dada2/issues/30#issuecomment-128410481.

spholmes commented 9 years ago

It loaded...

On Thu, Aug 6, 2015 at 11:34 AM, benjjneb notifications@github.com wrote:

Load won't work, but library(dada2) and require(dada2) should work.

So it did successfully load after the above output (albeit with the listed complaints?) Or it failed to load?

On Thu, Aug 6, 2015 at 11:27 AM, spholmes notifications@github.com wrote:

Here are a few more details, also require(dada2) loaded the package and load(dada2) doesn't.

  • DONE (dada2) > load(dada2) Error in load(dada2) : object 'dada2' not found > load("dada2") Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'dada2', probable reason 'No such file or directory' > require("dada2") Loading required package: dada2 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 object is masked from ‘package:stats’:

xtabs

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

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

Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges

Attaching package: ‘IRanges’

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

distance

Loading required package: XVector Loading required package: Rcpp Warning messages: 1: package ‘Biostrings’ was built under R version 3.2.1 2: package ‘S4Vectors’ was built under R version 3.2.1 3: package ‘IRanges’ was built under R version 3.2.1 4: replacing previous import by ‘data.table::tables’ when loading ‘dada2’

— Reply to this email directly or view it on GitHub https://github.com/benjjneb/dada2/issues/30#issuecomment-128410481.

— Reply to this email directly or view it on GitHub https://github.com/benjjneb/dada2/issues/30#issuecomment-128411905.

Susan Holmes Professor, Statistics and BioX John Henry Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

joey711 commented 9 years ago

I will update my version and run a package check. Is it safe to say we're in the "prepare for BioC" mode?