Hi,
Currently the build for `recount` is failing in the Linux build
machine http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
It's been failing with the same error message for a while. The build
message ends with:
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
Quitting from lines 400-406 (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
UCSC library operation failed
Execution halted
The lines of code from the recount vignette this refers to are:
## Define expressed regions for study SRP009615, only for chromosome Y
regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
maxClusterGap = 3000L)
## Briefly explore the resulting regions
regions
The UCSC error is something I've seen in previous versions of
rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
version 0.99.25 (which is the one from the build report) had under
suggests rtracklayer (>= 1.33.11). I thought that this would mean that
the build would fail if rtracklayer below version 1.33.11 was being
used. I'm no longer sure, which is why in recount version 0.99.27 I
moved rtracklayer to imports to test this. The latest build report
shows that rtracklayer 1.33.11 did build correctly in the Linux
machine.
Everything seems to be working fine in my local tests and in R Travis
https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
some code showing that everything is working as expected in my local
Linux test. So I'm a tad confused and can't reproduce this issue when
using rtracklayer version 1.33.11. Which is why I'm guessing that
somehow the Linux build machine is not using rtracklayer >= 1.33.11.
## The url redirects as expected to the correct url
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, xtabs
The following objects are masked from ?package:base?:
anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: ?S4Vectors?
The following objects are masked from ?package:base?:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
## Define expressed regions for study SRP009615, only for chromosome Y
regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
+ maxClusterGap = 3000L)
2016-08-09 14:16:59 loadCoverage: loading BigWig file
http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
2016-08-09 14:17:01 loadCoverage: applying the cutoff to the merged data
2016-08-09 14:17:02 filterData: originally there were 57227415 rows,
now there are 57227415 rows. Meaning that 0 percent was filtered.
2016-08-09 14:17:02 findRegions: identifying potential segments
2016-08-09 14:17:02 findRegions: segmenting information
2016-08-09 14:17:02 .getSegmentsRle: segmenting with cutoff(s) 5
2016-08-09 14:17:02 findRegions: identifying candidate regions
2016-08-09 14:17:03 findRegions: identifying region clusters
Note that in my local test, I installed rtracklayer from the
Bioconductor-mirror. In my Travis test, rtracklayer gets installed
using biocLite().
I know that the latest Windows build failed, but that's because of the
recurrent zlibbioc issue. I've seen it build and pass R CMD check
before in moscato1.
I let this issue linger because we wanted to post our pre-print to
bioRxiv before @bioconductor automatically tweeted about the recount
package. However, now that the pre-print is up, we'd like to have the
recount page http://bioconductor.org/packages/recount/ built (which I
know depends on the Linux build working).
Best,
Leo