[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Aug 9 20:46:32 CEST 2016
1.33.11 is the latest version in svn.
https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html will tell you (with a reasonable degree of accuracy) which version of which package is installed on zin1, it reports that it has version 1.33.11 installed.
The issue with recount looks like it's a (hopefully transient) UCSC connection problem.
Dan
----- Original Message -----
> From: "lcollado" <lcollado at jhu.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Cc: "Jeff Leek" <jtleek at gmail.com>, "Andrew Jaffe" <andrewejaffe at gmail.com>, "Ben Langmead" <langmea at cs.jhu.edu>, "Abhi
> Nellore" <anellore at gmail.com>
> Sent: Tuesday, August 9, 2016 11:33:50 AM
> Subject: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
> 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
>> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
> [1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata"
>> library('recount')
> 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
>>
>> ## Briefly explore the resulting regions
>> regions
> GRanges object with 808 ranges and 6 metadata columns:
> seqnames ranges strand | value area
> <Rle> <IRanges> <Rle> | <numeric> <numeric>
> 1 chrY [2929794, 2929829] * | 14.7265009482702 530.154034137726
> 2 chrY [2956678, 2956701] * | 12.8106340567271 307.45521736145
> 3 chrY [2977203, 2977227] * | 5.34908433914185 133.727108478546
> 4 chrY [2977957, 2977994] * | 6.46976616508082 245.851114273071
> 5 chrY [2978850, 2978871] * | 5.7976552139629 127.548414707184
> ... ... ... ... . ... ...
> 804 chrY [26614511, 26614546] * | 7.28189378314548 262.148176193237
> 805 chrY [26614548, 26614553] * | 5.48768202463786 32.9260921478271
> 806 chrY [26614779, 26614808] * | 6.64339276949565 199.301783084869
> 807 chrY [26626808, 26626848] * | 12.6038152648181 516.756425857544
> 808 chrY [26626971, 26627028] * | 14.1673366941255 821.705528259277
> indexStart indexEnd cluster clusterL
> <integer> <integer> <Rle> <Rle>
> 1 2929794 2929829 1 36
> 2 2956678 2956701 2 24
> 3 2977203 2977227 3 2750
> 4 2977957 2977994 3 2750
> 5 2978850 2978871 3 2750
> ... ... ... ... ...
> 804 26614511 26614546 224 298
> 805 26614548 26614553 224 298
> 806 26614779 26614808 224 298
> 807 26626808 26626848 225 221
> 808 26626971 26627028 225 221
> -------
> seqinfo: 1 sequence from an unspecified genome
>>
>> options(width = 120)
>> devtools::session_info()
> Session info
> -----------------------------------------------------------------------------------------------------------
> setting value
> version R version 3.3.1 Patched (2016-07-11 r70891)
> system x86_64, linux-gnu
> ui X11
> language (EN)
> collate en_US.UTF-8
> tz <NA>
> date 2016-08-09
>
> Packages
> ---------------------------------------------------------------------------------------------------------------
> package * version date source
> acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0)
> AnnotationDbi 1.35.4 2016-07-22 Bioconductor
> Biobase * 2.33.0 2016-05-08 Bioconductor
> BiocGenerics * 0.19.2 2016-07-22 Bioconductor
> BiocParallel 1.7.6 2016-08-09 cran (@1.7.6)
> biomaRt 2.29.2 2016-06-07 Bioconductor
> Biostrings 2.41.4 2016-07-22 Bioconductor
> bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
> BSgenome 1.41.2 2016-07-22 Bioconductor
> bumphunter 1.13.1 2016-07-22 Bioconductor
> chron 2.3-47 2015-06-24 CRAN (R 3.3.0)
> cluster 2.0.4 2016-04-18 CRAN (R 3.3.1)
> codetools 0.2-14 2015-07-15 CRAN (R 3.3.1)
> colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0)
> data.table 1.9.6 2015-09-19 CRAN (R 3.3.1)
> DBI 0.4-1 2016-05-08 CRAN (R 3.3.0)
> derfinder 1.7.9 2016-07-22 Bioconductor
> derfinderHelper 1.7.3 2016-07-22 Bioconductor
> devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
> digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
> doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
> downloader 0.4 2015-07-09 cran (@0.4)
> foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
> foreign 0.8-66 2015-08-19 CRAN (R 3.3.1)
> Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
> GenomeInfoDb * 1.9.4 2016-07-22 Bioconductor
> GenomicAlignments 1.9.6 2016-07-22 Bioconductor
> GenomicFeatures 1.25.15 2016-07-22 Bioconductor
> GenomicFiles 1.9.11 2016-07-22 Bioconductor
> GenomicRanges * 1.25.93 2016-08-09 cran (@1.25.93)
> GEOquery 2.39.3 2016-06-15 Bioconductor
> ggplot2 2.1.0 2016-03-01 CRAN (R 3.3.1)
> gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
> gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
> Hmisc 3.17-4 2016-05-02 CRAN (R 3.3.1)
> httr 1.2.1 2016-07-03 cran (@1.2.1)
> IRanges * 2.7.12 2016-08-09 cran (@2.7.12)
> iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
> jsonlite 1.0 2016-07-01 CRAN (R 3.3.1)
> lattice 0.20-33 2015-07-14 CRAN (R 3.3.1)
> latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
> locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
> magrittr 1.5 2014-11-22 CRAN (R 3.3.1)
> Matrix 1.2-6 2016-05-02 CRAN (R 3.3.1)
> matrixStats 0.50.2 2016-04-24 CRAN (R 3.3.1)
> memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
> munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
> nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
> pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
> plyr 1.8.4 2016-06-08 CRAN (R 3.3.1)
> qvalue 2.5.2 2016-07-22 Bioconductor
> R6 2.1.2 2016-01-26 CRAN (R 3.3.0)
> RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
> Rcpp 0.12.6 2016-07-19 CRAN (R 3.3.1)
> RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
> recount * 0.99.27 2016-08-09 Github (leekgroup/recount at 922e7a6)
> registry 0.3 2015-07-08 CRAN (R 3.3.0)
> rentrez 1.0.2 2016-04-21 cran (@1.0.2)
> reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0)
> rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
> rpart 4.1-10 2015-06-29 CRAN (R 3.3.1)
> Rsamtools 1.25.0 2016-07-22 Bioconductor
> RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0)
> rtracklayer 1.33.11 2016-07-22 Github
> (Bioconductor-mirror/rtracklayer at c12bd86)
> S4Vectors * 0.11.10 2016-07-22 Bioconductor
> scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
> stringi 1.1.1 2016-05-27 CRAN (R 3.3.0)
> stringr 1.0.0 2015-04-30 CRAN (R 3.3.1)
> SummarizedExperiment * 1.3.81 2016-08-09 cran (@1.3.81)
> survival 2.39-5 2016-06-26 CRAN (R 3.3.1)
> VariantAnnotation 1.19.8 2016-07-22 Bioconductor
> withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
> XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
> xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
> XVector 0.13.7 2016-08-09 cran (@0.13.7)
> zlibbioc 1.19.0 2016-05-08 Bioconductor
>>
>
> 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
>
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