[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
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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