[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

Leonardo Collado Torres lcollado at jhu.edu
Tue Aug 9 20:33:50 CEST 2016


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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