[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Leonardo Collado Torres
lcollado at jhu.edu
Fri Aug 12 19:44:20 CEST 2016
Thanks Dan for finding the /tmp/udcCache error and fixing it! I assume
that recount will build properly next time.
The error related to SRP009615-results.Rmd is likely related to
https://github.com/leekgroup/recount/blob/master/vignettes/Makefile.
I'm using that Makefile trick to include the HTML output of a
regionReport::DESeq2Report() created via
https://github.com/leekgroup/recount/blame/master/vignettes/recount-quickstart.Rmd#L343-L359
which re-writes SRP009615-results.Rmd. regionReport::DESeq2Report()
specifies the `software` variable which is then used when rendering
the Rmd file. Given that it works well on the OS build machine, I
suspect it'll work well now with Linux thanks to the /tmp/udcCache
issue you resolved. If you use R CMD build from a clean `recount` dir,
it should all work.
Best,
Leo
On Tue, Aug 9, 2016 at 2:30 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> Actually it looks like it was a permissions issue with the directory /tmp/udcCache. I removed this directory (as superuser) and that error no longer happens.
>
> Now I get a different error which seems unrelated:
>
> ...
> * creating vignettes ... ERROR
> Quitting from lines 2-32 (SRP009615-results.Rmd)
> Error: processing vignette 'SRP009615-results.Rmd' failed with diagnostics:
> object 'software' not found
> Execution halted
>
>
> Probably because of line 20:
>
> Basic `r software` results exploration
>
> `r software` is interpreted as a chunk of code to be executed by R.
>
>
> Dan
>
>
> ----- Original Message -----
>> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> To: "lcollado" <lcollado at jhu.edu>
>> Cc: "Jeff Leek" <jtleek at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>, "Andrew Jaffe" <andrewejaffe at gmail.com>,
>> "Ben Langmead" <langmea at cs.jhu.edu>, "Abhi Nellore" <anellore at gmail.com>
>> Sent: Tuesday, August 9, 2016 11:46:32 AM
>> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
>
>> 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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