[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Aug 9 21:30:26 CEST 2016
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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