[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Aug 12 21:27:02 CEST 2016
Well, I wrote my email to you on August 9th and the latest build report is from Aug 10 and we see the same error as before.
I just manually went to zin1 and was able to remove /tmp/udcCache without having to be a superuser, I could do it as the user that the build system runs as (biocbuild).
I then rebuilt the recount package (successfully, btw) and it created the /tmp/udcCache directory again (but again it was removable without superuser powers).
So I am not sure what is going on. Hopefully the next build will not have this error. Maybe when I touched it last time the build was already in progress and what I did came too late to affect the build.
Anyway it would be good to know which package is creating that /tmp/udcCache directory. Ideally that package would instead use tmpdir() and then the directory would be removed when recount is done building, and this issue would never come up again.
Dan
----- Original Message -----
> From: "lcollado" <lcollado at jhu.edu>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> 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: Friday, August 12, 2016 10:44:20 AM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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