[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Martin Morgan
martin.morgan at roswellpark.org
Sat Aug 13 01:43:59 CEST 2016
On 08/12/2016 03:27 PM, Dan Tenenbaum wrote:
> 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.
>
Only rtracklayer references this. it might not be such a good idea to
use tempdir(), because then the cache wouldn't be available for use
during the builds... in what sense was it a permissions issue?
Martin
> 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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