[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Dan Tenenbaum
dtenenba at fredhutch.org
Sat Aug 13 01:49:52 CEST 2016
----- Original Message -----
> From: "Martin Morgan" <martin.morgan at roswellpark.org>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "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: Friday, August 12, 2016 4:43:59 PM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
> 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?
>
When I initially went onto zin1 and installed and then stangled and sourced the vignette I saw some sort of permissions error with this directory. Unfortunately I did not save the exact error message.
When I initially tried
rm -rf /tmp/udcCache
...as the biocbuild user I got a permission denied error.
I should have investigated further to see which file(s) could not be deleted by biocbuild and what their permissions/ownership were but instead I just removed the entire directory as superuser.
So there was a permissions issue which caused the problem Leonardo reported.
Dan
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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