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" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, > "Andrew Jaffe" <andreweja...@gmail.com>, > "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@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 <dtene...@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" <dtene...@fredhutch.org> >>> To: "lcollado" <lcoll...@jhu.edu> >>> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, >>> "Andrew Jaffe" <andreweja...@gmail.com>, >>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@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" <lcoll...@jhu.edu> >>>> To: "bioc-devel" <bioc-devel@r-project.org> >>>> Cc: "Jeff Leek" <jtl...@gmail.com>, "Andrew Jaffe" >>>> <andreweja...@gmail.com>, >>>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi >>>> Nellore" <anell...@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@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@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@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
