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
