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" <[email protected]> > To: "lcollado" <[email protected]> > Cc: "Jeff Leek" <[email protected]>, "bioc-devel" <[email protected]>, > "Andrew Jaffe" <[email protected]>, > "Ben Langmead" <[email protected]>, "Abhi Nellore" <[email protected]> > 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" <[email protected]> >> To: "bioc-devel" <[email protected]> >> Cc: "Jeff Leek" <[email protected]>, "Andrew Jaffe" <[email protected]>, >> "Ben Langmead" <[email protected]>, "Abhi >> Nellore" <[email protected]> >> 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 >> >> _______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
