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
