----- Original Message ----- > From: "Martin Morgan" <martin.mor...@roswellpark.org> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "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: 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" <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 >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received > this message in error, please notify the sender immediately by e-mail and > delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
