[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?
Hi, recount has built well on the last 2 builds (Aug 14 and 11th) on Linux and I see that now https://bioconductor.org/packages/devel/bioc/html/recount.html is up. My guess is that the directory that Dan removed fixed things in time for the Aug 11th build. Thanks again! Best, Leo On Fri, Aug 12, 2016 at 7:31 PM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:
On 08/12/2016 07:49 PM, Dan Tenenbaum wrote:
----- Original Message -----
From: "Martin Morgan" <martin.morgan at roswellpark.org> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "lcollado" <lcollado at jhu.edu> Cc: "Jeff Leek" <jtleek at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>, "Andrew Jaffe" <andrewejaffe at gmail.com>, "Ben Langmead" <langmea at cs.jhu.edu>, "Abhi Nellore" <anellore at 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.
I'll ask Michael about a Sys.info()[["user"]]-specific cache.
Dan
Martin
Dan ----- Original Message -----
From: "lcollado" <lcollado at jhu.edu> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: "Jeff Leek" <jtleek at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>, "Andrew Jaffe" <andrewejaffe at gmail.com>, "Ben Langmead" <langmea at cs.jhu.edu>, "Abhi Nellore" <anellore at 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 <dtenenba at 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" <dtenenba at fredhutch.org> To: "lcollado" <lcollado at jhu.edu> Cc: "Jeff Leek" <jtleek at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>, "Andrew Jaffe" <andrewejaffe at gmail.com>, "Ben Langmead" <langmea at cs.jhu.edu>, "Abhi Nellore" <anellore at 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" <lcollado at jhu.edu>
To: "bioc-devel" <bioc-devel at r-project.org>
Cc: "Jeff Leek" <jtleek at gmail.com>, "Andrew Jaffe"
<andrewejaffe at gmail.com>,
"Ben Langmead" <langmea at cs.jhu.edu>, "Abhi
Nellore" <anellore at 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')
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 at 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 at 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
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