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
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