[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

----- 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.

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')
[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 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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[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

Thread (7 messages)