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

Leonardo Collado Torres lcollado at jhu.edu
Tue Aug 16 08:25:50 CEST 2016


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')
>>>>>>>>
>>>>>>>> [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
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
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