Question: Can't access devel version of ExperimentHub in Travis CI
0
gravatar for Kyle Johnsen
6 months ago by
Kyle Johnsen20
United States/Brigham Young University
Kyle Johnsen20 wrote:

I use Travis CI for developing my Bioconductor package, and it's been working well so far. But now that I rely on ExperimentHub (and new data in ExperimentHub at that), I'm running into problems getting the most recent snapshots. I'm using the bioc-devel option in the .travis.yml file, and in the log I can see that Bioconductor version 3.8 is installed, as well as the devel version of ExperimentHub (1.7.6). Yet I seem to only be getting snapshots from the release version of Bioconductor, back in April.

Does anyone know why this is and how I can access devel snapshots of ExperimentHub? I've attached relevant parts of my Travis CI log.

 

* installing *source* package 鈥楤iocInstaller鈥� ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
    鈥�/tmp/Rtmp4kTGXF/downloaded_packages鈥�
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/BiocInstaller_1.31.3.tar.gz'
Content type 'application/x-gzip' length 19476 bytes (19 KB)
==================================================
downloaded 19 KB

* installing *source* package 鈥楤iocInstaller鈥� ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.
Bioconductor version 3.8 (BiocInstaller 1.31.3), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
    鈥�/tmp/Rtmp4kTGXF/downloaded_packages鈥�
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Bioconductor version 3.8 (BiocInstaller 1.31.3), ?biocLite for help
'BiocInstaller' changed to version 1.31.3
Warning message:
'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.

 

...

 

Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2017-01-27)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       UTC                         
 date     2018-10-01                  

Packages ----------------------------------------------------------------------
 package                * version   date      
 AnnotationDbi            1.43.1    2018-06-13
 AnnotationForge          1.23.3    2018-08-03
 AnnotationHub            2.13.7    2018-09-26
 AnnotationHubData        1.11.3    2018-08-09
 assertthat               0.2.0     2017-04-11
 backports                1.1.2     2017-12-13
 base                   * 3.5.1     2018-07-26
 base64enc                0.1-3     2015-07-28
 BH                       1.66.0-1  2018-02-13
 bindr                    0.1.1     2018-03-13
 bindrcpp                 0.2.2     2018-03-29
 Biobase                  2.41.2    2018-07-18
 BiocCheck                1.17.23   2018-08-13
 BiocGenerics             0.27.1    2018-06-17
 BiocInstaller            1.31.3    2018-08-08
 BiocManager              1.30.2    2018-08-24
 BiocParallel             1.15.12   2018-09-13
 biocViews                1.49.8    2018-09-07
 biomaRt                  2.37.6    2018-09-06
 Biostrings               2.49.1    2018-08-04
 bit                      1.1-14    2018-05-29
 bit64                    0.9-7     2017-05-08
 bitops                   1.0-6     2013-08-17
 blob                     1.1.1     2018-03-25
 boot                     1.3-20    2017-08-06
 brew                     1.0-6     2011-04-13
 BSgenome                 1.49.3    2018-07-27
 callr                    3.0.0     2018-08-24
 class                    7.3-14    2015-08-30
 cli                      1.0.1     2018-09-25
 cluster                  2.0.7-1   2018-04-13
 codetools                0.2-15    2016-10-05
 commonmark               1.5       2018-04-28
 compiler                 3.5.1     2018-07-26
 crayon                   1.3.4     2017-09-16
 curl                     3.2       2018-03-28
 data.table               1.11.8    2018-09-30
 datasets               * 3.5.1     2018-07-26
 DBI                      1.0.0     2018-05-02
 DelayedArray             0.7.42    2018-09-22
 desc                     1.2.0     2018-05-01
 devtools                 1.13.6    2018-06-27
 digest                   0.6.17    2018-09-12
 dplyr                    0.7.6     2018-06-29
 ensemblVEP               1.23.0    2018-06-13
 evaluate                 0.11      2018-07-17
 ExperimentHub            1.7.6     2018-10-01
 ExperimentHubData        1.7.2     2018-08-29
 fansi                    0.3.0     2018-08-13
 foreign                  0.8-70    2017-11-28
 formatR                  1.5       2017-04-25
 futile.logger            1.4.3     2016-07-10
 futile.options           1.0.1     2018-04-20
 GenomeInfoDb             1.17.2    2018-09-26
 GenomeInfoDbData         1.1.0     2018-09-27
 GenomicAlignments        1.17.3    2018-07-18
 GenomicFeatures          1.33.2    2018-08-13
 GenomicRanges            1.33.14   2018-09-20
 getopt                   1.20.2    2018-02-16
 git2r                    0.23.0    2018-07-17
 glue                     1.3.0     2018-07-17
 gmapR                    1.23.1    2018-08-30
 graph                    1.59.0    2018-06-13
 graphics               * 3.5.1     2018-07-26
 grDevices              * 3.5.1     2018-07-26
 grid                     3.5.1     2018-07-26
 highr                    0.7       2018-06-09
 hms                      0.4.2     2018-03-10
 htmltools                0.3.6     2017-04-28
 httpuv                   1.4.5     2018-07-19
 httr                     1.3.1     2017-08-20
 interactiveDisplayBase   1.19.2    2018-09-06
 IRanges                  2.15.18   2018-09-20
 jsonlite                 1.5       2017-06-01
 KernSmooth               2.23-15   2015-06-29
 knitr                    1.20      2018-02-20
 lambda.r                 1.2.3     2018-05-17
 later                    0.7.5     2018-09-18
 lattice                  0.20-35   2017-03-25
 magrittr                 1.5       2014-11-22
 markdown                 0.8       2017-04-20
 MASS                     7.3-50    2018-04-30
 Matrix                   1.2-14    2018-04-13
 matrixStats              0.54.0    2018-07-23
 memoise                  1.1.0     2017-04-21
 methods                * 3.5.1     2018-07-26
 mgcv                     1.8-24    2018-06-23
 mime                     0.5       2016-07-07
 MMAPPR2data              0.99.0    2018-10-01
 mockery                  0.4.1.1   2018-08-19
 nlme                     3.1-137   2018-04-07
 nnet                     7.3-12    2016-02-02
 openssl                  1.0.2     2018-07-30
 optparse                 1.6.0     2018-06-17
 OrganismDbi              1.23.2    2018-07-16
 parallel                 3.5.1     2018-07-26
 pillar                   1.3.0     2018-07-14
 pkgbuild                 1.0.1     2018-09-18
 pkgconfig                2.0.2     2018-08-16
 pkgload                  1.0.0     2018-07-07
 plogr                    0.2.0     2018-03-25
 praise                   1.0.0     2015-08-11
 prettyunits              1.0.2     2015-07-13
 processx                 3.2.0     2018-08-16
 progress                 1.2.0     2018-06-14
 promises                 1.0.1     2018-04-13
 ps                       1.1.0     2018-08-10
 purrr                    0.2.5     2018-05-29
 R6                       2.2.2     2017-06-17
 RBGL                     1.57.0    2018-06-13
 rBiopaxParser            2.21.1    2018-08-30
 Rcpp                     0.12.19   2018-10-01
 RCurl                    1.95-4.11 2018-07-15
 rlang                    0.2.2     2018-08-16
 roxygen2                 6.1.0     2018-07-27
 rpart                    4.1-13    2018-02-23
 rprojroot                1.3-2     2018-01-03
 Rsamtools                1.33.5    2018-09-04
 RSQLite                  2.1.1     2018-05-06
 rstudioapi               0.7       2017-09-07
 rtracklayer              1.41.5    2018-08-31
 RUnit                    0.4.32    2018-05-18
 S4Vectors                0.19.20   2018-09-29
 shiny                    1.1.0     2018-05-17
 snow                     0.4-3     2018-09-14
 sourcetools              0.1.7     2018-04-25
 spatial                  7.3-11    2015-08-30
 splines                  3.5.1     2018-07-26
 stats                  * 3.5.1     2018-07-26
 stats4                   3.5.1     2018-07-26
 stringdist               0.9.5.1   2018-06-08
 stringi                  1.2.4     2018-07-20
 stringr                  1.3.1     2018-05-10
 SummarizedExperiment     1.11.6    2018-07-17
 survival                 2.42-3    2018-04-16
 tcltk                    3.5.1     2018-07-26
 testthat                 2.0.0     2017-12-13
 tibble                   1.4.2     2018-01-22
 tidyr                    0.8.1     2018-05-18
 tidyselect               0.2.4     2018-02-26
 tools                    3.5.1     2018-07-26
 utf8                     1.1.4     2018-05-24
 utils                  * 3.5.1     2018-07-26
 VariantAnnotation        1.27.5    2018-09-26
 VariantTools             1.23.0    2018-06-13
 whisker                  0.3-2     2013-04-28
 withr                    2.1.2     2018-03-15
 XML                      3.98-1.16 2018-08-19
 xml2                     1.2.0     2018-01-24
 xtable                   1.8-3     2018-08-29
 XVector                  0.21.3    2018-06-23
 yaml                     2.2.0     2018-07-25
 zlibbioc                 1.27.0    2018-06-13
ADD COMMENTlink modified 6 months ago • written 6 months ago by Kyle Johnsen20
Hi Kyle, Can you provide the GitHub repository of your package and a link to the Travis build page? Thanks, Marcel
ADD REPLYlink written 6 months ago by Marcel Ramos ♦♦ 360

Yes, here's the link to the repository (the problem is on the refactor-data branch): https://github.com/kjohnsen/MMAPPR2/tree/refactor-data

And here's a link to the failing build:

https://travis-ci.org/kjohnsen/MMAPPR2/builds/433856348

ADD REPLYlink written 6 months ago by Kyle Johnsen20
Have you tried to delete your Travis CI cache and re-running the build?
ADD REPLYlink written 6 months ago by Marcel Ramos ♦♦ 360

Yes, I have...here's a more recent log where I ran possibleDates() and confirmed that only release snapshots are available:
https://api.travis-ci.org/v3/job/436206153/log.txt

ADD REPLYlink written 6 months ago by Kyle Johnsen20

Maybe also try updating to use BiocManager instead of BiocInstaller and install instead of biocLite.

install.package("BiocManager") 
BiocManager::install(version="devel") 
BiocManager::install(ask=FALSE)

When I searched the above log, I could not find where you ran possibleDates() or where ExperimentHub was installed?

ADD REPLYlink modified 6 months ago • written 6 months ago by shepherl ♦♦ 1.3k

I restarted the build above after deleting all caches on Travis, thinking that could make a difference, and didn't realize the old log would be overwritten. So it's re-running right now.

As for using BiocManager, I already tried it, and install(version='devel') failed inexplicably. Here are the build results:

https://travis-ci.org/kjohnsen/MMAPPR2/builds/435888190

ADD REPLYlink written 6 months ago by Kyle Johnsen20

There's an issue with (CRAN) BiocManager when switching to devel. Can you try using the GitHub version of BiocManager?

remotes::install_github("Bioconductor/BiocManager")

ADD REPLYlink modified 6 months ago • written 6 months ago by Marcel Ramos ♦♦ 360

I tried it (using the r_github_packages option on the .travis.yml), and again BiocManager::install(version='devel') fails.

If you look at the package versions, the most recent version of BiocManager is definitely there (v1.30.2.9003).

Travis build: https://travis-ci.org/kjohnsen/MMAPPR2/jobs/436394517

 

 

ADD REPLYlink written 6 months ago by Kyle Johnsen20
2

Try also adding ask='FALSE' to the argument

remotes::install_github("Bioconductor/BiocManager")
BiocManager::install(version='devel', ask=FALSE)

And assuming that we can get this devel version issue straightened out for BiocManager. I would still recommend installing BiocManager at the top of the script instead of BiocInstaller and removing the BiocInstaller lines of code - BiocInstaller is being deprecated and will not be supported after the next release. Install all packages using BiocManager.

ADD REPLYlink written 6 months ago by shepherl ♦♦ 1.3k
Answer: Can't access devel version of ExperimentHub in Travis CI
2
gravatar for Kyle Johnsen
6 months ago by
Kyle Johnsen20
United States/Brigham Young University
Kyle Johnsen20 wrote:

Installing bioc-devel in the before_script using BiocManager::install(version='devel', ask=FALSE) fixed it.

Thank you Lori!

ADD COMMENTlink written 6 months ago by Kyle Johnsen20
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