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Kyle Johnsen
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30
@kyle-johnsen-11443
Last seen 5.9 years ago
United States/Brigham Young University
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
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
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
Maybe also try updating to use BiocManager instead of BiocInstaller and install instead of biocLite.
When I searched the above log, I could not find where you ran
possibleDates()or whereExperimentHubwas installed?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
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")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
Try also adding ask='FALSE' to the argument
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.