stable

libsbml-5.16.0-8.fc28, libsedml-0.4.3-10.fc28, & 126 more

FEDORA-2018-050da4f07f created by spot 5 years ago for Fedora 28

Update R to 3.5.0. Rebuild rpy and rkward to match. rpy updated to 2.9.3 in Fedora 28.

All compiled R packages rebuilt (except for R-shogun, because shogun doesn't build right now). Most updated to the latest version.

How to install

Updates may require up to 24 hours to propagate to mirrors. If the following command doesn't work, please retry later:

sudo dnf upgrade --refresh --advisory=FEDORA-2018-050da4f07f

This update has been submitted for testing by spot.

5 years ago

This update has been pushed to testing.

5 years ago
User Icon qulogic commented & provided feedback 5 years ago
karma

Same problem as the F27 update:

$ mock -r fedora-28-x86_64 --install R-core-3.5.0-1.fc28 --enablerepo=updates-testing R-Rcpp
$ mock -r fedora-28-x86_64 --no-clean --shell
# R
> library(Rcpp)
Error: package or namespace load failed for ‘Rcpp’:
 package ‘Rcpp’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version

Bodhi is disabling automatic push to stable due to negative karma. The maintainer may push manually if they determine that the issue is not severe.

5 years ago
User Icon basilrabi commented & provided feedback 5 years ago
karma

Works great! Thanks.

@qulogic: For R-Rcpp, report the issue to the maintainer. This is not directly related to R. R-Rcpp must be rebuilt against R 3.5.0. In the meantime, you should remove R-Rcpp and use the CRAN version via install.packages(Rcpp) instead.

R-Rcpp should be submitted as part of the same update, just like soname bumps.

spot edited this update.

New build(s):

  • R-qtl-1.42.8-1.fc28
  • R-acepack-1.4.1-7.fc28
  • R-affyio-1.50.0-1.fc28
  • R-affy-1.58.0-1.fc28
  • R-ape-5.1-1.fc28
  • R-argon2-0.2.0-2.fc28
  • R-backports-1.1.2-3.fc28
  • R-base64enc-0.1.3-3.fc28
  • R-biglm-0.9.1-13.fc28
  • R-bindrcpp-0.2.2-2.fc28
  • R-Biobase-2.40.0-1.fc28
  • R-BiocParallel-1.14.1-1.fc28
  • R-Biostrings-2.48.0-1.fc28
  • R-bit64-0.9.7-3.fc28
  • R-bitops-1.0.6-9.fc28
  • R-bit-1.1.13-1.fc28
  • R-BufferedMatrix-1.44.0-1.fc28
  • R-BufferedMatrixMethods-1.44.0-1.fc28
  • R-Cairo-1.5.9-4.fc28
  • R-callr-2.0.4-1.fc28
  • R-caTools-1.17.1-8.fc28
  • R-colorspace-1.3.2-2.fc28
  • R-commonmark-1.5-2.fc28
  • R-corpus-0.10.0-2.fc28
  • R-curl-3.2-2.fc28
  • R-date-1.2.38-2.fc28
  • R-deldir-0.1.15-2.fc28
  • R-digest-0.6.15-2.fc28
  • R-expm-0.999.2-6.fc28
  • R-fastmatch-1.1.0-2.fc28
  • R-filehash-2.4.1-3.fc28
  • R-FMStable-0.1.2-2.fc28
  • R-fts-0.9.9-2.fc28
  • R-gamlss.dist-5.0.5-2.fc28
  • R-gdtools-0.1.7-3.fc28
  • R-geepack-1.2.1-3.fc28
  • R-gee-4.13.19-2.fc28
  • R-GenomicAlignments-1.16.0-1.fc28
  • R-GenomicRanges-1.32.3-1.fc28
  • R-getPass-0.2.2-2.fc28
  • R-git2r-0.21.0-2.fc28
  • R-gmp-0.5.13.1-2.fc28
  • R-gss-2.1.9-2.fc28
  • R-gtools-3.5.0-2.fc28
  • R-hexbin-1.27.2-2.fc28
  • R-highlight-0.4.7.2-1.fc28
  • R-htmltools-0.3.6-4.fc28
  • R-httpuv-1.4.3-2.fc28
  • R-IRanges-2.14.10-1.fc28
  • R-jpeg-0.1.8-5.fc28
  • R-jsonlite-1.5-7.fc28
  • R-later-0.7.2-2.fc28
  • R-lazyeval-0.2.1-2.fc28
  • libsbml-5.16.0-8.fc28
  • R-littler-0.3.3-4.fc28
  • R-lmtest-0.9.36-1.fc28
  • R-lubridate-1.7.4-2.fc28
  • R-maanova-1.50.0-1.fc28
  • R-markdown-0.8-5.fc28
  • R-matrixStats-0.53.1-2.fc28
  • R-mime-0.5-3.fc28
  • R-mlbench-2.1.1-2.fc28
  • R-mnormt-1.5.5-2.fc28
  • R-msm-1.6.6-1.fc28
  • R-multtest-2.36.0-1.fc28
  • R-mvtnorm-1.0.7-1.fc28
  • R-openssl-1.0.1-2.fc28
  • R-pbdZMQ-0.3.3-2.fc28
  • R-pdftools-1.7-1.fc28
  • R-plyr-1.8.4-6.fc28
  • R-png-0.1.7-5.fc28
  • R-poLCA-1.4.1-2.fc28
  • R-polyclip-1.8.7-1.fc28
  • R-preprocessCore-1.42.0-1.fc28
  • R-processx-3.1.0-1.fc28
  • R-promises-1.0.1-2.fc28
  • R-Rcompression-0.93.2-20.fc28
  • R-RcppCCTZ-0.2.3-3.fc28
  • R-Rcpp-0.12.16-2.fc28
  • R-RCurl-1.95.4.10-2.fc28
  • R-reshape2-1.4.3-4.fc28
  • R-reticulate-1.7-2.fc28
  • R-rgdal-1.2.20-2.fc28
  • R-rgeos-0.3.26-2.fc28
  • R-RInside-0.2.14-7.fc28
  • R-rlang-0.2.0-2.fc28
  • R-rlecuyer-0.3.4-5.fc28
  • R-Rmpfr-0.7.0-2.fc28
  • R-ROC-1.56.0-1.fc28
  • R-RODBC-1.3.15-5.fc28
  • R-Rsamtools-1.32.0-1.fc28
  • R-Rsolid-0.9.31-24.fc28
  • R-RSQLite-2.1.1-2.fc28
  • R-rtracklayer-1.40.2-1.fc28
  • R-S4Vectors-0.18.2-1.fc28
  • libsedml-0.4.3-10.fc28
  • R-sourcetools-0.1.7-2.fc28
  • R-sp-1.2.7-2.fc28
  • R-statmod-1.4.30-1.fc28
  • R-statnet.common-4.0.0-2.fc28
  • R-stringdist-0.9.4.7-2.fc28
  • R-stringi-1.2.2-1.fc28
  • R-testthat-2.0.0-2.fc28
  • R-tikzDevice-0.11-2.fc28
  • R-tkrplot-0.0.23-2.fc28
  • R-utf8-1.1.3-2.fc28
  • R-uuid-0.1.2-5.fc28
  • R-V8-1.5-5.fc28
  • R-waveslim-1.7.5-8.fc28
  • R-wavethresh-4.6.8-5.fc28
  • R-webp-0.4-2.fc28
  • R-webutils-0.6-2.fc28
  • R-xml2-1.2.0-4.fc28.1
  • R-XML-3.98.1.11-1.fc28
  • R-XVector-0.20.0-1.fc28
  • R-yaml-2.1.19-2.fc28
  • R-zoo-1.8.1-1.fc28
  • R-DBI-1.0.0-1.fc28
  • R-plogr-0.2.0-1.fc28
  • R-prettyunits-1.0.2-1.fc28
  • R-blob-1.1.1-2.fc28
  • R-BiocGenerics-0.26.0-1.fc28
  • R-GenomeInfoDb-1.16.0-1.fc28
  • R-SummarizedExperiment-1.10.1-1.fc28
  • v8-314-3.14.5.10-10.fc28

Karma has been reset.

5 years ago

This update has been submitted for testing by spot.

5 years ago

This update has been pushed to testing.

5 years ago
User Icon basilrabi commented & provided feedback 5 years ago
karma

Works great!

User Icon sobek commented & provided feedback 5 years ago
karma

Thank you! Looks good to me.

User Icon besser82 commented & provided feedback 5 years ago
karma

Works great! LGTM! =)

This update has reached the stable karma threshold and can be pushed to stable now if the maintainer wishes.

5 years ago
User Icon qulogic commented & provided feedback 5 years ago
karma

I ran:

$ mock -r fedora-28-x86_64 --dnf-cmd -- install 'R-*' --skip-broken
$ mock -r fedora-28-x86_64 --dnf-cmd list 'R-*' | awk '{print $1}' | sed -e 's/\.[^.]\+$//g' -e 's/^R-//' -e 's/-devel$//' | sort -u > pkgs
$ mock -r fedora-28-x86_64 --copyin pkgs /
$ mock -r fedora-28-x86_64 --shell
# for p in `cat pkgs`; do echo "library($p); quit()" | R --quiet --vanilla; done &> results
$ mock -r fedora-28-x86_64 --copyout /results results-f28

then did it again with --enablerepo=updates-testing, and diffed the results.

With this update, we are now able to also install:

  • R-blob,
  • R-orcutt, and
  • R-prettyunits.

Also, now able to correctly load:

  • R-affy,
  • R-affydata,
  • R-lmtest,
  • R-maanova,
  • R-msm,
  • R-multcomp,
  • R-mvtnorm,
  • R-preprocessCore,
  • R-RM2,
  • R-sandwich,
  • R-statmod,
  • R-systemfit, and
  • R-waveslim.

But now these packages are broken:

  • R-chron,
  • R-COPASI,
  • R-GeneR,
  • R-quadprog,
  • R-reshape, and
  • R-roxygen2.

I have rebuilt R-chron, R-quadprog, R-reshape, and R-roxygen2, but I don't have permissions to build the other two. If you don't want to wait another week, I can submit these as a separate update.

Ugh, I added +1s on a bunch of the FTBFS bugs, but bodhi didn't save it.

qulogic, thanks for the follow-up. Let's go ahead and let this update land, and do the others as a separate update.

R-COPASI did get rebuilt, but the maintainer put it into an update of its own (then, deleted it).

This update has been submitted for batched by spot.

5 years ago

This update has been submitted for batched by spot.

5 years ago

This update has been submitted for stable by spot.

5 years ago

This update has been pushed to stable.

5 years ago

Please login to add feedback.

Metadata
Type
bugfix
Karma
2
Signed
Content Type
RPM
Test Gating
Builds
128
Settings
Unstable by Karma
-3
Stable by Karma
disabled
Stable by Time
disabled
Dates
submitted
5 years ago
in testing
5 years ago
in stable
5 years ago
modified
5 years ago
BZ#1405667 R-zoo-1.8-1 is available
0
0
BZ#1555498 R-Biostrings: FTBFS in F28
0
0
BZ#1555515 R-ROC: FTBFS in F28
0
0
BZ#1555516 R-RODBC: FTBFS in F28
0
0
BZ#1555521 R-Rsolid: FTBFS in F28
0
0
BZ#1555525 R-XML: FTBFS in F28
0
0
BZ#1555528 R-affy: FTBFS in F28
0
0
BZ#1555530 R-affyio: FTBFS in F28
0
0
BZ#1555532 R-bitops: FTBFS in F28
0
0
BZ#1555533 R-caTools: FTBFS in F28
0
0
BZ#1555547 R-maanova: FTBFS in F28
0
0
BZ#1555552 R-msm: FTBFS in F28
0
0
BZ#1555555 R-multtest: FTBFS in F28
0
0
BZ#1555556 R-mvtnorm: FTBFS in F28
0
0
BZ#1555561 R-preprocessCore: FTBFS in F28
0
0
BZ#1555564 R-rlecuyer: FTBFS in F28
0
0
BZ#1555569 R-statmod: FTBFS in F28
0
0
BZ#1555574 R-waveslim: FTBFS in F28
0
0
BZ#1555575 R-wavethresh: FTBFS in F28
0
0
BZ#1556527 v8-314: FTBFS in F28
0
0
BZ#1560254 R-curl-3.2 is available
0
0
BZ#1563656 R-lmtest-0.9-36 is available
0
0
BZ#1567573 rpy-2.9.3 is available
0
0
BZ#1570804 R-3.5.0 is available
0
0
BZ#1574116 R-stringi-1.2.2 is available
0
0
BZ#1575172 R-httpuv-1.4.3 is available
0
0
BZ#1578961 Review Request: R-prettyunits - Pretty, Human Readable Formatting of Quantities
0
0
BZ#1578963 Review Request: R-blob - A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
0
0

Automated Test Results