FEDORA-2018-050da4f07f — bugfix update for libsbml, libsedml, & 126 more

stable

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

FEDORA-2018-050da4f07f created by spot 6 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.

6 years ago

This update has been pushed to testing.

6 years ago

qulogic commented & provided feedback 6 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.

6 years ago

basilrabi commented & provided feedback 6 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.

qulogic commented 6 years ago

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.

6 years ago

This update has been submitted for testing by spot.

6 years ago

This update has been pushed to testing.

6 years ago

basilrabi commented & provided feedback 6 years ago

karma

Works great!

sobek commented & provided feedback 6 years ago

karma

Thank you! Looks good to me.

besser82 commented & provided feedback 6 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.

6 years ago

qulogic commented & provided feedback 6 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.

qulogic commented 6 years ago

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