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 4 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

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

This update has been submitted for testing by spot.

4 years ago

This update has been pushed to testing.

4 years ago

qulogic commented & provided feedback 4 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.

4 years ago

basilrabi commented & provided feedback 4 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 4 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.

4 years ago

This update has been submitted for testing by spot.

4 years ago

This update has been pushed to testing.

4 years ago

basilrabi commented & provided feedback 4 years ago

karma

Works great!

sobek commented & provided feedback 4 years ago

karma

Thank you! Looks good to me.

besser82 commented & provided feedback 4 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.

4 years ago

qulogic commented & provided feedback 4 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 4 years ago

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