FEDORA-2018-b11015006b — bugfix update for libsbml, libsedml, & 119 more

stable

libsbml-5.16.0-8.fc27, libsedml-0.4.3-10.fc27, & 119 more

FEDORA-2018-b11015006b created by spot 6 years ago for Fedora 27

Update R to 3.5.0. Rebuild rpy and rkward to match. rpy updated to 2.9.3 in Fedora 28. Rebuild all compiled R modules, except R-shogun (shogun does not build right now).

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-b11015006b

This update has been submitted for testing by spot.

6 years ago

This update has been pushed to testing.

6 years ago

qulogic commented 6 years ago

Much like a minor Python version bump, this appears to require rebuilding all R packages. For example,

$ mock -r fedora-27-x86_64 --install R-core-3.5.0-1.fc27 --enablerepo=updates-testing R-Rcpp
$ mock -r fedora-27-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

qulogic commented & provided feedback 6 years ago

karma

Not sure why negative karma did not get posted before.

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

spot edited this update.

New build(s):

R-blob-1.1.1-2.fc27
R-prettyunits-1.0.2-1.fc27
R-zoo-1.8.1-1.fc27
R-yaml-2.1.19-2.fc27
R-XVector-0.16.0-4.fc27
R-XML-3.98.1.7-4.fc27
R-xml2-1.2.0-4.fc27
R-webutils-0.6-2.fc27
R-webp-0.4-2.fc27
R-wavethresh-4.6.8-5.fc27
R-waveslim-1.7.5-8.fc27
R-V8-1.5-5.fc27
R-uuid-0.1.2-5.fc27
R-utf8-1.1.3-2.fc27
R-tkrplot-0.0.23-2.fc27
R-tikzDevice-0.11-2.fc27
R-testthat-1.0.2-6.fc27
R-stringi-1.2.2-1.fc27
R-stringdist-0.9.4.7-2.fc27
R-statnet.common-4.0.0-2.fc27
R-statmod-1.4.30-1.fc27
R-sp-1.2.7-2.fc27
R-sourcetools-0.1.7-2.fc27
libsedml-0.4.3-10.fc27
R-S4Vectors-0.14.3-4.fc27
R-rtracklayer-1.36.3-4.fc27
R-RSQLite-1.1.2-5.fc27
R-Rsolid-0.9.31-24.fc27
R-Rsamtools-1.28.0-4.fc27
R-RODBC-1.3.15-5.fc27
R-ROC-1.46.0-6.fc27
R-Rmpfr-0.7.0-2.fc27
R-rlecuyer-0.3.4-5.fc27
R-rlang-0.2.0-2.fc27
R-RInside-0.2.14-7.fc27
R-rgeos-0.3.26-2.fc27
R-rgdal-1.2.20-2.fc27
R-reticulate-1.7-2.fc27
R-reshape2-1.4.3-4.fc27
R-RCurl-1.95.4.8-4.fc27
R-Rcpp-0.12.16-2.fc27
R-RcppCCTZ-0.2.3-3.fc27
R-Rcompression-0.93.2-20.fc27
R-qtl-1.42.8-1.fc27
R-processx-2.0.0.1-2.fc27
R-preprocessCore-1.38.1-4.fc27
R-polyclip-1.8.7-1.fc27
R-poLCA-1.4.1-2.fc27
R-png-0.1.7-5.fc27
R-plyr-1.8.4-6.fc27
R-pdftools-1.7-1.fc27
R-pbdZMQ-0.3.3-2.fc27
R-openssl-1.0.1-2.fc27
R-mvtnorm-1.0.7-1.fc27
R-multtest-2.36.0-1.fc27
R-msm-1.6.4-4.fc27
R-mnormt-1.5.5-2.fc27
R-mlbench-2.1.1-2.fc27
R-mime-0.5-3.fc27
R-matrixStats-0.52.2-4.fc27
R-markdown-0.8-5.fc27
R-maanova-1.46.1-4.fc27
R-lubridate-1.7.3-5.fc27
R-lmtest-0.9.36-1.fc27
R-littler-0.3.3-4.fc27
libsbml-5.16.0-8.fc27
R-lazyeval-0.2.1-2.fc27
R-later-0.7.2-2.fc27
R-jsonlite-1.5-7.fc27
R-jpeg-0.1.8-5.fc27
R-IRanges-2.10.1-4.fc27
R-httpuv-1.3.6.2-3.fc27
R-htmltools-0.3.6-4.fc27
R-highlight-0.4.7.2-1.fc27
R-hexbin-1.27.2-2.fc27
R-gtools-3.5.0-2.fc27
R-gss-2.1.9-2.fc27
R-gmp-0.5.13.1-2.fc27
R-git2r-0.21.0-2.fc27
R-getPass-0.2.2-2.fc27
R-GenomicRanges-1.28.3-4.fc27
R-GenomicAlignments-1.12.1-4.fc27
R-gee-4.13.19-2.fc27
R-geepack-1.2.1-3.fc27
R-gdtools-0.1.7-3.fc27
R-gamlss.dist-5.0.5-2.fc27
R-fts-0.9.9-2.fc27
R-FMStable-0.1.2-2.fc27
R-filehash-2.4.1-3.fc27
R-fastmatch-1.1.0-2.fc27
R-expm-0.999.2-6.fc27
R-digest-0.6.12-4.fc27
R-deldir-0.1.15-2.fc27
R-date-1.2.38-2.fc27
R-curl-3.2-2.fc27
R-corpus-0.10.0-2.fc27
R-commonmark-1.5-2.fc27
R-colorspace-1.3.2-2.fc27
R-caTools-1.17.1-8.fc27
R-callr-2.0.3-2.fc27
R-Cairo-1.5.9-4.fc27
R-BufferedMatrixMethods-1.44.0-1.fc27
R-BufferedMatrix-1.44.0-1.fc27
R-bit64-0.9.7-3.fc27
R-bitops-1.0.6-9.fc27
R-bit-1.1.13-1.fc27
R-Biostrings-2.44.0-4.fc27
R-BiocParallel-1.10.1-3.fc27
R-Biobase-2.36.2-4.fc27
R-bindrcpp-0.2.2-2.fc27
R-biglm-0.9.1-13.fc27
R-base64enc-0.1.3-3.fc27
R-backports-1.1.2-3.fc27
R-argon2-0.2.0-2.fc27
R-ape-5.1-1.fc27
R-affy-1.54.0-4.fc27
R-affyio-1.46.0-4.fc27
R-acepack-1.4.1-7.fc27

Karma has been reset.

6 years ago

This update has been submitted for testing by spot.

6 years ago

This update has obsoleted R-polyclip-1.8.4-1.fc27, and has inherited its bugs and notes.

6 years ago

spot edited this update.

New build(s):

R-blob-1.1.1-2.fc27
R-prettyunits-1.0.2-1.fc27
R-zoo-1.8.1-1.fc27
R-yaml-2.1.19-2.fc27
R-XVector-0.16.0-4.fc27
R-XML-3.98.1.7-4.fc27
R-xml2-1.2.0-4.fc27
R-webutils-0.6-2.fc27
R-webp-0.4-2.fc27
R-wavethresh-4.6.8-5.fc27
R-waveslim-1.7.5-8.fc27
R-V8-1.5-5.fc27
R-uuid-0.1.2-5.fc27
R-utf8-1.1.3-2.fc27
R-tkrplot-0.0.23-2.fc27
R-tikzDevice-0.11-2.fc27
R-testthat-1.0.2-6.fc27
R-stringi-1.2.2-1.fc27
R-stringdist-0.9.4.7-2.fc27
R-statnet.common-4.0.0-2.fc27
R-statmod-1.4.30-1.fc27
R-sp-1.2.7-2.fc27
R-sourcetools-0.1.7-2.fc27
libsedml-0.4.3-10.fc27
R-S4Vectors-0.14.3-4.fc27
R-rtracklayer-1.36.3-4.fc27
R-RSQLite-1.1.2-5.fc27
R-Rsolid-0.9.31-24.fc27
R-Rsamtools-1.28.0-4.fc27
R-RODBC-1.3.15-5.fc27
R-ROC-1.46.0-6.fc27
R-Rmpfr-0.7.0-2.fc27
R-rlecuyer-0.3.4-5.fc27
R-rlang-0.2.0-2.fc27
R-RInside-0.2.14-7.fc27
R-rgeos-0.3.26-2.fc27
R-rgdal-1.2.20-2.fc27
R-reticulate-1.7-2.fc27
R-reshape2-1.4.3-4.fc27
R-RCurl-1.95.4.8-4.fc27
R-Rcpp-0.12.16-2.fc27
R-RcppCCTZ-0.2.3-3.fc27
R-Rcompression-0.93.2-20.fc27
R-qtl-1.42.8-1.fc27
R-processx-2.0.0.1-2.fc27
R-preprocessCore-1.38.1-4.fc27
R-polyclip-1.8.7-1.fc27
R-poLCA-1.4.1-2.fc27
R-png-0.1.7-5.fc27
R-plyr-1.8.4-6.fc27
R-pdftools-1.7-1.fc27
R-pbdZMQ-0.3.3-2.fc27
R-openssl-1.0.1-2.fc27
R-mvtnorm-1.0.7-1.fc27
R-multtest-2.36.0-1.fc27
R-msm-1.6.4-4.fc27
R-mnormt-1.5.5-2.fc27
R-mlbench-2.1.1-2.fc27
R-mime-0.5-3.fc27
R-matrixStats-0.52.2-4.fc27
R-markdown-0.8-5.fc27
R-maanova-1.46.1-4.fc27
R-lubridate-1.7.3-5.fc27
R-lmtest-0.9.36-1.fc27
R-littler-0.3.3-4.fc27
libsbml-5.16.0-8.fc27
R-lazyeval-0.2.1-2.fc27
R-later-0.7.2-2.fc27
R-jsonlite-1.5-7.fc27
R-jpeg-0.1.8-5.fc27
R-IRanges-2.10.1-4.fc27
R-httpuv-1.3.6.2-3.fc27
R-htmltools-0.3.6-4.fc27
R-highlight-0.4.7.2-1.fc27
R-hexbin-1.27.2-2.fc27
R-gtools-3.5.0-2.fc27
R-gss-2.1.9-2.fc27
R-gmp-0.5.13.1-2.fc27
R-git2r-0.21.0-2.fc27
R-getPass-0.2.2-2.fc27
R-GenomicRanges-1.28.3-4.fc27
R-GenomicAlignments-1.12.1-4.fc27
R-gee-4.13.19-2.fc27
R-geepack-1.2.1-3.fc27
R-gdtools-0.1.7-3.fc27
R-gamlss.dist-5.0.5-2.fc27
R-fts-0.9.9-2.fc27
R-FMStable-0.1.2-2.fc27
R-filehash-2.4.1-3.fc27
R-fastmatch-1.1.0-2.fc27
R-expm-0.999.2-6.fc27
R-digest-0.6.12-4.fc27
R-deldir-0.1.15-2.fc27
R-date-1.2.38-2.fc27
R-curl-3.2-2.fc27
R-corpus-0.10.0-2.fc27
R-commonmark-1.5-2.fc27
R-colorspace-1.3.2-2.fc27
R-caTools-1.17.1-8.fc27
R-callr-2.0.3-2.fc27
R-Cairo-1.5.9-4.fc27
R-BufferedMatrixMethods-1.44.0-1.fc27
R-BufferedMatrix-1.44.0-1.fc27
R-bit64-0.9.7-3.fc27
R-bitops-1.0.6-9.fc27
R-bit-1.1.13-1.fc27
R-Biostrings-2.44.0-4.fc27
R-BiocParallel-1.10.1-3.fc27
R-Biobase-2.36.2-4.fc27
R-bindrcpp-0.2.2-2.fc27
R-biglm-0.9.1-13.fc27
R-base64enc-0.1.3-3.fc27
R-backports-1.1.2-3.fc27
R-argon2-0.2.0-2.fc27
R-ape-5.1-1.fc27
R-affy-1.54.0-4.fc27
R-affyio-1.46.0-4.fc27
R-acepack-1.4.1-7.fc27

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

This update has reached 7 days in testing and can be pushed to stable now if the maintainer wishes

6 years ago

qulogic commented 6 years ago

I ran:

$ mock -r fedora-27-x86_64 --dnf-cmd -- install 'R-*' --skip-broken
$ mock -r fedora-27-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-27-x86_64 --copyin pkgs /
$ mock -r fedora-27-x86_64 --shell
# for p in `cat pkgs`; do echo "library($p); quit()" | R --quiet --vanilla; done &> results
$ mock -r fedora-27-x86_64 --copyout /results results-f27

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

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

R-blob, and
R-prettyunits.

Also, now able to correctly load:

R-future,
R-listenv,
R-promises,
R-R.cache, and
R-R.rsp.

But now these packages are broken:

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

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

qulogic commented 6 years ago

Those 4 rebuilds have spent their week in testing; is this update going to get pushed to stable?

This update has been submitted for batched by spot.

6 years ago

This update has been submitted for stable by spot.

6 years ago

This update has been pushed to stable.

6 years ago