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

sudo dnf upgrade --advisory=FEDORA-2018-b11015006b

This update has been submitted for testing by spot.

2 years ago

This update has been pushed to testing.

2 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
User Icon qulogic commented & provided feedback 2 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.

2 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.

2 years ago

This update has been submitted for testing by spot.

2 years ago

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

2 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.

2 years ago

This update has been submitted for testing by spot.

2 years ago

This update has been pushed to testing.

2 years ago

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

2 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.

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.

2 years ago

This update has been submitted for stable by spot.

2 years ago

This update has been pushed to stable.

2 years ago
User Icon kkofler commented & provided feedback 2 years ago
karma

Please login to add feedback.

Metadata
Type
bugfix
Karma
-1
Signed
Content Type
RPM
Test Gating
Builds
121
Settings
Unstable by Karma
-3
Dates
submitted
2 years ago
in testing
2 years ago
in stable
2 years ago
modified
2 years ago
BZ#1567573 rpy-2.9.3 is available
0
0
BZ#1570804 R-3.5.0 is available
0
0
libsbml-5.16.0-8.fc27
libsedml-0.4.3-10.fc27
R-3.5.0-1.fc27
R-acepack-1.4.1-7.fc27
R-affy-1.54.0-4.fc27
R-affyio-1.46.0-4.fc27
R-ape-5.1-1.fc27
R-argon2-0.2.0-2.fc27
R-backports-1.1.2-3.fc27
R-base64enc-0.1.3-3.fc27
R-biglm-0.9.1-13.fc27
R-bindrcpp-0.2.2-2.fc27
R-Biobase-2.36.2-4.fc27
R-BiocParallel-1.10.1-3.fc27
R-Biostrings-2.44.0-4.fc27
R-bit-1.1.13-1.fc27
R-bit64-0.9.7-3.fc27
R-bitops-1.0.6-9.fc27
R-blob-1.1.1-2.fc27
R-BufferedMatrix-1.44.0-1.fc27
R-BufferedMatrixMethods-1.44.0-1.fc27
R-Cairo-1.5.9-4.fc27
R-callr-2.0.3-2.fc27
R-caTools-1.17.1-8.fc27
R-colorspace-1.3.2-2.fc27
R-commonmark-1.5-2.fc27
R-corpus-0.10.0-2.fc27
R-curl-3.2-2.fc27
R-date-1.2.38-2.fc27
R-deldir-0.1.15-2.fc27
R-digest-0.6.12-4.fc27
R-expm-0.999.2-6.fc27
R-fastmatch-1.1.0-2.fc27
R-filehash-2.4.1-3.fc27
R-FMStable-0.1.2-2.fc27
R-fts-0.9.9-2.fc27
R-gamlss.dist-5.0.5-2.fc27
R-gdtools-0.1.7-3.fc27
R-gee-4.13.19-2.fc27
R-geepack-1.2.1-3.fc27
R-GenomicAlignments-1.12.1-4.fc27
R-GenomicRanges-1.28.3-4.fc27
R-getPass-0.2.2-2.fc27
R-git2r-0.21.0-2.fc27
R-gmp-0.5.13.1-2.fc27
R-gss-2.1.9-2.fc27
R-gtools-3.5.0-2.fc27
R-hexbin-1.27.2-2.fc27
R-highlight-0.4.7.2-1.fc27
R-htmltools-0.3.6-4.fc27
R-httpuv-1.3.6.2-3.fc27
R-IRanges-2.10.1-4.fc27
R-jpeg-0.1.8-5.fc27
R-jsonlite-1.5-7.fc27
rkward-0.6.5-15.fc27
R-later-0.7.2-2.fc27
R-lazyeval-0.2.1-2.fc27
R-littler-0.3.3-4.fc27
R-lmtest-0.9.36-1.fc27
R-lubridate-1.7.3-5.fc27
R-maanova-1.46.1-4.fc27
R-markdown-0.8-5.fc27
R-matrixStats-0.52.2-4.fc27
R-mime-0.5-3.fc27
R-mlbench-2.1.1-2.fc27
R-mnormt-1.5.5-2.fc27
R-msm-1.6.4-4.fc27
R-multtest-2.36.0-1.fc27
R-mvtnorm-1.0.7-1.fc27
R-openssl-1.0.1-2.fc27
R-pbdZMQ-0.3.3-2.fc27
R-pdftools-1.7-1.fc27
R-plyr-1.8.4-6.fc27
R-png-0.1.7-5.fc27
R-poLCA-1.4.1-2.fc27
R-polyclip-1.8.7-1.fc27
R-preprocessCore-1.38.1-4.fc27
R-prettyunits-1.0.2-1.fc27
R-processx-2.0.0.1-2.fc27
rpy-2.8.6-7.fc27
R-qtl-1.42.8-1.fc27
R-Rcompression-0.93.2-20.fc27
R-Rcpp-0.12.16-2.fc27
R-RcppCCTZ-0.2.3-3.fc27
R-RCurl-1.95.4.8-4.fc27
R-reshape2-1.4.3-4.fc27
R-reticulate-1.7-2.fc27
R-rgdal-1.2.20-2.fc27
R-rgeos-0.3.26-2.fc27
R-RInside-0.2.14-7.fc27
R-rlang-0.2.0-2.fc27
R-rlecuyer-0.3.4-5.fc27
R-Rmpfr-0.7.0-2.fc27
R-ROC-1.46.0-6.fc27
R-RODBC-1.3.15-5.fc27
R-Rsamtools-1.28.0-4.fc27
R-Rsolid-0.9.31-24.fc27
R-RSQLite-1.1.2-5.fc27
R-rtracklayer-1.36.3-4.fc27
R-S4Vectors-0.14.3-4.fc27
R-sourcetools-0.1.7-2.fc27
R-sp-1.2.7-2.fc27
R-statmod-1.4.30-1.fc27
R-statnet.common-4.0.0-2.fc27
R-stringdist-0.9.4.7-2.fc27
R-stringi-1.2.2-1.fc27
R-testthat-1.0.2-6.fc27
R-tikzDevice-0.11-2.fc27
R-tkrplot-0.0.23-2.fc27
R-utf8-1.1.3-2.fc27
R-uuid-0.1.2-5.fc27
R-V8-1.5-5.fc27
R-waveslim-1.7.5-8.fc27
R-wavethresh-4.6.8-5.fc27
R-webp-0.4-2.fc27
R-webutils-0.6-2.fc27
R-xml2-1.2.0-4.fc27
R-XML-3.98.1.7-4.fc27
R-XVector-0.16.0-4.fc27
R-yaml-2.1.19-2.fc27
R-zoo-1.8.1-1.fc27

Automated Test Results